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{1578} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
God Help us, let's try to understand AI monosemanticity Commentary: To some degree, superposition seems like a geometric "hack" invented in the process of optimization to squeeze a great many (largely mutually-exclusive) sparse features into a limited number of neurons. GPT3 has a latent dimension of only 96 * 128 = 12288, and with 96 layers this is only 1.17 M neurons (*). A fruit fly has 100k neurons (and can't speak). All communication must be through that 12288 dimensional vector, which is passed through LayerNorm many times (**), so naturally the network learns to take advantage of locally linear subspaces. That said, the primate visual system does seem to use superposition, though not via local subspaces; instead, neurons seem to encode multiple axes somewhat linearly (e.g. global spaces: linearly combined position and class) That was a few years ago, and I suspect that new results may contest this. The face area seems to do a good job of disentanglement, for example. Treating everything as high-dimensional vectors is great for analogy making, like the wife - husband + king = queen example. But having fixed-size vectors for representing arbitrary-dimensioned relationships inevitably leads to compression ~= superposition. Provided those subspaces are semantically meaningful, it all works out from a generalization standpoint -- but this is then equivalent to allocating an additional axis for said relationship or attribute. Additional axes would also put less decoding burden on the downstream layers, and make optimization easier. Google has demonstrated allocation in transformers. It's also prevalent in the cortex. Trick is getting it to work! (*) GPT4 is unlikely to have more than an order of magnitude more 'neurons'; PaLM-540B has only 2.17 M. Given that GPT-4 is something like 3-4x larger, it should have 6-8 M neurons, which is still 3 orders of magnitude fewer than the human neocortex (nevermind the cerebellum ;-) (**) I'm of two minds on LayerNorm. PV interneurons might be seen to do something like this, but it's all local -- you don't need everything to be vector rotations. (LayerNorm effectively removes one degree of freedom, so really it's a 12287 dimensional vector) Update: After reading https://transformer-circuits.pub/2023/monosemantic-features/index.html, I find the idea of local manifolds / local codes to be quite appealing: why not represent sparse yet conditional features using superposition? This also expands the possibility of pseudo-hierarchical representation, which is great. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Sketch - Program synthesis by sketching
The essential algorithm, in words: Take the sketch, expand it to a set of parameterized variables, holes, and calling contexts. Convert these to a DAG aka (?) data-code flow graph w/ dependencies. Try to simplify the DAG, one-hot encode integers, and convert to either a conjunctive-normal-form (CNF) SAT problem for MiniSat, or to a boolean circuit for the ABC solver. Apply MiniSat or ABC to the problem to select a set of control values = values for the holes & permutations that satisfy the boolean constraints. Using this solution, use the SAT solver to find a input variable configuration that does not satisfy the problem. This serves as a counter-example. Run this through the validator function (oracle) to see what it does; use the counter-example and (inputs and outputs) to add clauses to the SAT problem. Run several times until either no counter-examples can be found or the problem is `unsat`. Though the thesis describes a system that was academic & relatively small back in 2008, Sketch has enjoyed continuous development, and remains used. I find the work that went into it to be remarkable and impressive -- even with incremental improvements, you need accurate expansion of the language & manipulations to show proof-of-principle. Left wondering what limits its application to even larger problems -- need for a higher-level loop that further subdivides / factorizes the problem, or DFS for filling out elements of the sketch? Interesting links discovered in while reading the dissertation:
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{1576} |
ref: -0
tags: GFlowNet Bengio probabilty modelling reinforcement learing
date: 10-29-2023 19:17 gmt
revision:3
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Put this in ~/.config/gtk-3.0/gtk.css and ~/.config/gtk-4.0/gtk.css to make scrollbars larger & permanently visible on high-DPI screens. ref .scrollbar { -GtkScrollbar-has-backward-stepper: 1; -GtkScrollbar-has-forward-stepper: 1; -GtkRange-slider-width: 16; -GtkRange-stepper-size: 16; } scrollbar slider { /* Size of the slider */ min-width: 16px; min-height: 16px; border-radius: 16px; /* Padding around the slider */ border: 2px solid transparent; } .scrollbar.vertical slider, scrollbar.vertical slider { min-height: 16px; min-width: 16px; } .scrollbar.horizontal.slider, scrollbar.horizontal slider { min-width: 16px; min-height: 16px; } /* Scrollbar trough squeezes when cursor hovers over it. Disabling that */ .scrollbar.vertical:hover:dir(ltr), .scrollbar.vertical.dragging:dir(ltr) { margin-left: 0px; } .scrollbar.vertical:hover:dir(rtl), .scrollbar.vertical.dragging:dir(rtl) { margin-right: 0px; } .scrollbar.horizontal:hover, .scrollbar.horizontal.dragging, .scrollbar.horizontal.slider:hover, .scrollbar.horizontal.slider.dragging { margin-top: 0px; } undershoot.top, undershoot.right, undershoot.bottom, undershoot.left { background-image: none; } undershoot.top, undershoot.right, undershoot.bottom, undershoot.left { background-image: none; } Also add: export GTK_OVERLAY_SCROLLING=0to your ~/.bashrc This does not work with GTK4, though -- to do that, put the following in ~/.config/gtk-4.0/settings.ini: [Settings] gtk-overlay-scrolling = false To make the scrollbars a bit easier to see in QT5 applications, run qt5ct (after apt-getting it), and add in a new style sheet, /usr/share/qt5ct/qss/scrollbar-simple-backup.qss /* SCROLLBARS (NOTE: Changing 1 subcontrol means you have to change all of them)*/ QScrollBar{ background: palette(alternate-base); } QScrollBar:horizontal{ margin: 0px 0px 0px 0px; } QScrollBar:vertical{ margin: 0px 0px 0px 0px; } QScrollBar::handle{ background: #816891; border: 1px solid transparent; border-radius: 1px; } QScrollBar::handle:hover, QScrollBar::add-line:hover, QScrollBar::sub-line:hover{ background: palette(highlight); } QScrollBar::add-line{ subcontrol-origin: none; } QScrollBar::add-line:vertical, QScrollBar::sub-line:vertical{ height: 0px; } QScrollBar::add-line:horizontal, QScrollBar::sub-line:horizontal{ width: 0px; } QScrollBar::sub-line{ subcontrol-origin: none; } | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1574} |
ref: -0
tags: ocaml application functional programming
date: 10-11-2022 21:36 gmt
revision:2
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https://stackoverflow.com/questions/26475765/ocaml-function-with-variable-number-of-arguments From this I learned that in ocaml you can return not just functions (e.g. currying) but appliations of yet-to-be named functions. let sum f = f 0 ;; let arg a b c = c ( b + a ) ;; let z a = a ;; then sum (arg 1) ;; is well-typed as (int -> `a) -> `a = <fun> e.g. an application of a function that converts int to `a. Think of it as the application of Xa to argument ( 0 + 1 ), where Xa is the argument (per type signature). Zero is supplied by the definition of 'sum'. sum (arg 1) (arg 2);; can be parsed as (sum (arg 1)) (arg 2) ;; '(arg 2)' outputs an application of an int & a yet-to be determined function to 'a, E.g. it's typed as int -> (int -> `a) -> `a = <fun>. So, you can call it Xa passed to above. Or, Xa = Xb( ( 0 + 1 ) + 2) where, again, Xb is a yet-to-be defined function that is supplied as an argument. Therefore, you can collapse the whole chain with the identity function z. But, of course, it could be anything else -- square root perhaps for MSE? All very clever. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-36070680 Extracellular vesicles mediate the communication of adipose tissue with brain and promote cognitive impairment associated with insulin resistance
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One model for the learning of language
A more interesting result is Deep symbolic regression for recurrent sequences, where the authors (facebook/meta) use a Transformer -- in this case, directly taken from Vaswini 2017 (8-head, 8-layer QKV w/ a latent dimension of 512) to do both symbolic (estimate the algebraic recurrence relation) and numeric (estimate the rest of the sequence) training / evaluation. Symbolic regression generalizes better, unsurprisingly. But both can be made to work even in the presence of (log-scaled) noise! While the language learning paper shows that small generative programs can be inferred from a few samples, the Meta symbolic regression shows that Transformers can evince either amortized memory (less likely) or algorithms for perception -- both new and interesting. It suggests that 'even' abstract symbolic learning tasks are sufficiently decomposable that the sorts of algorithms available to an 8-layer transformer can give a useful search heuristic. (N.B. That the transformer doesn't spit out perfect symbolic or numerical results directly -- it also needs post-processing search. Also, the transformer algorithm has search (in the form of softmax) baked in to it's architecture.) This is not a light architecture: they trained the transformer for 250 epochs, where each epoch was 5M equations in batches of 512. Each epoch took 1 hour on 16 Volta GPUs w 32GB of memory. So, 4k GPU-hours x ~10 TFlops = 1.4e20 Flops. Compare this with grammar learning above; 7 days on 32 cores operating at ~ 3Gops/sec is 1.8e15 ops. Much, much smaller compute. All of this is to suggest a central theme of computer science: a continuum between search and memorization.
Most interesting for a visual neuroscientist (not that I'm one per se, but bear with me) is where on these axes (search, heuristic, memory) visual perception is. Clearly there is a high degree of recurrence, and a high degree of plasticity / learning. But is there search or local optimization? Is this coupled to the recurrence via some form of energy-minimizing system? Is recurrence approximating E-M? | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1572} |
ref: -2019
tags: Piantadosi cogntion combinators function logic
date: 09-05-2022 01:57 gmt
revision:0
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Kickback cuts Backprop's red-tape: Biologically plausible credit assignment in neural networks Bit of a meh -- idea is, rather than propagating error signals backwards through a hierarchy, you propagate only one layer + use a signed global reward signal. This works by keeping the network ‘coherent’ -- positive neurons have positive input weights, and negative neurons have negative weights, such that the overall effect of a weight change does not change sign when propagated forward through the network. This is kind of a lame shortcut, imho, as it limits the types of functions that the network can model & the computational structure of the network. This is already quite limited by the dot-product-rectifier common structure (as is used here). Much more interesting and possibly necessary (given much deeper architectures now) is to allow units to change sign. (Open question as to whether they actually frequently do!). As such, the model is in the vein of "how do we make backprop biologically plausible by removing features / communication" rather than "what sorts of signals and changes does the brain use perceive and generate behavior". This is also related to the literature on what ResNets do; what are the skip connections for? Amthropic has some interesting analyses for Transformer architectures, but checking the literature on other resnets is for another time. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1569} |
ref: -2022
tags: symbolic regression facebook AI transformer
date: 05-17-2022 20:25 gmt
revision:0
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Deep symbolic regression for recurrent sequences Surprisingly, they do not do any network structure changes; it’s Vaswini 2017w/ a 8-head, 8 layer transformer (sequence to sequence, not decoder only) with a latent dimension of 512. Significant work was in feature / representation engineering (e.g. base-10k representations of integers and fixed-precision representations of floating-point numbers. (both of these involve a vocabulary size of ~10k ... amazing still that this works..)) + the significant training regimen they worked with (16 Turing GPUs, 32gb ea). Note that they do perform a bit of beam-search over the symbolic regressions by checking how well each node fits to the starting sequence, but the models work even without this degree of refinement. (As always, there undoubtedly was significant effort spent in simply getting everything to work) The paper does both symbolic (estimate the algebraic recurence relation) and numeric (estimate the rest of the sequence) training / evaluation. Symbolic regression generalizes better, unsurprisingly. But both can be made to work even in the presence of (log-scaled) noise! Analysis of how the transformers work for these problems is weak; only one figure showing that the embeddings of the integers follows some meandering but continuous path in t-SNE space. Still, the trained transformer is able to usually best hand-coded sequence inference engine(s) in Mathematica, and does so without memorizing all of the training data. Very impressive and important result, enough to convince that this learned representation (and undiscovered cleverness, perhaps) beats human mathematical engineering, which probably took longer and took more effort. It follows, without too much imagination (but vastly more compute), that you can train an 'automatic programmer' in the very same way. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Burst-dependent synaptic plasticity can coordinate learning in hierarchical circuits
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{1567} |
ref: -0
tags: evolution simplicity symmetry kolmogorov complexity polyominoes protein interactions
date: 04-21-2022 18:22 gmt
revision:5
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Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution
The paper features a excellent set of references, including:
Letter to a friend following her article Machine learning in evolutionary studies comes of age Read your PNAS article last night, super interesting that you can get statistical purchase on long-lost evolutionary 'sweeps' via GANs and other neural network models. I feel like there is some sort of statistical power issue there? DNNs are almost always over-parameterized... slightly suspicious. This morning I was sleepily mulling things over & thought about a walking conversation that we had a long time ago in the woods of NC: Why is evolution so effective? Why does it seem to evolve to evolve? Thinking more -- and having years more perspective -- it seems almost obvious in retrospect: it's a consequence of Bayes' rule. Evolution finds solutions in spaces that have overwhelming prevalence of working solutions. The prior has an extremely strong effect. These representational / structural spaces by definition have many nearby & associated solutions, hence appear post-hoc 'evolvable'. (You probably already know this.) I think proteins very much fall into this category: AA were added to the translation machinery based on ones that happened to solve a particular problem... but because of the 'generalization prior' (to use NN parlance), they were useful for many other things. This does not explain the human-engineering-like modularity of mature evolved systems, but maybe that is due to the strong simplicity prior [1] Very very interesting to me is how the science of evolution and neural networks are drawing together, vis a vis the lottery ticket hypothesis. Both evince a continuum of representational spaces, too, from high-dimensional vectoral (how all modern deep learning systems work) to low-dimensional modular, specific, and general (phenomenological human cognition). I suspect that evolution uses a form of this continuum, as seen in the human high-dimensional long-range gene regulatory / enhancer network (= a structure designed to evolve). Not sure how selection works here, though; it's hard to search a high-dimensional space. The brain has an almost identical problem: it's hard to do 'credit assignment' in a billions-large, deep and recurrent network. Finding which set of synapses caused a good / bad behaviior takes a lot of bits. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Interactions between learning and evolution
Altogether (historically) interesting, but some of these ideas might well have been anticipated by some simple hand calculations. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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“Visualizing data using t-SNE”
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Distilling free-form natural laws from experimental data
Since his Phd, Michael Schmidt has gone on to found Nutonian, which produced Eurequa software, apparently without dramatic new features other than being able to use the cloud for equation search. (Probably he improved many other detailed facets of the software..). Nutonian received $4M in seed funding, according to Crunchbase. In 2017, Nutonian was acquired by Data Robot (for an undisclosed amount), where Michael has worked since, rising to the title of CTO. Always interesting to follow up on the authors of these classic papers! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{1558} |
ref: -2021
tags: hippocampal behavior scale plasticity Magee Romani Bittner
date: 12-20-2021 22:39 gmt
revision:0
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Bidirectional synaptic plasticity rapidly modifies hippocampal representations
I'm still not 100% sure that this excludes any influence on presynaptic activity ... they didn't control for that. But certainly LTD in their model does not require postsynaptic activity; indeed, it may only require net-synaptic homeostasis. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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The fact that sVD works at all, and pulls out some structure is interesting! Not nearly as good as word2vec. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1556} |
ref: -0
tags: concept net NLP transformers graph representation knowledge
date: 11-04-2021 17:48 gmt
revision:0
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Symbolic Knowledge Distillation: from General Language Models to Commonsense Models
Human-designed knowledge graphs are described here: ConceptNet 5.5: An Open Multilingual Graph of General Knowledge And employed for profit here: https://www.luminoso.com/ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Recently I've been underwhelmed by the performance of adaptive optics (AO) for imaging head-fixed cranial-window mice. There hasn't been much of an improvement, despite significant optimization effort. This begs the question: where are AO microscopes used? When the purpose of a paper is to explain and qualify an novel AO approach, the improvement is always good, >> 2x. Yet, in the one paper (first below) when the purpose was neuroscience, not optics, the results are less inspiring. Are the results from the optics papers cherry-picked? Thalamus provides layer 4 of primary visual cortex with orientation- and direction-tuned inputs Wenzhi Sun, Zhongchao Tan, Brett D Mensh & Na Ji 2016 https://www.nature.com/articles/nn.4196
Direct wavefront sensing for high-resolution in vivo imaging in scattering tissue Kai Wang, Wenzhi Sun, Christopher T. Richie, Brandon K. Harvey, Eric Betzig & Na Ji, 2015 https://www.nature.com/articles/ncomms8276
Multiplexed aberration measurement for deep tissue imaging in vivo Chen Wang, Rui Liu, Daniel E Milkie, Wenzhi Sun, Zhongchao Tan, Aaron Kerlin, Tsai-Wen Chen, Douglas S Kim & Na Ji 2014 https://www.nature.com/articles/nmeth.3068
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{1554} |
ref: -2021
tags: FIBSEM electron microscopy presynaptic plasticity activity Funke
date: 10-12-2021 17:03 gmt
revision:0
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Ultrastructural readout of in vivo synaptic activity for functional connectomics
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DreamCoder: Growing generalizable, interpretable knowledge with wake-sleep Bayesian program learning
This paper describes a system for adaptively finding programs which succinctly and accurately produce desired output. These desired outputs are provided by the user / test system, and come from a number of domains:
Also in the lineage is the EC2 algorithm, which most of the same authors above published in 2018. EC2 centers around the idea of "explore - compress" : explore solutions to your program induction problem during the 'wake' phase, then compress the observed programs into a library by extracting/factoring out commonalities during the 'sleep' phase. This of course is one of the core algorithms of human learning: explore options, keep track of both what worked and what didn't, search for commonalities among the options & their effects, and use these inferred laws or heuristics to further guide search and goal-setting, thereby building a buffer attack the curse of dimensionality. Making the inferred laws themselves functions in a programming library allows hierarchically factoring the search task, making exploration of unbounded spaces possible. This advantage is unique to the program synthesis approach. This much is said in the introduction, though perhaps with more clarity. DreamCoder is an improved, more-accessible version of EC2, though the underlying ideas are the same. It differs in that the method for constructing libraries has improved through the addition of a powerful version space for enumerating and evaluating refactors of the solutions generated during the wake phase. (I will admit that I don't much understand the version space system.) This version space allows DreamCoder to collapse the search space for re-factorings by many orders of magnitude, and seems to be a clear advancement. Furthermore, DreamCoder incorporates a second phase of sleep: "dreaming", hence the moniker. During dreaming the library is used to create 'dreams' consisting of combinations of the library primitives, which are then executed with training data as input. These dreams are then used to train up a neural network to predict which library and atomic objects to use in given contexts. Context in this case is where in the parse tree a given object has been inserted (it's parent and which argument number it sits in); how the data-context is incorporated to make this decision is not clear to me (???). This neural dream and replay-trained neural network is either a GRU recurrent net with 64 hidden states, or a convolutional network feeding into a RNN. The final stage is a linear ReLu (???) which again is not clear how it feeds into the prediction of "which unit to use when". The authors clearly demonstrate that the network, or the probabalistic context-free grammar that it controls (?) is capable of straightforward optimizations, like breaking symmetries due to commutativity, avoiding adding zero, avoiding multiplying by one, etc. Beyond this, they do demonstrate via an ablation study that the presence of the neural network affords significant algorithmic leverage in all of the problem domains tested. The network also seems to learn a reasonable representation of the sub-type of task encountered -- but a thorough investigation of how it works, or how it might be made to work better, remains desired. I've spent a little time looking around the code, which is a mix of python high-level experimental control code, and lower-level OCaml code responsible for running (emulating) the lisp-like DSL, inferring type in it's polymorphic system / reconciling types in evaluated program instances, maintaining the library, and recompressing it using aforementioned version spaces. The code, like many things experimental, is clearly a work-in progress, with some old or unused code scattered about, glue to run the many experiments & record / analyze the data, and personal notes from the first author for making his job talks (! :). The description in the supplemental materials, which is satisfyingly thorough (if again impenetrable wrt version spaces), is readily understandable, suggesting that one (presumably the first) author has a clear understanding of the system. It doesn't appear that much is being hidden or glossed over, which is not the case for all scientific papers. With the caveat that I don't claim to understand the system to completion, there are some clear areas where the existing system could be augmented further. The 'recognition' or perceptual module, which guides actual synthesis of candidate programs, realistically can use as much information as is available in DreamCoder as is available: full lexical and semantic scope, full input-output specifications, type information, possibly runtime binding of variables when filling holes. This is motivated by the way that humans solve problems, at least as observed by introspection:
Critical to making this work is to have, as I've written in my notes many years ago, a 'self compressing and factorizing memory'. The version space magic + library could be considered a working example of this. In the realm of ANNs, per recent OpenAI results with CLIP and Dall-E, really big transformers also seem to have strong compositional abilities, with the caveat that they need to be trained on segments of the whole web. (This wouldn't be an issue here, as Dreamcoder generates a lot of its own training data via dreams). Despite the data-inefficiency of DNN / transformers, they should be sufficient for making something in the spirit of above work, with a lot of compute, at least until more efficient models are available (which they should be shortly; see AlphaZero vs MuZero). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1553} |
ref: -2020
tags: excitatory inhibitory balance E-I synapses
date: 10-06-2021 17:50 gmt
revision:1
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We mapped over 90,000 E and I synapses across twelve L2/3 PNs and uncovered structured organization of E and I synapses across dendritic domains as well as within individual dendritic segments. Despite significant domain-specific variation in the absolute density of E and I synapses, their ratio is strikingly balanced locally across dendritic segments. Computational modeling indicates that this spatially precise E/I balance dampens dendritic voltage fluctuations and strongly impacts neuronal firing output. I think this would be tenuous, but they did do patch-clamp recording to back it up, but it's vitally interesting from a structural standpoint. Plus, this is a enjoyable, well-written paper :-) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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The HSIC Bottleneck: Deep learning without Back-propagation In this work, the authors use a kernelized estimate of statistical independence as part of a 'information bottleneck' to set per-layer objective functions for learning useful features in a deep network. They use the HSIC, or Hilbert-schmidt independence criterion, as the independence measure. The information bottleneck was proposed by Bailek (spikes..) et al in 1999, and aims to increase the mutual information between the layer representation and the labels while minimizing the mutual information between the representation and the input:
Where is the hidden representation at layer i (later output), is the layer input, and are the labels. By replacing with the HSIC, and some derivation (?), they show that
Where are samples and labels, and -- that is, it's the kernel function applied to all pairs of (vectoral) input variables. H is the centering matrix. The kernel is simply a Gaussian kernel, . So, if all the x and y are on average independent, then the inner-product will be mean zero, the kernel will be mean one, and after centering will lead to zero trace. If the inner product is large within the realm of the derivative of the kernel, then the HSIC will be large (and negative, i think). In practice they use three different widths for their kernel, and they also center the kernel matrices. But still, the feedback is an aggregate measure (the trace) of the product of two kernelized (a nonlinearity) outer-product spaces of similarities between inputs. it's not unimaginable that feedback networks could be doing something like this... For example, a neural network could calculate & communicate aspects of joint statistics to reward / penalize weights within a layer of a network, and this is parallelizable / per layer / adaptable to an unsupervised learning regime. Indeed, that was done almost exactly by this paper: Kernelized information bottleneck leads to biologically plausible 3-factor Hebbian learning in deep networks albeit in a much less intelligible way. Robust Learning with the Hilbert-Schmidt Independence Criterion Is another, later, paper using the HSIC. Their interpretation: "This loss-function encourages learning models where the distribution of the residuals between the label and the model prediction is statistically independent of the distribution of the instances themselves." Hence, given above nomenclature, (I'm not totally sure about the weighting, but might be required given the definition of the HSIC.) As I understand it, the HSIC loss is a kernellized loss between the input, output, and labels that encourages a degree of invariance to input ('covariate shift'). This is useful, but I'm unconvinced that making the layer output independent of the input is absolutely essential (??) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1552} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Modularizing Deep Learning via Pairwise Learning With Kernels
I think in general this is an important result, even if its not wholly unique / somewhat anticipated (it's a year old at the time of writing). Modular training of neural networks is great for efficiency, parallelization, and biological implementations! Transport of weights between layers is hence non-essential. Classes still are, but I wonder if temporal continuity can solve some of these problems? (There is plenty of other effort in this area -- see also {1544}) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1551} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Cell-based reporters reveal in vivo dynamics of dopamine and norepinephrine release in murine cortex
Referenced -- and used by the recent paper Reinforcement learning links spontaneous cortical dopamine impulses to reward, which showed that dopamine signaling itself can come under volitional, operant-conditioning (or reinforcement type) modulation. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1550} |
ref: -2011
tags: government polyicy observability submerged state America
date: 09-23-2021 22:06 gmt
revision:0
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The Submerged State -- How Invisible Government Policies Undermine American Democracy. By Suzanne Mettler (I've not read this book, just the blurb, but it looks like a defensible thesis) : Government polyicy, rather than distributing resources (money, infrastructure, services) as directly as possible to voters, have recently opted to distribute indirectly, through private companies. This gives the market & private organizations more perceived clout, perpetuates a level of corruption, and undermines American's faith in their government. So, we need a better 'debugger' for policy in america? Something like a discrete chain rule to help people figure out what policies (and who) are responsible for the good / bad things in their life? Sure seems that the bureaucracy is could use some cleanup / is failing under burgeoning complexity. This is probably not dissimilar to cruddy technical systems. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1548} |
ref: -2021
tags: gated multi layer perceptrons transformers ML Quoc_Le Google_Brain
date: 08-05-2021 06:00 gmt
revision:4
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Pretty remarkable that an industrial lab freely publishes results like this. I guess the ROI is that they get the resultant improved ideas? Or, perhaps, Google is in such a dominant position in terms of data and compute that even if they give away ideas and code, provided some of the resultant innovation returns to them, they win. The return includes trained people as well as ideas. Good for us, I guess! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1449} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
This was compiled from searching papers which referenced Olshausen and Field 1996 PMID-8637596 Emergence of simple-cell receptive field properties by learning a sparse code for natural images.
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{1546} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Local synaptic learning rules suffice to maximize mutual information in a linear network
x = randn(1000, 10); Q = x' * x; a = 0.001; Y = randn(10, 1); y = zeros(10, 1); for i = 1:1000 y = Y + (eye(10) - a*Q)*y; end y - pinv(Q)*Y / a % should be zero.
To this is added a 'sensing' learning and 'noise' unlearning phase -- one optimizes , the other minimizes . Everything is then applied, similar to before, to a gaussian-filtered one-dimensional white-noise stimuli. He shows this results in bandpass filter behavior -- quite weak sauce in an era where ML papers are expected to test on five or so datasets. Even if this was 1992 (nearly forty years ago!), it would have been nice to see this applied to a more realistic dataset; perhaps some of the following papers? Olshausen & Field came out in 1996 -- but they applied their algorithm to real images. In both Olshausen & this work, no affordances are made for multiple layers. There have to be solutions out there... | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1543} |
ref: -2019
tags: backprop neural networks deep learning coordinate descent alternating minimization
date: 07-21-2021 03:07 gmt
revision:1
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Beyond Backprop: Online Alternating Minimization with Auxiliary Variables
This is interesting in that the weight updates can be cone in parallel - perhaps more efficient - but you are still propagating errors backward, albeit via optimizing 'codes'. Given the vast infractructure devoted to auto-diff + backprop, I can't see this being adopted broadly. That said, the idea of alternating minimization (which is used eg for EM clustering) is powerful, and this paper does describe (though I didn't read it) how there are guarantees on the convexity of the alternating minimization. Likewise, the authors show how to improve the performance of the online / minibatch algorithm by keeping around memory variables, in the form of covariance matrices. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1542} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
https://github.com/wilicc/gpu-burn Mult-gpu stress test. Are your GPUs overclocked to the point of overheating / being unreliable? | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1541} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Like this blog but 100% better! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Two Routes to Scalable Credit Assignment without Weight Symmetry This paper looks at five different learning rules, three purely local, and two non-local, to see if they can work as well as backprop in training a deep convolutional net on ImageNet. The local learning networks all feature forward weights W and backward weights B; the forward weights (+ nonlinearities) pass the information to lead to a classification; the backward weights pass the error, which is used to locally adjust the forward weights. Hence, each fake neuron has locally the forward activation, the backward error (or loss gradient), the forward weight, backward weight, and Hebbian terms thereof (e.g the outer product of the in-out vectors for both forward and backward passes). From these available variables, they construct the local learning rules:
Each of these serves as a "regularizer term" on the feedback weights, which governs their learning dynamics. In the case of backprop, the backward weights B are just the instantaneous transpose of the forward weights W. A good local learning rule approximates this transpose progressively. They show that, with proper hyperparameter setting, this does indeed work nearly as well as backprop when training a ResNet-18 network. But, hyperparameter settings don't translate to other network topologies. To allow this, they add in non-local learning rules:
In "Symmetric Alignment", the Self and Decay rules are employed. This is similar to backprop (the backward weights will track the forward ones) with L2 regularization, which is not new. It performs very similarly to backprop. In "Activation Alignment", Amp and Sparse rules are employed. I assume this is supposed to be more biologically plausible -- the Hebbian term can track the forward weights, while the Sparse rule regularizes and stabilizes the learning, such that overall dynamics allow the gradient to flow even if W and B aren't transposes of each other. Surprisingly, they find that Symmetric Alignment to be more robust to the injection of Gaussian noise during training than backprop. Both SA and AA achieve similar accuracies on the ResNet benchmark. The authors then go on to explain the plausibility of non-local but approximate learning rules with Regression discontinuity design ala Spiking allows neurons to estimate their causal effect. This is a decent paper,reasonably well written. They thought trough what variables are available to affect learning, and parameterized five combinations that work. Could they have done the full matrix of combinations, optimizing just they same as the metaparameters? Perhaps, but that would be even more work ... Regarding the desire to reconcile backprop and biology, this paper does not bring us much (if at all) closer. Biological neural networks have specific and local uses for error; even invoking 'error' has limited explanatory power on activity. Learning and firing dynamics, of course of course. Is the brain then just an overbearing mess of details and overlapping rules? Yes probably but that doesn't mean that we human's can't find something simpler that works. The algorithms in this paper, for example, are well described by a bit of linear algebra, and yet they are performant. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
https://webautocats.com/epc/saab/sbd/ -- Online, free parts look-up for Saab cars. Useful. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1538} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-20596024 Sensitivity to perturbations in vivo implies high noise and suggests rate coding in cortex
Cortical reliability amid noise and chaos
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{1537} |
ref: -0
tags: cortical computation learning predictive coding reviews
date: 02-23-2021 20:15 gmt
revision:2
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PMID-30359606 Predictive Processing: A Canonical Cortical Computation
PMID-23177956 Canonical microcircuits for predictive coding
Control of synaptic plasticity in deep cortical networks
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{1536} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
From Protein Structure to Function with Bioinformatics
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{1532} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-23273272 A cellular mechanism for cortical associations: and organizing principle for the cerebral cortex
See also: PMID-25174710 Sensory-evoked LTP driven by dendritic plateau potentials in vivo
And: The binding solution?, a blog post covering Bittner 2015 that looks at rapid dendritic plasticity in the hippocampus as a means of binding stimuli to place fields. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1523} |
ref: -0
tags: tennenbaum compositional learning character recognition one-shot learning
date: 02-23-2021 18:56 gmt
revision:2
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One-shot learning by inverting a compositional causal process
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{1526} |
ref: -0
tags: neuronal assemblies maass hebbian plasticity simulation austria fMRI
date: 02-23-2021 18:49 gmt
revision:1
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PMID-32381648 A model for structured information representation in neural networks in the brain
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Reconciling modern machine-learning practice and the classical bias–variance trade-off A formal publication of the effect famously discovered at OpenAI & publicized on their blog. Goes into some details on fourier features & runs experiments to verify the OpenAI findings. The result stands. An interesting avenue of research is using genetic algorithms to perform the search over neural network parameters (instead of backprop) in reinforcement-learning tasks. Ben Phillips has a blog post on some of the recent results, which show that it does work for certain 'hard' problems in RL. Of course, this is the dual of the 'lottery ticket' hypothesis and the deep double descent, above; large networks are likely to have solutions 'close enough' to solve a given problem. That said, genetic algorithms don't necessarily perform gradient descent to tweak the weights for optimal behaviror once they are within the right region of RL behavior. See {1530} for more discussion on this topic, as well as {1525} for a more complete literature survey. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1534} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Going in circles is the way forward: the role of recurrence in visual inference I think the best part of this article are the references -- a nicely complete listing of, well, the current opinion in Neurobiology! (Note that this issue is edited by our own Karel Svoboda, hence there are a good number of Janelians in the author list..) The gestalt of the review is that deep neural networks need to be recurrent, not purely feed-forward. This results in savings in overall network size, and increase in the achievable computational complexity, perhaps via the incorporation of priors and temporal-spatial information. All this again makes perfect sense and matches my sense of prevailing opinion. Of course, we are left wanting more: all this recurrence ought to be structured in some way. To me, a rather naive way of thinking about it is that feed-forward layers cause weak activations, which are 'amplified' or 'selected for' in downstream neurons. These neurons proximally code for 'causes' or local reasons, based on the supported hypothesis that the brain has a good temporal-spatial model of the visuo-motor world. The causes then can either explain away the visual input, leading to balanced E-I, or fail to explain it, in which the excess activity is either rectified by engaging more circuits or engaging synaptic plasticity. A critical part of this hypothesis is some degree of binding / disentanglement / spatio-temporal re-assignment. While not all models of computation require registers / variables -- RNNs are Turning-complete, e.g., I remain stuck on the idea that, to explain phenomenological experience and practical cognition, the brain much have some means of 'binding'. A reasonable place to look is the apical tuft dendrites, which are capable of storing temporary state (calcium spikes, NMDA spikes), undergo rapid synaptic plasticity, and are so dense that they can reasonably store the outer-product space of binding. There is mounting evidence for apical tufts working independently / in parallel is investigations of high-gamma in ECoG: PMID-32851172 Dissociation of broadband high-frequency activity and neuronal firing in the neocortex. "High gamma" shows little correlation with MUA when you differentiate early-deep and late-superficial responses, "consistent with the view it reflects dendritic processing separable from local neuronal firing" | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1533} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Up until reading this, I had thought that the Balwin effect refers to the fact that when animals gain an ability to learn, this allows them to take new ecological roles without genotypic adaptation. This is a component of the effect, but is not the original meaning, which is opposite: when species adapt to a novel environment through phenotypic adptation (say adapting to colder weather through within-lifetime variation), evolution tends to push these changes into the germ line. This is something to the effect of Lamarkian evolution. In the case of house finches, as discussed in the link above, this pertains to increased brood variability and sexual dimorphism due to varied maternal habits and hormones due to environmental stress. This variance is then rapidly operated on by natural selection to tune the finch to it's new enviroment, including Montana, where the single author did most of his investigation. There are of course countless other details here, but still this is an illuminating demonstration of how evolution works to move information into the genome. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1531} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-24204224 The Convallis rule for unsupervised learning in cortical networks 2013 - Pierre Yger 1 , Kenneth D Harris This paper aims to unify and reconcile experimental evidence of in-vivo learning rules with established STDP rules. In particular, the STDP rule fails to accurately predict change in strength in response to spike triplets, e.g. pre-post-pre or post-pre-post. Their model instead involves the competition between two time-constant threshold circuits / coincidence detectors, one which controls LTD and another LTP, and is such an extension of the classical BCM rule. (BCM: inputs below a threshold will weaken a synapse; those above it will strengthen. ) They derive the model from optimization criteria that neurons should try to optimize the skewedness of the distribution of their membrane potential: much time spent either firing spikes or strongly inhibited. This maps to a objective function F that looks like a valley - hence the 'convallis' in the name (latin for valley); the objective is differentiated to yield a weighting function for weight changes; they also add a shrinkage function (line + heaviside function) to gate weight changes 'off' at resting membrane potential. A network of firing neurons successfully groups correlated rate-encoded inputs, better than the STDP rule. it can also cluster auditory inputs of spoken digits converted into cochleogram. But this all seems relatively toy-like: of course algorithms can associate inputs that co-occur. The same result was found for a recurrent balanced E-I network with the same cochleogram, and convalis performed better than STDP.  Meh. Perhaps the biggest thing I got from the paper was how poorly STDP fares with spike triplets: Pre following post does not 'necessarily' cause LTD; it's more complicated than that, and more consistent with the two different-timeconstant coincidence detectors. This is satisfying as it allows for apical dendritic depolarization to serve as a contextual binding signal - without negatively impacting the associated synaptic weights. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1530} |
ref: -2017
tags: deep neuroevolution jeff clune Uber genetic algorithms
date: 02-18-2021 18:27 gmt
revision:1
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Deep Neuroevolution: genetic algorithms are a competitive alternative for training deep neural networks for reinforcement learning* Uber AI labs; Jeff Clune.
The result is indeed surprising, but it also feels lazy -- the total effort or information that they put into writing the actual algorithm is small; as mentioned in the introduction, this is a case of old algorithms with modern levels of compute. Analogously, compare Go-Explore, also by Uber AI labs, vs Agent57 by DeepMind; the Agent57 paper blithely dismisses the otherwise breathless Go-Explore result as feature engineering and unrealistic free backtracking / game-resetting (which is true..) It's strange that they did not incorporate crossover aka recombination, as David MacKay clearly shows that recombination allows for much higher mutation rates and much better transmission of information through a population. (Chapter 'Why have sex'). They also perhaps more reasonably omit developmental encoding, where network weights are tied or controlled through development, again in an analogy to biology. A better solution, as they point out, would be some sort of hybrid GA / ES / A3C system which used both gradient-based tuning, random stochastic gradient-based exploration, and straight genetic optimization, possibly all in parallel, with global selection as the umbrella. They mention this, but to my current knowledge this has not been done. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1528} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Discovering hidden factors of variation in deep networks
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{1527} |
ref: -0
tags: inductive logic programming deepmind formal propositions prolog
date: 11-21-2020 04:07 gmt
revision:0
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Learning Explanatory Rules from Noisy Data
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{1490} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21527931 Two-photon absorption properties of fluorescent proteins
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Why deep learning works even though it shouldn't, instigated a fun thread thinking about "complexity of model" vs "complexity of solution".
The Lottery Ticket Hypothesis: Finding Sparse, Trainable Neural Networks
Stabilizing the lottery ticket hypothesis
Identifying and attacking the saddle point problem in high-dimensional non-convex optimization Rethinking Parameter Counting in Deep Models: Effective Dimensionality Revisited
Random deep neural networks are biased towards simple functions
Reconciling modern machine learning practice and the bias-variance trade-off
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{1524} |
ref: -2020
tags: replay hippocampus variational autoencoder
date: 10-11-2020 04:09 gmt
revision:1
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Brain-inspired replay for continual learning with artificial neural networks
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Schema networks: zero-shot transfer with a generative causal model of intuitive physics
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{1521} |
ref: -2005
tags: dimensionality reduction contrastive gradient descent
date: 09-13-2020 02:49 gmt
revision:2
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Dimensionality reduction by learning and invariant mapping
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PMID-15142952 Visual binding through reentrant connectivity and dynamic synchronization in a brain-based device
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Neuralink progress update August 28 2020 Some commentary. The good:
The mixed:
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{1417} |
ref: -0
tags: synaptic plasticity 2-photon imaging inhibition excitation spines dendrites synapses 2p
date: 08-14-2020 01:35 gmt
revision:3
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PMID-22542188 Clustered dynamics of inhibitory synapses and dendritic spines in the adult neocortex.
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{1478} |
ref: -2013
tags: 2p two photon STED super resolution microscope synapse synaptic plasticity
date: 08-14-2020 01:34 gmt
revision:3
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PMID-23442956 Two-Photon Excitation STED Microscopy in Two Colors in Acute Brain Slices
PMID-29932052 Chronic 2P-STED imaging reveals high turnover of spines in the hippocampus in vivo | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-31780899 Single Synapse LTP: A matter of context?
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PMID-26621426 Causal Inference and Explaining Away in a Spiking Network
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Super-Photostable Phosphole-Based Dye for Multiple-Acquisition Stimulated Emission Depletion Imaging
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Spent a while this evening reading about Qualified Immunity -- the law that permits government officials (e.g. police officers) immunity when 'doing their jobs'. It's perhaps one root of the George Floyd / racism protests, as it has set a precedent that US police can be violent and get away with it. (This is also related to police unions and collective liability loops... anyway) The supreme court has the option to take cases challenging the constitutionality of Qualified Immunity, which many on both sides of the political spectrum want them to do. It 'got' this power via Marbury vs. Madison. M v. M is self-referential genius:
As a person curious how systems gain complexity and feedback loops ... so much nerdgasm. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1512} |
ref: -0
tags: rutherford journal computational theory neumann complexity wolfram
date: 05-05-2020 18:15 gmt
revision:0
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The Structures for Computation and the Mathematical Structure of Nature
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{1510} |
ref: -2017
tags: google deepmind compositional variational autoencoder
date: 04-08-2020 01:16 gmt
revision:7
[6] [5] [4] [3] [2] [1] [head]
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SCAN: learning hierarchical compositional concepts
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Improved asymmetric locality sensitive hashing for maximum inner product search
Use case: Capsule: a camera based positioning system using learning
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{1500} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-31942076 A distributional code for value in dopamine based reinforcement learning
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Scalable and sustainable deep learning via randomized hashing
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Finding frequent items in data streams
Mission: Ultra large-scale feature selection using Count-Sketches
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PMID-30420685 Fast in-vivo voltage imaging using a red fluorescent indicator
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A 6-nm ultra-photostable DNA Fluorocube for fluorescence imaging Also including some correspondence with the authors: Me Nice work and nice paper, thanks for sharing .. and not at all what I had expected from Ron's comments! Below are some comments ... would love your opinion. I'd expect that the molar absorption coefficients for the fluorocubes should be ~6x larger than for the free dyes and the single dye cubes (measured?), yet the photon yields for all except Cy3N maybe are around the yield for one dye molecule. So the quantum yield must be decreased by ~6x? This in turn might be from a middling FRET which reduces lifetime, thereby the probability of ISC, photoelectron transfer, and hence photobleaching. I wonder if in the case of ATTO 647N Cy5 and Cy3, the DNA is partly shielding the fluorphores from solvent (ala ethidium bromide), which also helps with stability, just like in fluorescent proteins. ATTO 647N generates a lot of singlet oxygen, who knows what it's doing to DNA. Can you do a log-log autocorrelation of the blinking timeseries of the constructs? This may reveal different rate constants controlling dark/light states (though, for 6 coupled objects, might not be interpretable!) Also, given the effect of DNA shielding, have you compared to free dyes to single-dye cubes other than supp fig 10? The fact that sulfonation made such a huge effect in brightness is suggestive. Again, these are super interesting & exciting results! Author I haven't directly looked at the molar absorption coefficient but judging from the data that I collected for the absorption spectra, there is certainly an increase for the fluorocubes compared to single dyes. I agree that this would be an interesting experiment and I am planning collect data to measure the molar absorption coefficient. I would also expect a ~6 fold increase for the Fluorocubes. Yes, we suspect homo FRET to help reduce photobleaching. So far we only measured lifetimes in bulk but are planning to obtain lifetime data on the single-molecule level soon. We also wondered if the DNA is providing some kind of shield for the fluorophores but could not design an experiment to directly test this hypothesis. If you have a suggestion, that would be wonderful. The log-log autocorrelation of blinking events is indeed difficult to interpret. Already individual intensity traces of fluorocubes are difficult to analyze as many of them get brighter before they bleach. We are also wondering if some fluorocubes are emitting two photons simultaneously. We will hopefully be able to measure this soon. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-18204458 High-speed, low-photodamage nonlinear imaging using passive pulse splitters
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{1502} |
ref: -0
tags: rhodamine derivatives imidazole bacterial resistance
date: 02-19-2020 19:10 gmt
revision:2
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PMID-24877017 Optimal lens design and use in laser-scanning microscopy
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{1498} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Optimization and functionalization of red-shifted rhodamine dyes
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{1495} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Why multifactor?
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{1497} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-26659050 Human level concept learning through probabalistic program induction
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{1496} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-29123069 A neural algorithm for a fundamental computing problem
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{1494} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-25258080 A critical time window for dopamine actions on the structural plasticity of dendritic spines
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{1493} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-27690349 Nonlinear Hebbian Learning as a Unifying Principle in Receptive Field Formation
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{1489} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1487} |
ref: -0
tags: adaptive optics sensorless retina fluorescence imaging optimization zernicke polynomials
date: 11-15-2019 02:51 gmt
revision:0
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PMID-26819812 Wavefront sensorless adaptive optics fluorescence biomicroscope for in vivo retinal imaging in mice
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{1486} |
ref: -2019
tags: non degenerate two photon excitation fluorophores fluorescence OPO optical parametric oscillator
date: 10-31-2019 20:53 gmt
revision:0
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Efficient non-degenerate two-photon excitation for fluorescence microscopy | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1485} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-26352471 Labelling and optical erasure of synaptic memory traces in the motor cortex
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{1484} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Carbon capture links:
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{1483} |
ref: -0
tags: Lucy Flavin mononucelotide FAD FMN fluorescent protein reporter
date: 10-17-2019 19:54 gmt
revision:1
[0] [head]
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PMID-25906065 LucY: A Versatile New Fluorescent Reporter Protein
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{1481} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
How much energy is thermodynamically required to concentrate from one liter of air? concentration is 400ppm, or 0.4%. 1l of air is 1/22.4 or 44mMol. From wikipedia, the entropy of mixing is: where and are the fraction of air and (0.996 and 0.004) This works out to . At STP, 300K, this means you need only about to extract the carbon dioxide. A car driving 1 km emits about 150g carbon dioxide. This is 3.4 moles, which will diffuse into 852 moles of air, or 19e3 liters of air (19 cubic meters). To pull this back out of the air then you'd need at minimum 55.3 kJ. This is not much at all -- a car produces 100kW mechanical power, or 100kJ every second, and presumably it takes a minute to drive that 1km. But such perfectly efficient purification is not possible. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1480} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-25342811 Lattice Light Sheet Microscopy: Imaging Molecules to Embryos at High Spatiotemporal Resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{208} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-22388818 Corticostriatal plasticity is necessary for learning intentional neuroprosthetic skills.
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{99} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15928412[0] Naive coadaptive Control May 2005. see notes ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{331} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17021028[0] Correlations Between the Same Motor Cortex Cells and Arm Muscles During a Trained Task, Free Behavior, and Natural Sleep in the Macaque Monkey
____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1477} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-31495645 Can One Concurrently Record Electrical Spikes from Every Neuron in a Mammalian Brain?
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{1476} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-22831554 Swept field laser confocal microscopy for enhanced spatial and temporal resolution in live-cell imaging.
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{1475} |
ref: -2017
tags: two photon holographic imaging Arch optogenetics GCaMP6
date: 09-12-2019 19:24 gmt
revision:1
[0] [head]
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PMID-28053310 Simultaneous high-speed imaging and optogenetic inhibition in the intact mouse brain.
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{1473} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17179937 Major signal increase in fluorescence microscopy through dark-state relaxation (2007)
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{1472} |
ref: -0
tags: computational neuroscience opinion tony zador konrad kording lillicrap
date: 07-30-2019 21:04 gmt
revision:0
[head]
|
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Two papers out recently in Arxive and Biorxiv:
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{1471} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Edited Terrence Eden's script to average multiple frames when producing a time-lapse video from a continuous video. Frames are averaged together before decimation, rather than pure decimation, as with ffmpeg. Produces appealing results on subjects like water. Also, outputs a video directly, without having to write individual images. python #!/usr/bin/python import cv2 import sys # Video to read print str(sys.argv[1]) vidcap = cv2.VideoCapture(sys.argv[1]) # Which frame to start from, how many frames to go through start_frame = 0 frames = 61000 # Counters count = 0 save_seq = 0 decimate = 10 rolling = 16 # average over N output frames transpose = False if(transpose): h = vidcap.get(3) w = vidcap.get(4) else: w = vidcap.get(3) h = vidcap.get(4) fourcc = cv2.VideoWriter_fourcc(*'mp4v') writer = cv2.VideoWriter("timelapse.mp4", fourcc, 30, (int(w), int(h)), True) avglist = [] while True: # Read a frame success,image = vidcap.read() if not success: break if count > start_frame+frames: break if count >= start_frame: if (count % decimate == 0): # Extract the frame and convert to float avg = image.astype('uint16') # max 255 frames averaged. if (count % decimate > 0 and count % decimate <= (decimate-1)): avg = avg + image.astype('uint16') if (count % decimate == (decimate-1)): # Every 100 frames (3 seconds @ 30fps) avg = avg / decimate if(transpose): avg = cv2.transpose(avg) avg = cv2.flip(avg, 1) avg2 = avg; for a in avglist: avg2 = avg2 + a avg2 = avg2 / rolling; avglist.append(avg); if len(avglist) >= rolling: avglist.pop(0) # remove the first item. avg2 = avg2.astype('uint8') print("saving "+str(save_seq)) # Save Image # cv2.imwrite(filename+str('{0:03d}'.format(save_seq))+".png", avg) save_seq += 1 writer.write(avg2) if count == frames + start_frame: break count += 1 writer.release() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1470} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Large-Scale Optical Neural Networks based on Photoelectric Multiplication
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{1469} |
ref: -2016
tags: fluorescent proteins photobleaching quantum yield piston GFP
date: 06-19-2019 14:33 gmt
revision:0
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PMID-27240257 Quantitative assessment of fluorescent proteins.
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{1467} |
ref: -2017
tags: neuromorphic optical computing nanophotonics
date: 06-17-2019 14:46 gmt
revision:5
[4] [3] [2] [1] [0] [head]
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Progress in neuromorphic photonics
See also :
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{1468} |
ref: -2013
tags: microscopy space bandwidth product imaging resolution UCSF
date: 06-17-2019 14:45 gmt
revision:0
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How much information does your microscope transmit?
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{1418} |
ref: -0
tags: nanophotonics interferometry neural network mach zehnder interferometer optics
date: 06-13-2019 21:55 gmt
revision:3
[2] [1] [0] [head]
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Deep Learning with Coherent Nanophotonic Circuits
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{1464} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nanoelectronic Programmable Synapses Based on Phase Change Materials for Brain-Inspired Computing
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{1466} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Eminently useful. Source: https://ocw.mit.edu/courses/electrical-engineering-and-computer-science/6-974-fundamentals-of-photonics-quantum-electronics-spring-2006/lecture-notes/chapter7.pdf Laser Dye technology by Peter Hammond
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{1465} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Small gathering of links on Lenslet Labs / Lenslet inc. Founded in 1999.
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{1463} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
All-optical spiking neurosynaptic networks with self-learning capabilities
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{1460} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
A friend postulated using the triplet state phosphorescence as a magnetically-modulatable dye. E.g. magnetically slice a scattering biological sample, rather than slicing optically (light sheet, 2p) or mechanically. After a little digging:
I'd imagine that it should be possible to design a molecule -- a protein cage, perhaps a (fully unsaturated) terpine -- which isolates the excited state from oxygen quenching. Adam Cohen at Harvard has been working a bit on this very idea, albeit with fluorescence not phosphorescence --
Yet! Magnetic field effects do exist in solution:
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{1461} |
ref: -2019
tags: super-resolution microscopy fluorescent protein molecules
date: 05-28-2019 16:02 gmt
revision:3
[2] [1] [0] [head]
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PMID-30997987 Chemistry of Photosensitive Fluorophores for Single-Molecule Localization Microscopy
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{1459} |
ref: -2018
tags: Michael Levin youtube talk NIPS 2018 regeneration bioelectricity organism patterning flatworm
date: 04-09-2019 18:50 gmt
revision:1
[0] [head]
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What Bodies Think About: Bioelectric Computation Outside the Nervous System - NeurIPS 2018
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{1458} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-28739915 Interactions between feedback and lateral connections in the primary visual cortex
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{1457} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-25112683 Subcellular Neural Probes from Single-Crystal Gold Nanowires
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{1456} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21360044 Robust penetrating microelectrodes for neural interfaces realized by titanium micromachining
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{1455} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Conducting credit assignment by aligning local distributed representations
Lit review.
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{1454} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Building High-level Features Using Large Scale Unsupervised Learning
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{1441} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Assessing the Scalability of Biologically-Motivated Deep Learning Algorithms and Architectures
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PMID-22325196 Backpropagation through time and the brain
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PMID-22325196 How Does the Brain Solve Visual Object Recognition
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{305} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-101388[0] Fine control of operantly conditioned firing patterns of cortical neurons.
____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1451} |
ref: -2018
tags: sparse representation auditory cortex excitatation inhibition balance
date: 03-11-2019 20:47 gmt
revision:1
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PMID-30307493 Sparse Representation in Awake Auditory Cortex: Cell-type Dependence, Synaptic Mechanisms, Developmental Emergence, and Modulation.
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{1450} |
ref: -2015
tags: conjugate light electron tomography mouse visual cortex fluorescent label UNC cryoembedding
date: 03-11-2019 19:37 gmt
revision:1
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PMID-25855189 Mapping Synapses by Conjugate Light-Electron Array Tomography
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{1420} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-22278062 Conditional modulation of spike-timing-dependent plasticity for olfactory learning.
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PMID-15321069 Sparse coding of sensory inputs
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{1447} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16543459 Reward timing in the primary visual cortex
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{1446} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-29074582 A generative vision model that trains with high data efficiency and breaks text-based CAPTCHAs
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{1445} |
ref: -2018
tags: cortex layer martinotti interneuron somatostatin S1 V1 morphology cell type morphological recovery patch seq
date: 03-06-2019 02:51 gmt
revision:3
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{1444} |
ref: -2012
tags: parvalbumin interneurons V1 perceptual discrimination mice
date: 03-06-2019 01:46 gmt
revision:0
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PMID-22878719 Activation of specific interneurons improves V1 feature selectivity and visual perception
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{1443} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-27545715 High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA.
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{1442} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-30635577 Functional imaging of visual cortical layers and subplate in awake mice with optimized three photon microscopy
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{1440} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{1439} |
ref: -2006
tags: hinton contrastive divergence deep belief nets
date: 02-20-2019 02:38 gmt
revision:0
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PMID-16764513 A fast learning algorithm for deep belief nets.
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{1438} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{1437} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21280920 Optically sectioned in vivo imaging with speckle illumination HiLo microscopy
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{1436} |
ref: -0
tags: Airy light sheet microscopy attenuation compensation LSM imaging
date: 02-19-2019 04:51 gmt
revision:1
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Light-sheet microscopy with attenuation-compensated propagation-invariant beams
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{1434} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Audio AI: isolating vocals from stereo music using Convolutional Neural Networks
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{1426} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Training neural networks with local error signals
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{1415} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-28777724 Active inference, curiosity and insight. Karl J. Friston, Marco Lin, Christopher D. Frith, Giovanni Pezzulo,
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{1432} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Direct Feedback alignment provides learning in deep neural nets
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{1423} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-27824044 Random synaptic feedback weights support error backpropagation for deep learning.
Our proof says that weights W0 and W evolve to equilibrium manifolds, but simulations (Fig. 4) and analytic results (Supple- mentary Proof 2) hint at something more specific: that when the weights begin near 0, feedback alignment encourages W to act like a local pseudoinverse of B around the error manifold. This fact is important because if B were exactly W + (the Moore- Penrose pseudoinverse of W ), then the network would be performing Gauss-Newton optimization (Supplementary Proof 3). We call this update rule for the hidden units pseudobackprop and denote it by ∆hPBP = W + e. Experiments with the linear net- work show that the angle, ∆hFA ]∆hPBP quickly becomes smaller than ∆hFA ]∆hBP (Fig. 4b, c; see Methods). In other words feedback alignment, despite its simplicity, displays elements of second-order learning. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1431} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sparse and composite coherent lattices
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{1419} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
All-optical machine learning using diffractive deep neural networks
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{1430} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-28650477 Video rate volumetric Ca2+ imaging across cortex using seeded iterative demixing (SID) microscopy
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{1174} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Brains, sex, and machine learning -- Hinton google tech talk.
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{1429} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
New Evidence for the Strange Geometry of Thought
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{1427} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-27934860 Scanning superlens microscopy for non-invasive large field-of-view visible light nanoscale imaging
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{1425} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-29375323 Fear learning regulates cortical sensory representation by suppressing habituation
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Curiosity-driven exploration by Self-supervised prediction
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{1422} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-29205151 Towards deep learning with segregated dendrites https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716677/
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{1421} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-26516682 Retroactive modulation of spike timing-dependent plasticity by dopamine.
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After briefly searching the web, I could not find a chart of the top 100 occupations in the US. After downloading the data from the US Bureau of Labor Statistics, made this chart: Click for full-size. Surprising how very service heavy our economy is. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1416} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning data manifolds with a Cutting Plane method
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{1413} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-24711417 Evidence for a causal inverse model in an avian cortico-basal ganglia circuit
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{1412} |
ref: -0
tags: deeplabcut markerless tracking DCN transfer learning
date: 10-03-2018 23:56 gmt
revision:0
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Markerless tracking of user-defined features with deep learning
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{1411} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-20544831 The decade of the dendritic NMDA spike.
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{1410} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Structure discovery in Nonparametric Regression through Compositional Kernel Search
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{1409} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Coevolution of Fitness Predictors
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{1408} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LDMNet: Low dimensional manifold regularized neural nets.
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PMID-21896383 Effect of Insertion Speed on Tissue Response and Insertion Mechanics of a Chronically Implanted Silicon-Based Neural Probe
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{1406} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-26436341 Three-dimensional macroporous nanoelectronic networks as minimally invasive brain probes.
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{1402} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-18336081 Adaptive integration in the visual cortex by depressing recurrent cortical circuits.
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{1384} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-28246640 Ultraflexible nanoelectronic probes form reliable, glial scar–free neural integration
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{1010} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-4708761 Design, Fabrication, and In Vivo Behavior of Chronic Recording Intracortical Microelectrodes
____References____ Salcman, Michael and Bak, Martin J. Design, Fabrication, and In Vivo Behavior of Chronic Recording Intracortical Microelectrodes Biomedical Engineering, IEEE Transactions on BME-20 4 253 -260 (1973) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1400} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-29220192 Fluidic Microactuation of Flexible Electrodes for Neural Recording.
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{1368} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-23451719 Synthetic Nanoelectronic Probes for Biological Cells and Tissue
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{1176} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-6170092 (pdf) An ultra-compliant, scalable neural probe with molded biodissolvable delivery vehicle
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{1236} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-23580530 Injectable, cellular-scale optoelectronics with applications for wireless optogenetics.
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{1399} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-25128375 Chronic tissue response to carboxymethyl cellulose based dissolvable insertion needle for ultra-small neural probes.
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{1057} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19666051[0] Insertion shuttle with carboxyl terminated self-assembled monolayer coatings for implanting flexible polymer neural probes in the brain.
____References____
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{1398} |
ref: -0
tags: platinum parylene electrodes brush dissolving stiffener gelatin
date: 12-28-2017 02:44 gmt
revision:0
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PMID-27159159 Embedded Ultrathin Cluster Electrodes for Long-Term Recordings in Deep Brain Centers.
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{1397} |
ref: -0
tags: polyimide electrodes immune response foreign body inflammation stiffener steiglitz
date: 12-28-2017 02:37 gmt
revision:0
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PMID-27534649 Intracortical polyimide electrodes with a bioresorbable coating.
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{1396} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-27791052 Ultrathin, transferred layers of thermally grown silicon dioxide as biofluid barriers for biointegrated flexible electronic systems
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{1395} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-25574019 Biomaterials. Electronic dura mater for long-term multimodal neural interfaces.
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{1394} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Materials and technologies for soft implantable neuroprostheses
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{1393} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11327505 Flexible polyimide-based intracortical electrode arrays with bioactive capability.
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{1392} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-29109247 Highly scalable multichannel mesh electronics for stable chronic brain electrophysiology
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{1391} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks
Summary thoughts: This is a highly interesting study, insofar that the authors show substantial support for their hypotheses that phenotypes can be explored through random-walk non-lethal mutations of the genotype, and this is somewhat invariant to the source of carbon for known biochemical reactions. What gives me pause is the use of linear programming / optimization when setting the relative concentrations of biomolecules, and the permissive criteria for accepting these networks; real life (I would imagine) is far more constrained. Relative and absolute concentrations matter. Still, the study does reflect some robustness. I suggest that a good control would be to ‘fuzz’ the list of available reactions based on statistical criteria, and see if the results still hold. Then, go back and make the reactions un-biological or less networked, and see if this destroys the measured degrees of robustness. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1389} |
ref: -0
tags: photoacoustic tomography mouse imaging q-switched laser
date: 05-11-2017 05:23 gmt
revision:1
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{1390} |
ref: -0
tags: photoacoustic tomography mouse imaging q-switched laser
date: 05-11-2017 05:21 gmt
revision:0
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{1239} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Quick review of electrode area / impedance within m8ta:
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{1356} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-27705958 Chronic in vivo stability assessment of carbon fiber microelectrode arrays.
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{1388} |
ref: -0
tags: PEDOT PSS electroplate eletrodeposition neural recording michigan probe stimulation CSC
date: 04-27-2017 01:36 gmt
revision:1
[0] [head]
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PMID-19543541 Poly(3,4-ethylenedioxythiophene) as a micro-neural interface material for electrostimulation
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{1387} |
ref: -1977
tags: polyethylene surface treatment plasma electron irradiation mechanical testing saline seawater accelerated lifetime
date: 04-15-2017 06:06 gmt
revision:0
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Enhancement of resistance of polyethylene to seawater-promoted degradation by surface modification
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{1385} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Method of electropolishing tungsten wire US 3287238 A
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{1250} |
ref: -0
tags: polyimide electrodes thermosonic bonding Stieglitz adhesion delamination
date: 03-06-2017 21:58 gmt
revision:7
[6] [5] [4] [3] [2] [1] [head]
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IEEE-6347149 (pdf) Improved polyimide thin-film electrodes for neural implants 2012
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{747} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17517431[0] Neural probe design for reduced tissue encapsulation in CNS.
____References____
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{1163} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-8263001[0] Biocompatibility of silicon-based electrode arrays implanted in feline cortical tissue.
____References____
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{1383} |
ref: -0
tags: carbon nanotube densification conductivity strength
date: 02-23-2017 02:52 gmt
revision:2
[1] [0] [head]
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Super-strong and highly conductive carbon nanotube ribbons from post-treatment methods
High-strength carbon nanotube fibre-like ribbon with high ductility and high electrical conductivity | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1382} |
ref: -0
tags: iridium oxide nanotube intracellular recording electroplate MEA
date: 02-22-2017 22:41 gmt
revision:0
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PMID-24487777 Iridium oxide nanotube electrodes for sensitive and prolonged intracellular measurement of action potentials. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1381} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-28084398 Highly Stable Glassy Carbon Interfaces for Long-Term Neural Stimulation and Low-Noise Recording of Brain Activity
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{1380} |
ref: -0
tags: myoelectric EMG recording TMR prosthetics
date: 02-13-2017 20:43 gmt
revision:0
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PMID: Man/machine interface based on the discharge timings of spinal motor neurons after targeted muscle reinnervation
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{1378} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-25803728 Neural stimulation and recording with bidirectional, soft carbon nanotube fiber microelectrodes.
PMID-23307737 Strong, light, multifunctional fibers of carbon nanotubes with ultrahigh conductivity.
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{1374} |
ref: -0
tags: nanoprobe transmembrane intracellular thiol gold AFM juxtacellular
date: 02-06-2017 23:45 gmt
revision:3
[2] [1] [0] [head]
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PMID-20212151 Fusion of biomimetic stealth probes into lipid bilayer cores
PMID-21469728 '''Molecular Structure Influences the Stability of Membrane Penetrating Biointerfaces.
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{1377} |
ref: -0
tags: nanopore membrane nanostraws melosh surface adhesion intracellular
date: 02-06-2017 23:34 gmt
revision:0
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PMID-22166016 Nanostraws for Direct Fluidic Intracellular Access
PMID-24710350, Quantification of nanowire penetration into living cells.
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{1376} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-24677434 A Review of Organic and Inorganic Biomaterials for Neural Interfaces
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PMID-22905231 Neuronal recordings with solid-conductor intracellular nanoelectrodes (SCINEs).
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Contenders for high-modulus pitch-based carbon fiber: "
Tensile and Flextural Prperties of single carbon fibers
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{1372} |
ref: -0
tags: bone marrow transplant chimera immune response to indwelling electrode implant capadona inflammation
date: 02-02-2017 23:24 gmt
revision:1
[0] [head]
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PMID-24973296 The roles of blood-derived macrophages and resident microglia in the neuroinflammatory response to implanted intracortical microelectrodes.
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{1371} |
ref: -0
tags: nanotube tracking extracellular space fluorescent
date: 02-02-2017 22:13 gmt
revision:0
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PMID-27870840 Single-nanotube tracking reveals the nanoscale organization of the extracellular space in the live brain
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{1370} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-27256971 Multisite electrophysiological recordings by self-assembled loose-patch-like junctions between cultured hippocampal neurons and mushroom-shaped microelectrodes.
PMID-23380931 Multi-electrode array technologies for neuroscience and cardiology
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{1369} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-22231664 Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits.
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{1367} |
ref: -0
tags: microstimulation rat cortex measurement ICMS spread
date: 01-26-2017 02:52 gmt
revision:0
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PMID-12878710 Spatiotemporal effects of microstimulation in rat neocortex: a parametric study using multielectrode recordings.
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{1366} |
ref: -0
tags: direct electrical stimulation neural mapping review
date: 01-26-2017 02:28 gmt
revision:0
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PMID-22127300 Direct electrical stimulation of human cortex -- the gold standard for mapping brain functions?
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PMID-25705966 Robust and fragile aspects of cortical blood flow in relation to the underlying angioarchitecture.
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{1365} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Dianhydride: Dianiline / diamine: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-18672003[0] Neurotrophic electrode: method of assembly and implantation into human motor speech cortex.
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PMID-9237542 Activity of single action potentials in monkey motor cortex during long-term task learning. Kennedy PR1, Bakay RA.'''
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{1362} |
ref: -0
tags: serial electron microscopy Lichtman reconstruction nervous tissue
date: 01-17-2017 23:32 gmt
revision:0
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PMID-26232230 Saturated Reconstruction of a Volume of Neocortex.
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{1361} |
ref: -0
tags: neural coding rats binary permutation retrosplenial basolateral amygdala tetrode
date: 12-19-2016 07:39 gmt
revision:1
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PMID-27895562 Brain Computation Is Organized via Power-of-Two-Based Permutation Logic.
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{1360} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-22750248 In vivo effects of L1 coating on inflammation and neuronal health at the electrode-tissue interface in rat spinal cord and dorsal root ganglion.
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{1359} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
https://www.zeusinc.com/materials/lcp-liquid-crystal-polymer
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{1358} |
ref: -0
tags: china trustwothiness social engineering communism
date: 10-31-2016 05:42 gmt
revision:1
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China 'social credit': Beijing sets up huge system So long as it purports to measure just one social variable -- 'trustworthiness' -- it might be a good idea. Many commerce websites (.. ebay ..) have these sort of rating systems already, and they are useful. When humans live in smaller communities something like this is in the shared consciousness. Peering into everyone's purchasing habits and hobbies, however, seems like it will be grossly myopic and, as the article says, Orwellian. Likely they will train a deep-belief network on past data of weakly and communist party defined success, with all purchasing and social media as the input data, and use that in the proprietary algorithm for giving people their scalars to optimize. This would be the ultimate party control tool -- a great new handle for controlling people's minds, even 'better' than capitalism. Surprising that the article only hints at this, and that the Chinese themselves seem rather clueless that it's a power play. In this sense, it's a very clever play to link it to reproduction. Other comments: These sorts of systems may be necessary in highly populated countries, where freedom and individuality are less valued and social cohesion is requisite. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1357} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Physical Metallurgy of Refactory Metals and Alloys Properties of tungsten-rhenium alloys
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{1353} |
ref: -0
tags: PEDOT electropolymerization electroplating gold TFB borate counterion acetonitrile
date: 10-18-2016 07:49 gmt
revision:3
[2] [1] [0] [head]
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PMID-20715789 Investigation of near ohmic behavior for poly(3,4-ethylenedioxythiophene): a model consistent with systematic variations in polymerization conditions.
PMID-24576579 '''Improving the performance of poly(3,4-ethylenedioxythiophene) for brain–machine interface applications"
PEDOT-modified integrated microelectrodes for the detection of ascorbic acid, dopamine and uric acid
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{1354} |
ref: -0
tags: David Kleinfeld penetrating arterioles perfusion cortex vasculature
date: 10-17-2016 23:24 gmt
revision:1
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PMID-17190804 Penetrating arterioles are a bottleneck in the perfusion of neocortex.
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{1270} |
ref: -0
tags: gold micrograin recording electrodes electroplating impedance
date: 10-17-2016 20:28 gmt
revision:5
[4] [3] [2] [1] [0] [head]
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PMID-23071004 Gold nanograin microelectrodes for neuroelectronic interfaces.
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{1352} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-27571550 Stable long-term chronic brain mapping at the single-neuron level.
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PMID-20345247 Neural mechanisms for interacting with a world full of choices
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{1350} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
A Wireless 32-Channel Implantable Bidirectional Brain Machine Interface
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{1349} |
ref: -0
tags: bone regrowth hyperelastic 3d print implant hydroxyapatite polycaptolactone
date: 09-30-2016 18:27 gmt
revision:0
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Heller Lecture - Prof. David Kleinfeld
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{1347} |
ref: -0
tags: laser induced breakdown spectroscopy for surgery tissue differentiation
date: 09-22-2016 19:26 gmt
revision:0
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PMID-25426327 Laser induced breakdown spectroscopy for bone and cartilage differentiation - ex vivo study as a prospect for a laser surgery feedback mechanism.
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{1346} |
ref: -0
tags: super resolution imaging PALM STORM fluorescence
date: 09-21-2016 05:57 gmt
revision:0
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PMID-23900251 Parallel super-resolution imaging
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{1345} |
ref: -0
tags: nucleus accumbens caudate stimulation learning enhancement MIT
date: 09-20-2016 23:51 gmt
revision:1
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http://amasci.com/tesla/Tap_Drill_Chart.html by way of: https://m.reddit.com/r/engineering/comments/4ry07t/does_anyone_have_a_stored_copy_of_this_tap_and/ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1341} |
ref: -0
tags: image registration optimization camera calibration sewing machine
date: 07-15-2016 05:04 gmt
revision:20
[19] [18] [17] [16] [15] [14] [head]
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Recently I was tasked with converting from image coordinates to real world coordinates from stereoscopic cameras mounted to the end-effector of a robot. The end goal was to let the user (me!) click on points in the image, and have the robot record that position & ultimately move to it. The overall strategy is to get a set of points in both image and RW coordinates, then fit some sort of model to the measured data. I began by printing out a grid of (hopefully evenly-spaced and perpendicular) lines via a laserprinter; spacing was ~1.1 mm. This grid was manually aligned to the axes of robot motion by moving the robot along one axis & checking that the lines did not jog. The images were modeled as a grating with quadratic phase in texture coordinates: (1) (2) (3) The 1000 was used to make the parameter search distribution more spherical; were bias terms to seed the solver; 0.97 was a duty-cycle term fit by inspection to the image data; (3) is a modified sigmoid. was then optimized over the parameters using a GPU-accelerated (CUDA) nonlinear stochastic optimization: (4) Optimization was carried out by drawing parameters from a normal distribution with a diagonal covariance matrix, set by inspection, and mean iteratively set to the best solution; horizontal and vertical optimization steps were separable and carried out independently. The equation (4) was sampled 18k times, and equation (3) 34 billion times per frame. Hence the need for GPU acceleration. This yielded a set of 10 parameters (again, and were bias terms and kept constant) which modeled the data (e.g. grid lines) for each of the two cameras. This process was repeated every 0.1 mm from 0 - 20 mm height (z) from the target grid, resulting in a sampled function for each of the parameters, e.g. . This required 13 trillion evaluations of equation (3). Now, the task was to use this model to generate the forward and reverse transform from image to world coordinates; I approached this by generating a data set of the grid intersections in both image and world coordinates. To start this process, the known image origin was used to find the corresponding roots of the periodic axillary functions : (5) (6) Or .. (7) (8) From this, we get variables which are the offsets to align the sine functions with the physical origin. Now, the reverse (world to image) transform was needed, for which a two-stage newton scheme was used to solve equations (7) and (8) for . Note that this is an equation of phase, not image intensity -- otherwise this direct method would not work! First, the equations were linearized with three steps of (9-11) to get in the right ballpark:
(9) (10) and (11) where mldivide is the Matlab operator. Then three steps with the full Jacobian were made to attain accuracy: (12) (13) (14) Solutions were verified by plugging back into equations (7) and (8) & verifying were the same. Inconsistent solutions were discarded; solutions outside the image space were also discarded. The process (10) - (14) was repeated to tile the image space with gird intersections, as indicated in (9), and this was repeated for all in , resulting in a large (74k points) dataset of , which was converted to full real-world coordinates based on the measured spacing of the grid lines, . Between individual z steps, was re-estimated to minimize (for a current ): (15) with grid-search, and the method of equations (9-14). This was required as the stochastic method used to find original image model parameters was agnostic to phase, and so phase (via parameter ) could jump between individual measurements (the origin did not move much between successive measurements, hence (15) fixed the jumps.) To this dataset, a model was fit: (16) Where , , , and . was introduced as an axillary variable to assist in perspective mapping, ala computer graphics. Likewise, were scaled so the quadratic nonlinearity better matched the data. The model (16) was fit using regular linear regression over all rows of the validated dataset. This resulted in a second set of coefficients for a model of world coordinates to image coordinates; again, the model was inverted using Newton's method (Jacobian omitted here!). These coefficients, one set per camera, were then integrated into the C++ program for displaying video, and the inverse mapping (using closed-form matrix inversion) was used to convert mouse clicks to real-world coordinates for robot motor control. Even with the relatively poor wide-FOV cameras employed, the method is accurate to , and precise to . | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{711} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19299587[0] Optical Deconstruction of Parkinsonian Neural Circuitry.
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* Watch the [http://homes.cs.washington.edu/~todorov/index.php?video=MordatchSIGGRAPH12&paper=Mordatch,%20SIGGRAPH%202012 movies! Discovery of complex behaviors through contact-invariant optimization]
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ZeroMQ -- much better sockets framework than native TCP/UDP sockets.
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Useful numbers for estimating molecular mean-free-path in vacuum systems: "
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A contact lens with embedded sensor for monitoring tear glucose level
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What are the concentrations of the monoamines in the brain? (Purpose: estimate the required electrochemical sensing area & efficiency)
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PMID-26627311 Monolithically Integrated μLEDs on Silicon Neural Probes for High-Resolution Optogenetic Studies in Behaving Animals.
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META II: Digital Vellum in the Digital Scriptorium: Revisiting Schorre's 1962 compiler-compiler
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PMID-21867803[0] Can histology solve the riddle of the nonfunctioning electrode? Factors influencing the biocompatibility of brain machine interfaces.
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Utah/blackrock group has been working on improving the longevity of their parlyene encapsulation with the addition of ~50nm Al2O3.
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PMID-25627426 Rapid evaluation of the durability of cortical neural implants using accelerated aging with reactive oxygen species.
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https://mitpress.mit.edu/sites/default/files/titles/free_download/9780262526548_Art_of_Insight.pdf | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Problem: have a Q-switched Nd:YAG laser, (flashlamp pumped, passively Q-switched) from ebay (see this album). Allegedly it outputs 1J pulses of 8ns duration; in practice, it may put several 100mJ pulses ~ 16ns long while the flashlamp is firing. It was sold as a tattoo removal machine. However, I'm employing it to drill micro-vias in fine polyimide films. When focused through a 10x objective via the camera mount of an Leica microscope, 532nm (KTP doubled, second harmonic generation (SHG)) laser pulses both ablates the material, but does not leave a clean, sharp hole: it looks more like 'blasting': the hole is ragged, more like a crater. This may be from excessive 1064nm heating (partial KTP conversion), or plasma/flame heating & expansion due to absorption of the 532nm / 1064nm light. It may also be due to excessive pulse duration (should the laser not actually be q-switched... photodiode testing suggests otherwise, but I'd like to verify that), excessive pulse power, insufficient pulse intensity, or insufficient polyimide absorption at 532nm. The solution to excessive plasma and insufficient polyimide absorption is to shift the wavelength to 355nm (NUV) via third harmonic generation, 1064 + 532 = 355nm. This requires sum frequency generation (SFG), for which LBO (lithium triborate) or BBO (beta-barium borate) seem the commonly accepted nonlinear optical materials. To get SHG or THG, phase and polarization matching of the incoming light is critical. The output of the Nd:YAG laser is, I assume, non-polarized (or randomly polarized), as the KTP crystal simply screws on the front, and so should be rotationally agnostic (and there are no polarizing elements in the simple laser head -- unless the (presumed) Cr:YAG passive Q-switch induces some polarization.) Output polarization of the KTP crystal will be perpendicular to the incoming beam; if the resulting THG / SFG crystal needs Type-1 phase matching (both in phase and parallel polarization), will need a half-wave plate for 1064nm; for Type-II phase matching, no plate is needed. For noncritical phase matching in LBO (which I just bought), an oven is required to heat the crystal to the correct temperature. This suggests 73C for THG, while this suggests 150C (for SHG?). Third harmonic frequency generation by type-I critically phase-matched LiB3O5 crystal by means of optically active quartz crystal Suggests most lasers operate in Type-1 SHG, and Type-II THG, but this is less efficient than dual Type-1; the quartz crystal is employed to rotate the polarizations to alignment. Both SHG and THG crystals are heated for optimum power output. Finally, Short pulse duration of an extracavity sum-frequency mixing with an LiB3O5 (LBO) crystal suggests that no polarization change is required, nor oven control LBO temperature. Tight focus and high energy density is required, of course (at the expense of reduced crystal lifetime). Likely this is the Type-1,Type-II scheme alluded to in the paper above. I'll try this first before engaging further complexity (efficiency is not very important, as the holes are very small & material removal may be slow.) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-25571176 Fabrication and characterization of a high-resolution neural probe for stereoelectroencephalography and single neuron recording. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Improvement in the adhesion of polyimide/epoxy joints using various curing agents
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Tantalum and chromium adhesion to polyimide. Part 2. Peel and locus of failure analyses
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Adhesion Evaluation of Adhesiveless Metal/Polyimide Substrate for MCM and high density packaging
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PMID-18640155 Characterization of flexible ECoG electrode arrays for chronic recording in awake rats.
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{1313} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Neural Stimulation and Recording with Bidirectional, Soft Carbon Nanotube Fiber Microelectrodes
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Central Neuroanatomy of Electrosensory Systems in Fish
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PMID-11889591 Spontaneous nerve activity and sensitivity in catfish ampullary electroreceptor organs after tetanus toxin application
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The physiology of low-frequency electrosensory systems
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{1251} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-938305 (pdf) High Density Interconnects and flexible hybrid assemblies for active biomedical implants
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{1308} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Kinetics of Alkaline Hydrolysis of a Polyimide Surface
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{1307} |
ref: -2000
tags: polyimide acrylic aluminum electro deposition imide insulation ultra thin
date: 02-27-2015 19:42 gmt
revision:0
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Ultrathin, Layered Polyamide and Polyimide Coatings on Aluminum
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{1304} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21379404 Creating low-impedance tetrodes by electroplating with additives
Conclusion: 75% PEG, commercial electropating solution, 0.1ua current pluses to 250K or less.
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{1302} |
ref: -0
tags: kevlar electrodes flexible polymer 12um McNaughton Utah
date: 10-11-2014 00:19 gmt
revision:0
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PMID-8982987 Metallized polymer fibers as leadwires and intrafascicular microelectrodes
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Adhesiveless copper on polyimide substrate with nickel-chromium tiecoat
Adhesion Between Polymers and Other Substances - A Review of Bonding Mechanisms, Systems and Testing
High-Performance Polymers (book) Guy Rabilloud (via google books.)
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{1300} |
ref: -0
tags: Peter Ledochowitsch ECoG parylene fabrication MEMS
date: 09-25-2014 16:54 gmt
revision:0
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IEEE-5734604 (pdf) Fabrication and testing of a large area, high density, parylene MEMS µECoG array
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{1299} |
ref: -0
tags: wirebonding finishes gold nickel palladium electroless electrolytic
date: 09-21-2014 02:53 gmt
revision:3
[2] [1] [0] [head]
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Why palladium? To prevent black nickel: http://tayloredge.com/reference/Electronics/PWB/BlackPad_ITRI_Round1.PD Introduction The use of electroless nickel / immersion gold (E.Ni/I.Au) as a circuit board finish has grown significantly in the last few years. It provides a flat board finish, is very solderable, provides a precious metal contact surface and the nickel strengthens the plated holes. However, as the usage of E.Ni/I.Au increased, a problem was found on BGA (Ball Grid Array) components. An open or fractured solder joint sometimes appears after board assembly on the occasional BGA pad. The solder had wet and dissolved the gold and formed a weak intermetallic bond to the nickel. This weak bond to the nickel readily fractures under stress or shock, leaving an open circuit. The incidence of this problem appears to be very sporadic and a low ppm level problem, but it is very unpredictable. A BGA solder joint cannot be touched-up without the component being removed. After the BGA component is removed, a black pad is observed at the affected pad site. This black pad is not readily solderable, but it can be repaired. From: http://www.smtnet.com/Forums/index.cfm?fuseaction=view_thread&Thread_ID=4430 You don't have enough gold. Your 2uin is too porous and is allowing the nickel to corrode. Prove that this by hand soldering to these pads with a more active flux, like a water soluble solder paste, than you are using. You must have at least 3uin of immersion gold. Seriously consider >5uin. Your nickel thickness is fine. Although if you wanted to trade costs, consider giving-up nickel to 150uin thickness, while increasing the gold thickness. Gold over electroless nickel creates brittle joints because of phosphorous in the nickel plating bath. The phosphorous migrates into the over-plating. Electrolytic nickel and gold plating should not be a problem. If you stay with the electroless nickel, keep the phosphorous at a mid [7 - 9%] level. Just as important, don't let the immersion gold get too aggressive. The immersion gold works by corroding the nickel. If it is too aggressive it takes away the nickel and leave phosphorous behind. This makes it look like the phosphorous level is too high in the nickel bath. Gold purity is very important for any type of wire bonding process. For aluminum wedge bonding, gold should have a purity of 99. 99% [no thalium] and the nickel becomes critical. No contaminates and the nickel wants to be plated a soft as possible. This requires good control of Ph and plating chemicals in the nickel-plating bath. Harman "Wire Bonding In Microelectronics" McGraw-Hill is a good resource for troubleshooting wire bonding. I reviewed it in the SMTnet Newsletter a couple of months ago. That said, electrolytic nickel + electrolytic gold does work well -- perhaps even better than ENEPIG: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-13539663 Subcortical threshold voltages as a function of sine wave frequencies Brown and Brackett
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PMID-4550167[1] Sensory responses elicited by subcortical high frequency electrical stimulation in man. -- everything innovative has already been done in the 70s!
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One of the goals/needs of the lab is to be able to stimluate and record nervous tissue at the same time. We do not have immediate access to optogenetic methods, but what about lower frequency EM stimulation? The idea: if you put the stimulation frequency outside the recording system bandwidth, there is no need to switch, and indeed no reason you can't stimulate and record at the same time. Hence, I very briefly checked for the effects of RF stimulation on nervous tissue.
Conclusion: worth a shot, especially given the paper by Alberts et al 1972.
____References____
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{1296} |
ref: -0
tags: physical principles of scalable neural recording marblestone
date: 08-25-2014 20:21 gmt
revision:0
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PMID-24187539 Physical principles for scalable neural recording.
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{1295} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Pretty solid hike yesterday. 25.25 miles (or likely more, given the limited resolution of my tracing) in about 7.5 hours for an average speed of 3.4 mph. Lots of different terrain and eosystems along the way -- redwoods to lakeside to golden grassy hilltops to manzanita / scrub forest. Would be good for mountain biking. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-1937509 A silicon-based, three-dimensional neural interface: manufacturing processes for an intracortical electrode array. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1212} |
ref: Nordhausen-1994.02
tags: Utah array electrodes optimization
date: 08-14-2014 01:24 gmt
revision:2
[1] [0] [head]
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PMID-8180807[0] Optimizing recording capabilities of the Utah Intracortical Electrode Array.
____References____
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{1291} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Weldability of Tungsten and Its Alloys
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{1112} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21301965[0] Novel multi-sided, microelectrode arrays for implantable neural applications.
____References____
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{1290} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-270699 Local control of neurite development by nerve growth factor.
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{1289} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
images/1289_1.pdf -- Debugging reinvented: Asking and Answering Why and Why not Questions about Program Behavior.
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{1288} |
ref: -0
tags: automatic programming inductive functional igor
date: 07-29-2014 02:07 gmt
revision:0
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Inductive Rule Learning on the Knowledge Level.
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{1277} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1416914 (pdf) Partial release and detachment of microfabricated metal and polymer structures by anodic metal dissolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1276} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Interfacial adhesion of polymeric coatings for microelectronic encapsulation
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{1287} |
ref: -0
tags: maleimide azobenzine glutamate photoswitch optogenetics
date: 06-16-2014 21:19 gmt
revision:0
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PMID-16408092 Allosteric control of an ionotropic glutamate receptor with an optical switch
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various:
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{1284} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-17521567 Remote control of neuronal activity with a light-gated glutamate receptor.
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{1282} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Polyimide insulators for multilevel interconnections Arthur M. Wilson
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{1281} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Various microelectrode patents:
Microelectronics:
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{1278} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-23860226 A carbon-fiber electrode array for long-term neural recording.
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Frequency-domain techniques for tissue spectroscopy and imaging
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{1271} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Community & housing links for San Francisco.
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{1269} |
ref: -0
tags: hinton convolutional deep networks image recognition 2012
date: 01-11-2014 20:14 gmt
revision:0
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{1268} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Simple perl scrip for removing duplicate files within sub-directories of a known depth: #!/usr/bin/perl -w @files = <*>; foreach $file (@files) { @files2 = <$file/*>; foreach $file2 (@files2) { print $file2 . "\n"; `rm -rf $file2/*_1.jpg`; `rm -rf $file2/*_2.jpg`; } } | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1203} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17027251[0] Flexible polyimide microelectrode array for in vivo recordings and current source density analysis.
____References____
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{1267} |
ref: -0
tags: stretchable nanoparticle conductors gold polyurethane flocculation
date: 12-13-2013 02:12 gmt
revision:5
[4] [3] [2] [1] [0] [head]
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PMID-23863931 Stretchable nanoparticle conductors with self-organized conductive pathways.
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{1264} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-23852172 A comparison of polymer substrates for photolithographic processing of flexible bioelectronics
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{1258} |
ref: -0
tags: polyimide platinum electrodes Spain longitudinal intrafasicular adhesion delamination
date: 10-05-2013 22:24 gmt
revision:4
[3] [2] [1] [0] [head]
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PMID-17278585 Assessment of biocompatibility of chronically implanted polyimide and platinum intrafascicular electrodes. 2007
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{1259} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-24062716 A highly compliant serpentine shaped polyimide interconnect for front-end strain relief in chronic neural implants.
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{1248} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Improved polyimide/metal adhesion by chemical modification approaches
IEEE-4936772 (pdf) Studies of adhesion of metal films to polyimide
IEEE-670747 (pdf) Adhesion evaluation of adhesiveless metal/polyimide substrate for MCM and high density packaging
On polyimide-polyimide interlayer adhesion: Diffusion and self-adhesion of the polyimide PMDA-ODA (1987)
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{1257} |
ref: -0
tags: Anna Roe optogenetics artificial dura monkeys intrinisic imaging
date: 09-30-2013 19:08 gmt
revision:3
[2] [1] [0] [head]
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PMID-23761700 Optogenetics through windows on the brain in nonhuman primates
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{1254} |
ref: -0
tags: woodchuck post-translational regulatory element
date: 09-30-2013 18:52 gmt
revision:2
[1] [0] [head]
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PMID-10074136 Woodchuck hepatitis virus posttranscriptional regulatory element enhances expression of transgenes delivered by retroviral vectors 1999
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{1256} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-23393413 Brain rhythms and neural syntax: implications for efficient coding of cognitive content and neuropsychiatric disease.
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{1255} |
ref: -0
tags: Disseroth Kreitzer parkinsons optogenetics D1 D2 6OHDA
date: 09-30-2013 18:15 gmt
revision:0
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PMID-20613723 Regulation of parkinsonian motor behaviors by optogenetic control of basal ganglia circuitry
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PMID-23142839 Ultrasmall implantable composite microelectrodes with bioactive surfaces for chronic neural interfaces.
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{1249} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21273316 Physiological clustering of visual channels in the mouse retina
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{1242} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
We're making parylene electrodes for neural recording, and one critical step is connecting them to recording electronics. Currently Berkeley uses ACF (anisotropic conductive film) for connection, which is widely used for connecting flex tape to LCD panels, or for connecting driver chips to LCD glass. According to the internet, pitches can be as low as 20um, with pad areas as low as 800um^2. source However, this does not seem to be a very reliable nor compact process with platinum films on parylene, possibly because ACF bonding relies on raised areas between mated conductors (current design has the Pt recessed into the parylene), and on rigid substrates. ACF consists of springy polymer balls coated in Ni and Au and embedded in a thermoset epoxy resin. The ACF film is put under moderate temperature (180C) and pressure (3mpa, 430psi), which causes the epoxy to cure in a state that leaves the gold/nickel/polymer balls to be compressed between the two conductors. Hence, even if the conductors move slightly due to thermal cycling, the small balls maintain good mechanical and electrical contact. The balls are dispersed sufficiently in the epoxy matrix that there is little to no chance of conduction between adjacent pads. (Or so I have learned from the internet.) Now, as mentioned, this is an imperfect method for joining Pt on parylene films, possibly because the parylene is so flexible, and the platinum foil is very thin (200-300 nm). Indeed, platinum does not bond very strongly to parylene, hence care must be taken to allow sufficient overlap to prevent water ingress. My proposed solution -- to be tested shortly -- is to use a low-melting temperature metal with strong wetting ability -- such as Field's metal (bismuth, tin, indium, melting point 149F, see http://www.gizmology.net/fusiblemetals.htm) to low-temperature solder the platinum to a carrier board (initially) or to a custom amplifier ASIC (later!). Parylene is stable to 200C (392F), so this should be safe. One worry is that the indium/bismuth will wet the parylene or polyimide, too; however I consider this unlikely due to the difficulty in attaching parylene to any metal. That said, there must be good reason why ACF is so popular, so perhaps a better ultimate solution is to stiffen the parylene (or ultimately polyimide) substrate so that it can support both the temperature/pressure of ACF bonding and the stress of a continued electrical/mechanical bond to polyimide fan-out board or ASIC. It may also be possible to gold or nickel electroplate the connector pads to be slightly raised instead of recessed. Update: ACF bond to rigid 1/2 oz copper, 4mil trace / space connector (3mil trace/space board): Note that the copper traces are raised, and the parylene is stretched over the uneven surface (this is much easier to see with the stereo microscope). To the left of the image, the ACF paste has been sqeezed out from between the FR4 and parylene. Also note that the platinum can make potential contact with vias in the PCB. Update 7/2: Fields metal (mentioned above) does stick to platinum reasonably well, but it also sticks to parylene (somewhat), and glass (exceptionally well!). In fact, I had a difficult time removing traces of field's metal from the Pyrex beakers that I was melting the metal with. These beakers were filled with boiling water, which may have been the problem. When I added flux (Kester flux-pen 951 No-clean MSDS), the metal became noticeably more shiny, and the contact angle increased on the borosilicate glass (e.g. looked more like mercury); this leads me to believe that it is not the metal itself that attaches to glass, but rather oxides of indium and bismuth. Kester 951 flux consists of:
After coating the parylene/platinum sample with flux, I raised the field's metal to the flux activation point, which released some smoke and left brown organic residues on the bottom of the glass dish. Then I dipped the parylene probe into the molten metal, causing the flux again to be activated, and partially wetting the platinum contacts. The figure below shows the result: Note the incomplete wetting, all the white solids left from the process, and how the field's metal caused the platinum to delaminate from the parylene when the cable was (accidentally) flexed. Tests with platinum foil revealed that the metal bond was not actually that strong, significantly weaker than that made with a flux-core SnPb solder. also, I'm not sure of the activation temperature of this flux, and think I may have overheated the parylene. Update 7/10: Am considering electrodeless Ni / Pt / Au deposition, which occurs in aqueous solution, hence at much lower temperatures than e-beam evaporation Electrodeless Ni ref. On polyimide substrates, there is extensive literature describing how to activate the surface for plating: Polyimides and Other High Temperature Polymers: Synthesis ..., Volume 4. Parylene would likely need a different possibly more aggressive treatment, as it does not have imide bonds to open. Furthermore, if the parylene / polyimide surface is *not* activated, the electrodeless plating could be specific to the exposed electrode and contact sites, which could help to solve the connector issue by strengthening & thickening the contact areas. The second fairly obvious solution is to planarize the contact site on the PCB, too, as seen above. ACF bonds can be quite reliable; last night I took apart (and successfully re-assembled) my 32" Samsung LCD monitor, and none of the flex-on-glass or chip-on-flex binds failed (despite my clumsy hands!). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1247} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Characterization of parylene-C film as an encapsulation material for neural interface devices
___Low Dielectric Constant Materials for Ic Applications___ edited by Paul Shin Ho, Jihperng Leu, Wei William Lee
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{1246} |
ref: -0
tags: parylene microchannel micromolding glass transition temperature microfluidics
date: 06-28-2013 17:34 gmt
revision:3
[2] [1] [0] [head]
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Parylene micromolding, a rapid low-cost fabrication method for parylene microchannel
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{1244} |
ref: -0
tags: polyimide electrodes ecog japan photosensitive
date: 06-28-2013 01:50 gmt
revision:0
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PMID-22719725 Photosensitive-polyimide based method for fabricating various neural electrode architectures
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IEEE-5734597 (pdf) A novel platinum nanowire-coated neural electrode and its electrochemical and biological characterization
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PMID-23010756[0] Comprehensive characterization and failure modes of tungsten microwire arrays in chronic neural implants.
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At Cornell I took a VLSI design class taught by Rajit Manohar (*), and even then - 2002/2003 - he was very excited about asynchronous circuit design. I was uncertain about the technology at the time, but generally I trusted his instinct. Seems that there is certainly some oil in those hills - Octasic has just released a new basestation IC based on asynchronous processor cores: http://www.octasic.com/en/products/oct2200/oct2224w.php The associated product-brief/technology whitepaper gives some good motivations for why asynchronous design is superior to classical synchronous design: (I'll quote, since I find this fascinating, hope they don't mind!)
Cool! I expect to see these techniques in many processors in the future - from embedded, very power sensitive MCUs to GPUs! (*) Rajit was a cool guy. Not only did he give us a good grade, but he even drove us 'downtown' (in the sense of down the hill, Ithaca doesn't really have a downtown) at one point to pick up some resistors and other electronic parts so we could test out MOSIS-fabricated ASIC. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1241} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://thesis.library.caltech.edu/4671/1/PhDThesisFinalChanglinPang.pdf
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So, a year and a half ago I bought a green 1995 900 SE convertible for $600. At that time, it didn't move or go in reverse. Since then, I've been fixing up random things here an there (or just straight modifying / breaking the car by other standards) and recently realized that I had better start keeping track of everything that's been done, in case my memory lapses or i need to know where some random part came from. I doubt this will be useful to anyone else - next time, pictures! Things that I've done to the green convertible, in approximate chronological order:
Things that need to be done to the 'vert:
Now, wonders of wonders, I have another of these cars - though a sedan, not a convertible. It cost much more (about 8x as much), and is hence in much better shape. That said, I've had to do the following:
And now the blue 1998 saab 900, sold to Adam:
Next, the saab 9000 aero:
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PMID-1601445 Factors influencing the biocompatibility of insertable silicon microshafts in cerebral cortex.
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PMID-21228307 Ultrasmall and customizable multichannel electrodes for extracellular recordings
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PMID-23428842 Chronic intracortical microelectrode arrays induce non-uniform, depth-related tissue responses.
This result is supported by previous papers:
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{1237} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19963267 Quantitative analysis of the tissue response to chronically implanted microwire electrodes in rat cortex.
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PMID-22726828 The Brain Activity Map Project and the Challenge of Functional Connectomics
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PMID-23514423 Nanotools for Neuroscience and Brain Activity Mapping
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{1230} |
ref: -0
tags: dissertation interconnect parylene flexible electrodes
date: 02-26-2013 00:30 gmt
revision:2
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http://docs.lib.purdue.edu/dissertations/AAI3444877/
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{1231} |
ref: -0
tags: parylene interconnect monolithic integration silicon DRIE
date: 02-26-2013 00:29 gmt
revision:1
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{1229} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21240559 Highly-compliant, microcable neuroelectrodes fabricated from thin-film gold and PDMS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{597} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16425835Reliability of signals from a chronically implanted, silicon-based electrode array in non-human primate primary motor cortex
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{999} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-4065599 (pdf) Comments on Microelectrodes
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{1227} |
ref: Ledochowitsch-2011.01
tags: Ledochowitsch transparent micro ECoG Peter
date: 01-30-2013 07:01 gmt
revision:2
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PMID-22254956[0] A transparent μECoG array for simultaneous recording and optogenetic stimulation.
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{1162} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11327505 Flexible Polyimide-Based Intracortical Electrode Arrays with Bioactive Capability
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{823} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-20577628[0] Seven years of recording from monkey cortex with a chronically implanted multiple electrode.
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{1225} |
ref: -0
tags: histology optical coherence tomography vasculature avoidance
date: 01-29-2013 06:46 gmt
revision:0
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PMID-9766311 Optical coherence tomography for neurosurgical imaging of human intracortical melanoma.
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PMID-19255461[0] Development and characterization of in vivo flexible electrodes compatible with large tissue displacements.
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{1223} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-12657694[0] High rate shear strain of three-dimensional neural cell cultures: a new in vitro traumatic brain injury model.
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{781} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16198003[0] Response of brain tissue to chronically implanted neural electrodes
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{946} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-1256090[0] A new chronic recording intracortical microelectrode
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{748} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-18485471[0] Characterization of microglial attachment and cytokine release on biomaterials of differing surface chemistry
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{1221} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21775782[0] Long-term stability of neural prosthetic control signals from silicon cortical arrays in rhesus macaque motor cortex (Shenoy)
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{1036} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Things to read! decoding:
electrodes:
other random scribblings: Vascularization {1027} histology {736},{737} and size {1028},{747},{1026}, insulation {1033}. How very very important -- as important or moreso than the recording technology. What has happened to {149} ? | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-12914963[0] Brain responses to micro-machined silicon devices.
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{1220} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-20577634 Biocompatibility of intracortical microelectrodes: current status and future prospects.
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PMID-18057508[0] Complex impedance spectroscopy for monitoring tissue responses to inserted neural implants.
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{1201} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17946847[0] Preliminary study of multichannel flexible neural probes coated with hybrid biodegradable polymer. ____References____
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{1177} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1196780 (pdf) 3D flexible multichannel neural probe array
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PMID-16921203[0] Effects of insertion conditions on tissue strain and vascular damage during neuroprosthetic device insertion.
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{1216} |
ref: Lee-2005.12
tags: micromotion silicon michigan array simulation strain
date: 01-28-2013 03:13 gmt
revision:1
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PMID-16317231[0] Biomechanical analysis of silicon microelectrode-induced strain in the brain.
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{1200} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-14741588[0] Chronic response of adult rat brain tissue to implants anchored to the skull.
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{895} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1605268 (pdf) Evaluation of the Stability of Intracortical Microelectrode Arrays
____References____ Xindong Liu and McCreery, D.B. and Bullara, L.A. and Agnew, W.F. Evaluation of the stability of intracortical microelectrode arrays Neural Systems and Rehabilitation Engineering, IEEE Transactions on 14 1 91 -100 (2006) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1114} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-22170970[0] A system for recording neural activity chronically and simultaneously from multiple cortical and subcortical regions in non-human primates. ____References____
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{898} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19486899[0] Toward a comparison of microelectrodes for acute and chronic recordings.
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{1214} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-7972766 Brain and cerebrospinal fluid motion: real-time quantification with M-mode MR imaging.
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{1213} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-20153370[0] A bio-friendly and economical technique for chronic implantation of multiple microelectrode arrays ____References____
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{78} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17067683[0] A floating metal microelectrode array for chronic implantation
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{311} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-9350963 A floating microwire technique for multichannel neural recording and stimulation in the awake rat
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{1105} |
ref: Bullara-1983.09
tags: electrode grinding insulation stimulation
date: 01-28-2013 00:27 gmt
revision:1
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PMID-6632958[0] A microelectrode for delivery of defined charge densities.
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{736} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-10498377[0] Stability of the interface between neural tissue and chronically implanted intracortical microelectrodes.
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PMID-21270781[0] How advances in neural recording affect data analysis.
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{746} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-10906696[0] Tissue response to single-polymer fibers of varying diameters: evaluation of fibrous encapsulation and macrophage density.
"
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{1211} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-9723616[0] Signal-dependent noise determines motor planning.
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PMID-21654037[0] In vivo deployment of mechanically adaptive nanocomposites for intracortical microelectrodes
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{750} |
ref: Menei-1994.09
tags: microspheres beads polycaprolactone biocompatible drug delivery histology
date: 01-27-2013 20:54 gmt
revision:3
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PMID-7814435 Fate and biocompatibility of three types of microspheres implanted into the brain.
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PMID-782142[0] The reaction of the cerebral cortex to chronically implanted plastic needles.
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{1196} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21867802[0] Reducing surface area while maintaining implant penetrating profile lowers the brain foreign body response to chronically implanted planar silicon microelectrode arrays.
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{1198} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-22049097[0] Mechanically adaptive intracortical implants improve the proximity of neuronal cell bodies.
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{1208} |
ref: Lewitus-2011.08
tags: dissolving polymer electrodes histology degrading
date: 01-25-2013 01:31 gmt
revision:2
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PMID-21609850[0] The fate of ultrafast degrading polymeric implants in the brain.
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PMID-15698656[0] A comparison of chronic multi-channel cortical implantation techniques: manual versus mechanical insertion.
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PMID-19703712[0] The insulation performance of reactive parylene films in implantable electronic devices.
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{1207} |
ref: -0
tags: Shenoy eye position BMI performance monitoring
date: 01-25-2013 00:41 gmt
revision:1
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PMID-18303802 Cortical neural prosthesis performance improves when eye position is monitored.
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{1206} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19164034 Cortical recording with polypyrrole microwire electrodes.
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{1202} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-22254391 Chronic intracortical implantation of saccharose-coated flexible shaft electrodes into the cortex of rats. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1111} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17409479[0] Thin microelectrodes reduce GFAP expression in the implant site in rodent somatosensory cortex.
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{737} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16045910[0] Neuronal cell loss accompanies the brain tissue response to chronically implanted silicon microelectrode arrays.
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{749} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17266019[0] The brain tissue response to implanted silicon microelectrode arrays is increased when the device is tethered to the skull. ____References____
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{1199} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-23091629 Multiple implants do not aggravate the tissue reaction in rat brain.
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{1024} |
ref: COLLIAS-1957.05
tags: histology microelectrode vasulature
date: 01-23-2013 23:56 gmt
revision:4
[3] [2] [1] [0] [head]
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PMID-13429398[0] Histopathological changes produced by implanted electrodes in cat brains; comparison with histopathological changes in human and experimental puncture wounds.
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{1194} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15858046[0] Redundancy and synergy of neuronal ensembles in motor cortex.
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PMID-21499255[0] Reversible large-scale modification of cortical networks during neuroprosthetic control.
Other notes:
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{270} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16838014[] Neuronal ensemble control of prosthetic devices by a human with tetraplegia
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{142} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11090763[0] EEG-based communication: presence of an error potential.
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{1052} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-5332822 (pdf) Neural prosthetic systems: Current problems and future directions
____References____ Chestek, C.A. and Cunningham, J.P. and Gilja, V. and Nuyujukian, P. and Ryu, S.I. and Shenoy, K.V. Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE 3369 -3375 (2009) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1192} |
ref: -2002
tags: sea slugs flexible electrodes polymide Washington
date: 01-04-2013 18:46 gmt
revision:0
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IEEE-1002325 (pdf) Silicon micro-needles with flexible interconnections
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{1040} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-22022568[0] Multiplexed, High Density Electrophysiology with Nanofabricated Neural Probes
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{1102} |
ref: Gilletti-2006.09
tags: electrode micromotion histology GFAP variable reluctance
date: 01-04-2013 02:28 gmt
revision:2
[1] [0] [head]
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PMID-16921202[0] Brain micromotion around implants in the rodent somatosensory cortex.
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{1190} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16045910[0] Neuronal cell loss accompanies the brain tissue response to chronically implanted silicon microelectrode arrays.
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{1058} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19596378 Magnetic insertion system for flexible electrode implantation.
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{1189} |
ref: -0
tags: microelectrode array flexible PDMS via interconnect Georgia
date: 01-04-2013 00:33 gmt
revision:0
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IEEE-6197244 (pdf) A PDMS-Based Integrated Stretchable Microelectrode Array (isMEA) for Neural and Muscular Surface Interfacing | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1188} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-906517 (pdf) Flexible microelectrode arrays with integrated insertion devices
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{1178} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-23160191 Novel flexible Parylene neural probe with 3D sheath structure for enhancing tissue integration
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{1187} |
ref: -0
tags: neural recording topologies circuits operational transconductance amplifiers
date: 01-02-2013 20:00 gmt
revision:0
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PMID-22163863 Recent advances in neural recording microsystems. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-20622860 Imaging brain electric signals with genetically targeted voltage-sensitive fluorescent proteins.
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PMID-22308458 Optically monitoring voltage in neurons by photo-induced electron transfer through molecular wires.
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PMID-22574249 High spatial and temporal resolution wide-field imaging of neuron activity using quantum NV-diamond.
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PMID-16050036 Imaging brain activity with voltage- and calcium-sensitive dyes.
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http://www.redshirtimaging.com/redshirt_neuro/neuro_lib_2.htm
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PMID-20844600 Detection of Neural Action Potentials Using Optical Coherence Tomography: Intensity and Phase Measurements with and without Dyes.
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PMID-19654752 Detecting intrinsic scattering changes correlated to neuron action potentials using optical coherence imaging.
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Demonstration of cortical recording using novel flexible polymer neural probes
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List of links from Moshe Looks google tech talk:
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Recently decided to move myopen's sorting program from sqlite-based persistent state to matlab persistent state, for better interoperability with lab rigs & easier introspection. For this I wrote a class for serializing STL / boost based one, two, and three dimensional resizeable containers to and from matlab files. The code has been tested (albeit not extensively), and therefore may be of use to someone else, even if as an example. See: http://code.google.com/p/myopen/source/browse/trunk/common_host/matStor.cpp As you can see from the header (below), the interface is nice and concise! #ifndef __MATSTOR_H__ #define __MATSTOR_H__ class MatStor{ typedef boost::multi_array<float, 3> array3; typedef boost::multi_array<float, 2> array2; std::string m_name; //name of the file. std::map<std::string, std::vector<float> > m_dat1; //one dimensional std::map<std::string, array2> m_dat2; //two dimensions std::map<std::string, array3> m_dat3; //three! public: MatStor(const char* fname); ~MatStor(); void save(); void setValue(int ch, const char* name, float val); void setValue2(int ch, int un, const char* name, float val); void setValue3(int ch, int un, const char* name, float* val, int siz); float getValue(int ch, const char* name, float def); float getValue2(int ch, int un, const char* name, float def); void getValue3(int ch, int un, const char* name, float* val, int siz); }; #endif | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{1169} |
ref: -0
tags: artificial intelligence projection episodic memory reinforcement learning
date: 08-15-2012 19:16 gmt
revision:0
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Projective simulation for artificial intelligence
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A frequent task in the lab is to sort spikes (extracellular neural action potentials) from background noise. In the lab we are working on doing this wirelessly; to minimize power consumption, spike sorting is done before the radio. In this way only times of spikes need be transmitted, saving bandwidth and power. (This necessitates a bidirectional radio protocol, but this is a worthy sacrifice). In most sorting programs (e.g. Plexon), the raw signal is first thresholded, then waveform snippets (typically 32 samples long) are compared to a template to accept/reject them, or to sort them into different units. The comparison metric is usually the mean-squared error, MSE, aka the L2 norm. This makes sense, as the spike shapes are assumed to be stereotyped (they may very well not be), and the noise white / uncorrelated (another debatable assumption). On the headstage we are working with for wireless neural recording, jumps and memory moves are expensive operations, hence we've elected to do no waveform extraction, and instead match continuously match. By using the built-in MPEG compression opcodes, we can compute the L1 norm at a rate of 4 samples / clock -- very efficient. However, this was more motivated by hardware considerations an not actual spike sorting practice. Literature suggests that for isolating a fixed-pattern signal embedded in noise, the best solution is instead a matched filter. Hence, a careful study of spike-sorting was attempted in matlab, given the following assumptions: fixed spike shape (this was extracted from real data), and uncorrelated band-limited noise. The later was just white noise passed through a bandpass filter, e.g. cheby1(3, 2, [500/15e3 7.5/15]) Where the passband edges are 500 Hz and 15kHz, at a sampling rate of 30kHz. (Actual rate is 31.25kHz). Since the spike times are known, we can rigorously compare the Receiver Operating Characteristic (ROC) and the area under curve (AUC) for different sorting algorithms. Four were tried: L1 (as mentioned above, motivated by the MPEG opcodes), L2 (Plexon), FIR matched filter, and IIR matched filter. The latter was very much an experiment -- IIR filters are efficiently implemented on the blackfin processor, and they generally require fewer taps than their equivalent FIR implementation. To find an IIR equivalent to a given FIR matched filter (whose impulse response closely looks like the actual waveshape, just time-reversed), the filter parameters were simply optimized to match the two impulse responses. To facilitate the search, the denominator was specified in terms of complex conjugate pole locations (thereby constraining the form of the filter), while the numerator coefficients were individually optimized. Note that this is not optimizing given the objective to maximize sorting quality -- rather, it is to make the IIR filter impulse response as close as possible to the FIR matched filter, hence computationally light. And yet: the IIR filter outperforms the FIR matched filter, even though the IIR filter has 1/3 the coefficients (10 vs 32)! Below is the AUC quality metric for the four methods. And here are representative ROC curves at varying spike SNR ratios. The remarkable thing is that even at very low SNR, the matched IIR filter can reliably sort cells from noise. (Note that the acceptable false positive here should be weighted more highly; in the present analysis true positive and false positive are weighted equally, which is decidedly non-Bayesian given most of the time there is no spike.) The matched IIR filter is far superior to the normal MSE to template / L2 norm method -- seems we've been doing it wrong all along? As for reliably finding spikes / templates / filters when the SNR < 0, the tests above - which assume an equal number of spike samples and non-spike samples -- are highly biased; spikes are not normally sortable when the SNR < 0. Upon looking at the code again, I realized three important things:
Including #1 above, as expected, dramatically increased the false positive rate, which is to be expected and how the filters will be used in the real world. #2 did not dramatically impact any of the discriminators, which is good. #3 alleviated the gap between the IIR and FIR filters, and indeed the FIR matched filter performance now slightly exceeds the IIR matched filer. Below, AUC metric for 4 methods. And corresponding ROC for 6 different SNR ratios (note the SNRs sampled are slightly different, due to the higher false positive rate). One thing to note: as implemented, the IIR filter requires careful matching of poles and zeros, and is may not work with 1.15 fixed-point math on the Blackfin. The method really deserves to be tested in vivo, which I shall do shortly. More updates: See www.aicit.org/jcit/ppl/JCIT0509_05.pdf -- they add an 'adjustment' function to the matched filter due to variance in the amplitude of spikes, which adds a little performance at low SNRs.
Sigma is the standard deviation of x(t), n and k determine 'zoom intensity and zoom center'. The paper is not particularly well written - there are some typos, and their idea seems unjustified. Still the references are interesting:
Update: It is not to difficult to convert FIR filters to IIR filters using simple numerical optimization. Within my client program, this is done using simulated annealing; have tested this using fminsearch in matlab. To investigate the IIR-filter fitting problem more fully, I sliced the 10-dimensional optimization space along pairs of dimensions about the optimum point as found using fminsearch. The parameters are as follows:
The figure below plots the +-1 beyond the optimum for each axis pair. Click for full resolution image. Note that the last parameter is discrete, hence steps in the objective function. Also note that the problem is perfectly quadratic for the numerator, as expected, which is why LMS works so well. Note that for the denominator pole locations, the volume of the optimum is small, and there are interesting features beyond this. Some spaces have multiple optima. The next figure plots +-0.1 beyond the optimum for each axis vs. every other one. It shows that, at least on a small scale, the problem becomes very quadratic in all axes hence amenable to line or conjugate gradient search. Moving away from planes that pass through a found optima, what does the space look like? E.g. From a naive start, how hard is it to find at least one workable solution? To test this, I perturbed the found optimum with white noise in the parameters std 0.2, and plotted the objective function as before, albeit at higher resolution (600 x 600 points for each slice). These figures show that there can be several optima in the denominator, but again it appears that a very rough exploration followed by gradient descent should arrive at an optima. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1168} |
ref: -0
tags: debian linux github persistent ssh authentication
date: 07-27-2012 01:40 gmt
revision:1
[0] [head]
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If you don't want to repeatedly enter in your username/password for github when commiting, you'll want to enable an RSA authetication key. -- http://www.debian.org/devel/passwordlessssh run ssh-keygen(with no options). -- then https://help.github.com/articles/working-with-ssh-key-passphrases ssh-keygen -pwith your github passphrase (I'm not totally sure this is essential). For me, pull and push aftwerard worked without needing to supply my password. Easy! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-22157115 Decoding 3D reach and grasp from hybrid signals in motor and premotor cortices: spikes, multiunit activity, and local field potentials.
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{1165} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1275580 (pdf) Ceramic-based Multisite Electrode array for Chronic Single-Neuron Recording | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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http://www.mdpi.com/1424-8220/8/10/6704/pdf NeuroMEMS: Neuro Probe Microtechnologies
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PMID-22096594[0] Comprehensive analysis of tissue preservation and recording quality from chronic multielectrode implants.
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PMID-10223510 Chronic recording capability of the Utah Intracortical Electrode Array in cat sensory cortex.
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{1161} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Just to my left, a woman in a walker rolled into the library, and promptly complained to the police officer on duty about chest pains. The library faces a square in the middle of Springfield where teenagers, shirtless hippies, skateboarders, and other non-mainstream people kill time in the warm afternoon. The library as such is a cool haven to read and access the internet -- several teenagers were playing WoW on the library computers, and I too am tapping into the resource. A possibly adrift artsy-type man of about my age similarly came to conduct his wayward business, having 'just ended up in Springfield', saying it as both and excuse and a badge of pride evincing his free spirit. The woman is one of the classic types of hypochondriac, and though I'm only listening to them the EMT and police men know this, but they also know that on the off chance of being wrong, not taking the situation seriously could be a disaster. And so they administered simple blood pressure and pulse rate tests, both which seemed normal, then went about convincing her that she needed to be taken to the hospital to be completely checked out, thereby shifting the burden of liability to a place better protected by the standard operating procedure of a battery of tests. The woman immediately protested, worried about the heavy cost of a ambulance ride, coupled with a paranoia that she would lose her walker. To this the EMT -- a short woman with her practical ponytail shoved through a baseball cap, as often they do -- let glints of irritation show through, asking her repeatedly to decide which hospital she wished to go to, and then asking her to arrange another means to the hospital. The woman protested, but the EMT could scarecly be blamed -- she is stuck in a system not of her design -- and somehow the smooth-souled librarian, who before had been placating library customers by putting holds on books, convinced both parties to go to the nearest hopsital. How exactly this was done I'll forever remain in ignorance, for another ambulance spun through the downtown circle at that instant, scattering sports cars, stopping sedans, and causing the skaters to pause their idling and look. The incident vaguely reminds me when I had similar issues in Brooklyn, when i was sufficiently pained to drive my ass through the dirty orange-lit streets to a hospital in Williamsburg. They proceeded to do drug tests on me, despite my insistences, but everything checked out fine. In retrospect, the pain was likely heartburn antagonized by psychological isolation; this was before I really learned to listen to myself, and take care of the social and more basic physiological needs. The walker woman fell through these same cracks in a likely preventable but now very expensive way. Meanwhile, a large black transsexual and a wrinkly white guy walk hurriedly past the plate glass windows of the library, talking animatedly. They may be in a fissure of sorts, but i doubt they consider it a fall... | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1159} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
I highly agree with this philosophy / this deconstruction of the flow of information in human structures: http://www.lostgarden.com/2012/04/loops-and-arcs.html On criticism as a meta-arc game: "In the past I've discussed criticism as a game that attempts to revisit an arc repeatedly and embellish it with additional meaning. The game is to generate essays superficially based on some piece of existing art. In turn, other players generate additional essays based off the first essays. This acts as both a referee mechanism and judge. Score is accumulated via reference counts and by rising through an organization hierarchy. It is a deliciously political game of wit that is both impenetrable to outsiders and nearly independent of the actual source arcs. Here creating an arc becomes a move in the larger game. " | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-22448159 Spike sorting of heterogeneous neuron types by multimodality-weighted PCA and explicit robust variational Bayes.
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PMID-22017994[0] Closed-loop deep brain stimulation is superior in ameliorating parkinsonism.
Other thoughts:
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PMID-15496658 Neuronal oscillations in the basal ganglia and movement disorders: evidence from whole animal and human recordings.
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PMID-21696996 The hippocampus: hub of brain network communication for memory
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PMID-11832222 Theta Oscillations in the Hippocampus
Original model for theta oscillation creation (figure 2):
LTP:
Conclusions:
Misc:
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http://web.cecs.pdx.edu/~greenwd/xmsnLine_notes.pdf -- Series termination will work, provided the impedance of the driver + series resistor is matched to the impedance of the transmission line being driven. School has been so long ago, I've forgotten these essentials! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-12629196[0] Stimulation of the Subthalamic Nucleus Changes the Firing Pattern of Pallidal Neurons
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{696} |
ref: Jarosiewicz-2008.12
tags: Schwartz BMI learning perturbation
date: 03-07-2012 17:11 gmt
revision:2
[1] [0] [head]
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PMID-19047633[0] Functional network reorganization during learning in a brain-computer interface paradigm.
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PMID-19744484 What can man do without basal ganglia motor output? The effect of combined unilateral subthalamotomy and pallidotomy in a patient with Parkinson's disease.
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PMID-16271465 The basal ganglia: learning new tricks and loving it
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{1018} |
ref: Rouse-2011.06
tags: BMI chronic DBS bidirectional stimulator Washington Medtronic ASIC translational
date: 03-05-2012 23:56 gmt
revision:3
[2] [1] [0] [head]
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PMID-21543839[0] A chronic generalized bi-directional brain-machine interface.
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PMID-19460368[0] Pathological subthalamic nucleus oscillations in PD: can they be the cause of bradykinesia and akinesia?
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PMID-19299613[0] Spinal cord stimulation restores locomotion in animal models of Parkinson's disease.
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PMID-18037630[0] Bilateral stimulation in the caudal zona incerta nucleus for tremor control
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PMID-6838141[0] Speculations on the Functional Anatomy of Basal Ganglia Disorders
Got some things completely wrong:
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PMID-17046697 Rapid alterations in corticostriatal ensemble coordination during acute dopamine-dependent motor dysfunction.
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{1149} |
ref: -0
tags: locomotion decerebrated monkeys spinal cord section STN stimulation
date: 03-01-2012 23:53 gmt
revision:0
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PMID-7326562 Locomotor control in macaque monkeys
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PMID-16153803[0] The robot basal ganglia: action selection by an embedded model of the basal ganglia
My thoughts:
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PMID-21147836[0] Resting oscillatory cortico-subthalamic connectivity in patients with Parkinson’s disease
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PMID-7411442 The monkey globus pallidus: neuronal discharge properties in relation to movement.
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PMID-9421169 Bilateral lesions of the subthalamic nucleus induce multiple deficits in an attentional task in rats.
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PMID-19109506 Parkinsonian beta oscillations in the external globus pallidus and their relationship with subthalamic nucleus activity.
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PMID-18448656[0] Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex.
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{1087} |
ref: Timmermann-2003.01
tags: DBS double tremor oscillations DICS beamforming parkinsons
date: 02-29-2012 00:39 gmt
revision:4
[3] [2] [1] [0] [head]
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PMID-12477707[0] The cerebral oscillatory network of parkinsonian resting tremor.
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PMID-15703229[0] Spontaneous pallidal neuronal activity in human dystonia: comparison with Parkinson's disease and normal macaque.
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{1146} |
ref: -0
tags: oscillations DBS globus pallidus parkinsons
date: 02-28-2012 17:24 gmt
revision:1
[0] [head]
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PMID-17880401 Late emergence of synchronized oscillatory activity in the pallidum during progressive Parkinsonism.
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PMID-15242667 Anatomical funneling, sparse connectivity and redundancy reduction in the neural networks of the basal ganglia
PMID-15233923 Coincident but distinct messages of midbrain dopamine and striatal tonically active neurons.
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PMID-7983514[0] The Primate Subthalamic Nucleus. 1. Functional Properties in Intact Animals.
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{1136} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11285003 Dopaminergic control of synaptic plasticity in the dorsal striatum.
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{1143} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11052216 Organization of the basal ganglia: the importance of axonal collateralization.
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{164} |
ref: DeLong-1985.02
tags: globus pallidus subthalamic STN electrophysiology Georgopoulos DeLong DBS
date: 02-24-2012 21:50 gmt
revision:5
[4] [3] [2] [1] [0] [head]
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PMID-3981228[0] Primate globus pallidus and subthalamic nucleus: functional organization
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{1140} |
ref: -0
tags: dopamine reward prediction striatum error striatum orbitofrontal reward
date: 02-24-2012 21:26 gmt
revision:1
[0] [head]
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PMID-11105648 Involvement of basal ganglia and orbitofrontal cortex in goal-directed behavior.
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{1141} |
ref: -0
tags: putamen functional organization basal ganglia
date: 02-24-2012 21:01 gmt
revision:0
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PMID-6705861 Single cell studies of the primate putamen. I. Functional organization.
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{1138} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-1483512 Role of the primate basal ganglia and frontal cortex in the internal generation of movements. I. Preparatory activity in the anterior striatum
PMID-1483513 Role of primate basal ganglia and frontal cortex in the internal generation of movements. II. Movement-related activity in the anterior striatum.
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{1139} |
ref: -0
tags: striatum microstimulation abnormal myclonus dyskinesia
date: 02-24-2012 19:44 gmt
revision:0
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PMID-21508304 Discontinuous Long-Train Stimulation in the Anterior Striatum in Monkeys Induces Abnormal Behavioral States
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PMID-20855421[0] Mapping Go-No-Go performance within the subthalamic nucleus region.
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{168} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-7284825[0] Connections of the subthalamic nucleus in the monkey.
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{171} |
ref: Boulet-2006.1
tags: hemiballismus PD parkinsons STN subtalamic DBS dyskinesia rats 2006 glutamate
date: 02-22-2012 18:58 gmt
revision:1
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PMID-17050715 Subthalamic Stimulation-Induced Forelimb Dyskinesias Are Linked to an Increase in Glutamate Levels in the Substantia Nigra Pars Reticulata
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PMID-9464684[0] Physiological aspects of information processing in the basal ganglia of normal and parkinsonian primates.
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PMID-18540149[0] Deep brain stimulation: how does it work?
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{1083} |
ref: Holgado-2010.09
tags: DBS oscillations beta globus pallidus simulation computational model
date: 02-22-2012 18:36 gmt
revision:4
[3] [2] [1] [0] [head]
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PMID-20844130[0] Conditions for the Generation of Beta Oscillations in the Subthalamic Nucleus–Globus Pallidus Network
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PMID-19050033[0] Levodopa enhances synaptic plasticity in the substantia nigra pars reticulata of Parkinson's disease patients
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PMID-20493764[0] Current-controlled deep brain stimulation reduces in vivo voltage fluctuations observed during voltage-controlled stimulation.
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{1073} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-12040070[0] Enhanced synchrony among primary motor cortex neurons in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine primate model of Parkinson's disease.
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{828} |
ref: RodriguezOroz-2001.09
tags: STN SNr parkinsons disease single unit recording spain 2001 tremor oscillations DBS somatotopy organization
date: 02-22-2012 18:24 gmt
revision:12
[11] [10] [9] [8] [7] [6] [head]
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PMID-11522580[0] The subthalamic nucleus in Parkinson's disease: somatotopic organization and physiological characteristics
Old notes:
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{829} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-12023310[0] Dependence of subthalamic nucleus oscillations on movement and dopamine in Parkinson's disease.
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{1076} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17017503[0] Synchronizing activity of basal ganglia and pathophysiology of Parkinson's disease.
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{159} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21723919[0] Pathological basal ganglia activity in movement disorders.
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PMID-21059746[0] Involvement of the subthalamic nucleus in impulse control disorders associated with Parkinson’s disease
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PMID-12495873[0] Relationship between oscillations in the basal ganglia and synchronization of cortical activity.
Also, random: the world's highest rate of Parkinson's disease is in the Amish in the NE US. More than twice that of anywhere else; http://www.viartis.net/parkinsons.disease/news/090801.htm ____References____
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PMID-12671940[0] Oscillatory nature of human basal ganglia activity: relationship to the pathophysiology of Parkinson's disease.
Conclusion: he really thinks that there is a strong dichotomy between HF, pro-kinetic, and MF, anti-kinetic oscillations. ____References____
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{237} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-8783253[0] The subthalamic nucleus and the external pallidum: two tightly interconnected structures that control the output of the basal ganglia in the monkey.
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{207} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11566503[0] Dopamine regulates the impact of the cerebral cortex on the subthalamic nucleus-globus pallidus network
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{242} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-12220881[] Move to the rhythm: oscillations in the subthalamic nucleus-external globus pallidus network.
my notes:
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{169} |
ref: Hamani-2004.01
tags: STN subthalamic nucleus movement disorders PD parkinsons basal_ganglia globus_pallidus anatomy DBS
date: 02-22-2012 15:03 gmt
revision:8
[7] [6] [5] [4] [3] [2] [head]
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PMID-14607789[0] The subthalamic nucleus in the context of movement disorders
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{654} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-18614691[0] Role for subthalamic nucleus neurons in switching from automatic to controlled eye movement.
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{1093} |
ref: Benabid-2009.01
tags: DBS historical perspective
date: 02-22-2012 14:54 gmt
revision:2
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PMID-19660668[0] Functional neurosurgery for movement disorders: a historical perspective.
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PMID-16549385[0] The effect of subthalamic nucleus deep brain stimulation on precision grip abnormalities in Parkinson's disease
See also PMID-19266149[1] Distal and proximal prehension is differentially affected by Parkinson‘s disease The effect of conscious and subconscious load cues
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PMID-19559747[0] Deep brain stimulation in neurological diseases and experimental models: from molecule to complex behavior.
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PMID-21875864 Dopamine cell transplantation in Parkinson's disease: challenge and perspective.
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PMID-20400953 Dissolvable films of silk fibroin for ultrathin conformal bio-integrated electronics.
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PMID-16758482 "Paradoxical kinesis" is not a hallmark of Parkinson's disease but a general property of the motor system.
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PMID-15272269 Stem cell therapy for human neurodegenerative disorders-how to make it work.
Stroke:
ALS:
Synthesis:
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There seems to be an interesting connection between excessive grip force, isometric muscle contraction causing coherence between motor cortex and EMG, lack of inhibition on delayed response and go-no-go task, and experiments with STN lesioned rats, and the high/low oscillation hypothesis. Rather tenuous, I suppose, but let me spell it out. ( My personal impression, post-hoc, is that this is an epiphenomena of something else; evidence is contradictory.)
footnote: how much is our search for oscillations informed by our available analytical techniques? Hypothesis: Impulsivity may be the cognitive equivalent of excess grip force; maintenance of consistent 'force' or delayed decision making benefits from Piper-band rhythms, something which PD abolishes (gradually, through brain adaptation). DBS disrupts the beta (resting, all synchronized) rhythm, and thereby permits movement. However it also effectively 'lesions' the STN, which leads to cognitive deficits and poor force control. (Wait .. DBS plus levodopa improves 40-60Hz energy -- this would argue against the hypothesis. Also, stroke in the STN in normal individuals causes hemiballismus, which resolves gradually; this is not consistent with oscillations, but rather connectivity and activity.) Testing this hypothesis: well, first of all, is there beta-band oscillations in our data? what about piper band? We did not ask the patients to delay response, so any tests thereof will be implicit. Can look at relative energy 10Hz-30Hz and 30Hz-60Hz in the spike traces & see if this is modulated by hand position. (PETH as usual). So. I made PETHs for beta / gamma power ratio of the spiking rate, controlled by shuffling the PETH triggers. Beta power was between 12 and 30 Hz; gamma between 30 and 75 Hz, as set by a noncausal IIR bandpass filter. The following is a non-normalized heatmap of all significant PETHs over all sessions triggered when the hand crossed the midpoint between targets. (A z-scored heatmap was made as well; it looked worse). X is session number, Y time, 0 = -1 sec. sampling rate = 200 Hz. In one file (the band) there seems to be selective gamma inhibition about 0.5 sec before peak movement. Likely it is an outlier. 65 neurons of 973 (single and multiunits together) were significantly 'tuned' = 6.6%; marginally significant by binomial test (p=0.02). Below is an example PETH, with the shuffled distribution represented by mean +- 1 STD in blue. The following heatmap is created from the significant PETHs triggered on target appearance. 80 of the 204 significant PETHs are from PLEX092606005_a. The total number of significant responses (204/1674, single units and multiunits) is significant by the binomial test p < 0.001, with and without Sept. 26 removed. Below is an example plot (092606005). Looks pretty damn good, actually. Let's see how stable this relationship is by doing a leave-half out cross-validation, 10 plies, in red below (all triggers plotted in black) Looks excellent! Problem is we are working with a ratio, which is prone to spikes. Fix: work in log space. Aggregate response remains about the same. 192 / 1674 significant (11.5%) In the above figure, positive indicates increased power relative to power. The square shape is likely relative to (negative lags) hold time and (positive lags) reaction time, though the squareness is somewhat concerning. Recording is from VIM. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1122} |
ref: Gale-2009.03
tags: STN DBS monkey comparison electrophysiology
date: 02-21-2012 16:34 gmt
revision:2
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PMID-19167367[0] Subthalamic nucleus discharge patterns during movement in the normal monkey and Parkinsonian patient.
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{1125} |
ref: -0
tags: active filter design Netherlands Gerrit Groenewold
date: 02-17-2012 20:27 gmt
revision:0
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IEEE-04268406 (pdf) Noise and Group Delay in Actvie Filters
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PMID-20850966[0] Basal ganglia contributions to motor control: a vigorous tutor.
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I recently wrote a matlab script to measure & plot the autocorrelation of a spike train; to test it, I generated a series of timestamps from a homogeneous Poisson process: function [x, isi]= homopoisson(length, rate) % function [x, isi]= homopoisson(length, rate) % generate an instance of a poisson point process, unbinned. % length in seconds, rate in spikes/sec. % x is the timestamps, isi is the intervals between them. num = length * rate * 3; isi = -(1/rate).*log(1-rand(num, 1)); x = cumsum(isi); %%find the x that is greater than length. index = find(x > length); x = x(1:index(1,1)-1, 1); isi = isi(1:index(1,1)-1, 1); The autocorrelation of a Poisson process is, as it should be, flat: Above:
The problem with my recordings is that there is generally high long-range correlation, correlation which is destroyed by shuffling. Above is a plot of 1/isi for a noise channel with very high mean 'firing rate' (> 100Hz) in blue. Behind it, in red, is 1/shuffled isi. Noise and changes in the experimental setup (bad!) make the channel very non-stationary. Above is the autocorrelation plotted in the same way as figure 1. Normally, the firing rate is binned at 100Hz and high-pass filtered at 0.005hz so that long-range correlation is removed, but I turned this off for the plot. Note that the suffled data has a number of different offsets, primarily due to differing long-range correlations / nonstationarities. Same plot as figure 3, with highpass filtering turned on. Shuffled data still has far more local correlation - why? The answer seems to be in the relation between individual isis. Shuffling isi order obviuosly does not destroy the distribution of isi, but it does destroy the ordering or pair-wise correlation between isi(n) and isi(n+1). To check this, I plotted these two distributions: -- Original log(isi(n)) vs. log(isi(n+1) -- Shuffled log(isi_shuf(n)) vs. log(isi_shuf(n+1) -- Close-up of log(isi(n)) vs. log(isi(n+1) using alpha-blending for a channel that seems heavily corrupted with electro-cauterizer noise. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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We have found the following types of neurons during acute intraoperative recrodings from the subthalamic nucleus (STN) of awake parkinson's patients. During the surgeries the patients opened and closed their hand, instrumented through a virtual-reality data glove, in order to move a cursor to randomly presented targets in a 1-dimensional field.
This plot shows a neuron which fires preferentially when a target appears and the patient moves to the left (again, in this graph: y = -1 indicates target appears to the left, + 1 target to the right, and 0 otherwise). Note that there is noticable oscillations, due to the fact that the patient's behavior was very periodic, with a period of around 2 seconds. The neuron was inhibited around the instant of target apperance, independent of direction, as indicated by the blue regions at y = -1 and 1 around lag 0.
This plot shows a neuron which is inhibited just before target apperance (in this plot, y = 1 400ms around target appearance, independent of direction). That is, the neuron stops firing upon sucessful completion of a movement. This neuron shows no pathological oscillatory tuning; therefore, it might be assumed that not all of the STN is incapacitated by Parkinson's disease.
Here is another example of a neuron that does not show oscillatory firing behavior. In this graph, y = 1 when the patient is opening or closing his hand (equivalently the cursor velocity exceeds a threshold); y = 0 otherwise. This neuron is therefore inhibited during periods of movement. Note that around a lag of 2.5 seconds, the neuron has a higher probability of firing (the red region), possibly indicating positive firing upon successful completion of a movement.
Another example of a neuron that is tuned to thresholded cursor velocity, though this time, the firing rate becomes positive just around the instant of movement. Note here there is evidence of highly periodic behavior, as seen in the green/yellow regions spaced about 1.6 seconds apart along y=1. The region at lag = 1.6 secons corresponds to the movement following target acquisition, hence exhibits a higher firing rate.
This neuron, like the one above, fires strongly whenever the hand moves. Interestingly, there appeared to be no directional information in either of these cells.
Finally, we discovered that there appears to be error-correlated firing within the STN. The neuron shown above is selectively inhibited around periods where the cursor and target positions differ. In the plot above y=1 indicates the absolute value of the target position - the cursor position exceeds a threshold of 20% of the total range (this is subtly different from the target apperance signal, as the patient can over shoot or under shoot the target position with the cursur, upon which this signal will be 1. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1123} |
ref: Berke-2009.09
tags: DBS oscillations high gamma synchronization
date: 02-16-2012 17:48 gmt
revision:1
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PMID-19659455[0] Fast oscillations in cortical-striatal networks switch frequency following rewarding events and stimulant drugs.
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PMID-17182916[0] Subthalamic and Striatal Neurons Concurrently Process Motor, Limbic, and Associative Information in Rats Performing an Operant Task
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IEEE-1580838 (pdf) Microfabricated cylindrical multielectrodes for neural stimulation.
____References____ Snow, S. and Jacobsen, S.C. and Wells, D.L. and Horch, K.W. Microfabricated cylindrical multielectrodes for neural stimulation Biomedical Engineering, IEEE Transactions on 53 2 320 -326 (2006) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-21270781 How advances in neural recording affect data analysis
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PMID-8836553[0] Single unit recording capabilities of a 100 microelectrode array. Nordhausen CT, Maynard EM, Normann RA.
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{1110} |
ref: -0
tags: Seymour thesis electrode lithography fabrication
date: 02-05-2012 17:35 gmt
revision:4
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Advanced polymer-based microfabricated neural probes using biologically driven designs.
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{1109} |
ref: -0
tags: Cogan 2008 electrodes recording stimulation
date: 02-05-2012 00:21 gmt
revision:0
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PMID-18429704 Neural stimulation and recording electrodes.
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PMID-11948749[0] Surgery of the motor thalamus: problems with the present nomenclatures. ____References____
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PMID-9504843 Axons, but not cell bodies, are activated by electrical stimulation in cortical gray matter. I. Evidence from chronaxie measurements.
PMID-9504844 Axons, but not cell bodies, are activated by electrical stimulation in cortical gray matter. II. Evidence from selective inactivation of cell bodies and axon initial segments.
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PMID-16317234 A finite-element model of the mechanical effects of implantable microelectrodes in the cerebral cortex.
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PMID-19286561[0] Human Substantia Nigra Neurons Encode Unexpected Financial Rewards
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PMID-18562098[0] Accurate timing but increased impulsivity following excitotoxic lesions of the subthalamic nucleus.
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PMID-20727974[0] Bursts and oscillations as independent properties of neural activity in the parkinsonian globus pallidus internus.
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PMID-14960502[0] Event-related beta desynchronization in human subthalamic nucleus correlates with motor performance.
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PMID-16973296[0] Subthalamic nucleus neurones in slices from MPTP-lesioned mice show irregular, dopamine-reversible firing pattern changes, but without synchronous activity
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{112} |
ref: Lee-2005.07
tags: STN subthalamic nucleus hemiballismus DBS
date: 01-26-2012 17:24 gmt
revision:3
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PMID-16032642[0] Common causes of hemiballism.
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PMID-10660885[0] Single-axon tracing study of neurons of the external segment of the globus pallidus in primate.
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PMID-7983515[0] The primate subthalamic nucleus. II. Neuronal activity in the MPTP model of parkinsonism
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PMID-83239[0] Projections of the precentral motor cortex and other cortical areas of the frontal lobe to the subthalamic nucleus in the monkey.
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PMID-19070616[0] Pathological synchronisation in the subthalamic nucleus of patients with Parkinson's disease relates to both bradykinesia and rigidity.
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PMID-17949812[0] Pathophysiology of the basal ganglia and movement disorders: From animal models to human clinical applications
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PMID-17962524[0] Hold your horses: impulsivity, deep brain stimulation, and medication in parkinsonism.
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{165} |
ref: Lehericy-2005.08
tags: fMRI motor_learning basal_ganglia STN subthalamic
date: 01-25-2012 00:20 gmt
revision:2
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PMID-16107540[0] Distinct basal ganglia territories are engaged in early and advanced motor sequence learning
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{12} |
ref: Breit-2006.1
tags: parkinsons basal_ganglia palladium substantia_nigra motor_control striate
date: 01-24-2012 22:10 gmt
revision:1
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I wish i could remember where i got these notes from, so as to verify the somewhat controversial statements. I found them written on the back of a piece of scrap paper.
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{566} |
ref: Sakai-2001.06
tags: voltage scensitive fluorescent protein flourophore VSFP1 endoscope
date: 01-24-2012 06:07 gmt
revision:5
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http://www.blackwell-synergy.com/doi/full/10.1046/j.0953-816x.2001.01617.x PMID-11454036[0]
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{162} |
ref: Krack-2001.09
tags: STN subthalamic nucleus stimulation PD parkinsons DBS
date: 01-24-2012 05:48 gmt
revision:1
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PMID-11746616[0] Mirthful laughter induced by subthalamic nucleus stimulation.
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{163} |
ref: Hilker-2004.01
tags: STN subthalamic DBS stimulation cortex cerebellum PET PD parkinsons
date: 01-24-2012 05:38 gmt
revision:1
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PMID-14688612[0] Subthalamic Nucleus Stimulation Restores Glucose Metabolism in Associative and Limbic Cortices and in Cerebellum: Evidence from a FDG-PET Study in Advanced Parkinson's Disease
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PMID-21603228[0] Dopaminergic Balance between Reward Maximization and Policy Complexity.
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Just fer kicks, I tested what happens to low-order butterworth filters when you maladjust one of the feedback coefficients. [B, A] = butter(2, 0.1); [h, w] = freqz(B,A); A(2) = A(2) * 0.9; [h2, ~] = freqz(B,A); hold off subplot(1,2,1) plot(w,abs(h)) hold on; plot(w,abs(h2), 'r') title('10% change in one FB filter coef 2nd order butterworth') xlabel('freq, rads / sec'); ylabel('filter response'); % do the same for a higher order filter. [B, A] = butter(3, 0.1); [h, w] = freqz(B,A); A(2) = A(2) * 0.9; [h2, ~] = freqz(B,A); subplot(1,2,2) hold on plot(w,abs(h), 'b') plot(w,abs(h2), 'r') title('10% change in one FB filter coef 3rd order butterworth') xlabel('freq, rads / sec'); ylabel('filter response'); The filters show a resonant peak, even though feedback was reduced. Not surprising, really; a lot of systems will show reduced phase margin and will begin to oscillate when poles are moved. Does this mean that a given coefficient (anatomical area) is responsible for resonance? By itself, of course not; one can not extrapolate one effect from one manipulation in a feedback system, especially a higher-order feedback system. This, of course hold in the mapping of digital (or analog) filters to pathology or anatomy. Pathology is likely reflective of how the loop is structured, not how one element functions (well, maybe). For a paper, see {1083} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-21096380[0] "A multi-channel low-power system-on-chip for single-unit recording and narrowband wireless transmission of neural signal."
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PMID-6869036[0] The Piper rhythm--a phenomenon related to muscle resonance characteristics?
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PMID-11765129[0] Cortical network resonance and motor activity in humans.
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PMID-11923450[0] Synchronized neuronal discharge in the basal ganglia of parkinsonian patients is limited to oscillatory activity.
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{255} |
ref: BarGad-2003.12
tags: information dimensionality reduction reinforcement learning basal_ganglia RDDR SNR globus pallidus
date: 01-16-2012 19:18 gmt
revision:3
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PMID-15013228[] Information processing, dimensionality reduction, and reinforcement learning in the basal ganglia (2003)
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PMID-4966614[] Relation of pyramidal tract activity to force exerted during voluntary movement
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{931} |
ref: Deco-2009.05
tags: stochastic dynamics Romo memory computation
date: 01-16-2012 18:54 gmt
revision:1
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PMID-19428958[0] Stochastic dynamics as a principle of brain function
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PMID-8036499[0] Direct cortical representation of drawing ____References____
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PMID-20161810[0] Bridging the Divide between Neuroprosthetic Design, Tissue Engineering and Neurobiology
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IEEE-5969351 (pdf) New class of chronic recording multichannel neural probes with post-implant self-deployed satellite recording sites | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-21719340 Modelization of a self-opening peripheral neural interface: a feasibility study. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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IEEE-1201998 (pdf) A low-power low-noise CMOS amplifier for neural recording applications
Harrison, R.R. and Charles, C. A low-power low-noise CMOS amplifier for neural recording applications Solid-State Circuits, IEEE Journal of 38 6 958 - 965 (2003) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-19199762[0] Optical Detection of Brain Cell Activity Using Plasmonic Gold Nanoparticles
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PMID-16200750[0] Wireless Multichannel Biopotential Recording Using an Integrated FM Telemetry Circuit Pedram Mohseni, Khalil Najafi, Steven Eliades, Xiaoquin Wang.
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{1054} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-20089393[0] Electrical interfacing between neurons and electronics via vertically integrated sub-4 microm-diameter silicon probe arrays fabricated by vapor-liquid-solid growth.
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PMID-17913908[0] Single-Neuron Stability during Repeated Reaching in Macaque Premotor Cortex
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PMID-19067174[0] Integrated wireless neural interface based on the Utah electrode array
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{1049} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-4353193 (pdf) A Sub-Microwatt Low-Noise Amplifier for Neural Recording
____References____ Holleman, J. and Otis, B. Engineering in Medicine and Biology Society, 2007. EMBS 2007. 29th Annual International Conference of the IEEE 3930 -3933 (2007) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1050} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1643411 (pdf) A TinyOS-enabled MICA2-BasedWireless neural interface
____References____ Farshchi, S. and Nuyujukian, P.H. and Pesterev, A. and Mody, I. and Judy, J.W. A TinyOS-enabled MICA2-BasedWireless neural interface Biomedical Engineering, IEEE Transactions on 53 7 1416 -1424 (2006) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1051} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-5226763 (pdf) An Implantable 64-Channel Wireless Microsystem for Single-Unit Neural Recording
____References____ Sodagar, A.M. and Perlin, G.E. and Ying Yao and Najafi, K. and Wise, K.D. An Implantable 64-Channel Wireless Microsystem for Single-Unit Neural Recording Solid-State Circuits, IEEE Journal of 44 9 2591 -2604 (2009) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{979} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-14757342[0] A multichannel telemetry system for single unit neural recordings
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{1055} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-5230909 (pdf) A High Resolution Bi-Directional Communication through a Brain-Chip Interface
____References____ Maschietto, M. and Mahmud, M. and Stefano, G. and Vassanelli, S. Advanced Technologies for Enhanced Quality of Life, 2009. AT-EQUAL '09. 32 -35 (2009) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{729} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-4358095 (pdf) An Ultra-Low-Power Neural Recording Amplifier and its use in Adaptively-Biased Multi-Amplifier Arrays.
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{1025} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-335862 (pdf) A three-dimensional microelectrode array for chronic neural recording.
____References____ Hoogerwerf, A.C. and Wise, K.D. A three-dimensional microelectrode array for chronic neural recording Biomedical Engineering, IEEE Transactions on 41 12 1136 -1146 (1994) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1046} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1448388 (pdf) The Electrical Properties of Metal Microelectrodes
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{740} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-3957372[0] Solid-state electrodes for multichannel multiplexed intracortical neuronal recording.
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{1045} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-95711[0] Spike separation in multiunit records: A multivariate analysis of spike descriptive parameters
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{1037} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1546254 (pdf) A three-dimensional neural recording microsystem with implantable data compression circuitry
____References____ Olsson, R.H., III and Wise, K.D. A three-dimensional neural recording microsystem with implantable data compression circuitry Solid-State Circuits, IEEE Journal of 40 12 2796 - 2804 (2005) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{947} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-6392757[0] Instruments for sorting neuroelectric data: a review
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{1041} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1052457 (pdf) A monolithic signal processor for a neurophysiological telemetry system
____References____ Dorman, M.G. and Prisbe, M.A. and Meindl, J.D. A monolithic signal processor for a neurophysiological telemetry system Solid-State Circuits, IEEE Journal of 20 6 1185 - 1193 (1985) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1042} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-121568 (pdf) An implantable CMOS circuit interface for multiplexed microelectrode recording arrays
____References____ Ji, J. and Wise, K.D. ''An implantable CMOS circuit interface for multiplexed microelectrode recording arrays'' Solid-State Circuits, IEEE Journal of 27 3 433 -443 (1992) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1043} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1019051 (pdf) A multi channel chopper modulated neural recording system
____References____ Dagtekin, M. and Wentai Liu and Bashirullah, R. Engineering in Medicine and Biology Society, 2001. Proceedings of the 23rd Annual International Conference of the IEEE 1 757 - 760 vol.1 (2001) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1044} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-10522821[0] A 100-channel system for real time detection and storage of extracellular spike waveforms.
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{985} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1185151 (pdf) Two multichannel integrated circuits for neural recording and signal processing
____References____ Obeid, I. and Morizio, J.C. and Moxon, K.A. and Nicolelis, M.A.L. and Wolf, P.D. Two multichannel integrated circuits for neural recording and signal processing Biomedical Engineering, IEEE Transactions on 50 2 255 -258 (2003) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{316} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-12797724[0] A miniaturized neuroprosthesis suitable for implantation into the brain.
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{782} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-5067358 (pdf) Wireless, Ultra Low Power, Broadband Neural Recording Microsystem
____References____ Song, Y.-K. and Borton, D.A. and Park, S. and Patterson, W.R. and Bull, C.W. and Laiwalla, F. and Mislow, J. and Simeral, J.D. and Donoghue, J.P. and Nurmikko, A.V. Active Microelectronic Neurosensor Arrays for Implantable Brain Communication Interfaces Neural Systems and Rehabilitation Engineering, IEEE Transactions on 17 4 339 -345 (2009) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-19621062 Emergence of a stable cortical map for neuroprosthetic control.
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PMID-19255460[0] Lower layers in the motor cortex are more effective targets for penetrating microelectrodes in cortical prostheses.
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PMID-18018699[0] HermesB: a continuous neural recording system for freely behaving primates.
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{271} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16838020[0] A high-performance brain-computer interface
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PMID-16003903[0] Development of a chipscale integrated microelectrode/microelectronic device for brain implantable neuroengineering applications. -- second from this
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PMID-15247483[0] Cognitive control signals for Neural Prosthetics
PMID-15491902 Cognitive neural prosthetics
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{930} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1300783 (pdf) Transmission latencies in a telemetry-linked brain-machine interface
____References____ Bossetti, C.A. and Carmena, J.M. and Nicolelis, M.A.L. and Wolf, P.D. Transmission latencies in a telemetry-linked brain-machine interface Biomedical Engineering, IEEE Transactions on 51 6 919 -924 (2004.06) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{318} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-14624244[0] Learning to control a brain-machine interface for reaching and grasping by primates.
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{933} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-18923392[0] Direct control of paralysed muscles by cortical neurons.
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PMID-12052948[0] Direct Cortical Control of 3D Neuroprosthetic Devices
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IEEE-1214707 (pdf) Silicon-substrate intracortical microelectrode arrays for long-term recording of neuronal spike activity in cerebral cortex.
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PMID-11099043[0] Real-time prediction of hand trajectory by ensembles of cortical neurons in primates
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PMID-9665587[0] Restoration of neural output from a paralyzed patient by a direct brain connection.
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PMID-10896186[] Direct control of a computer from the human central nervous system
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PMID-19603074[0] Unscented Kalman filter for brain-machine interfaces.
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PMID-114271[0] Operant control of precentral neurons: the role of reinforcement schedules.
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PMID-7418770[0] Operant control of precentral neurons: the role of audio and visual feedback.
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PMID-7409057[0] Operant control of precentral neurons: comparison of fast and slow pyramidal tract neurons.
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PMID-6769536[0] Operant control of precentral neurons: Control of modal interspike intervals
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PMID-4196269[0] Operantly conditioned patterns on precentral unit activity and correlated responses in adjacent cells and contralateral muscles
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PMID-4974291[0] Operant conditioning of cortical unit activity
PMID-5000088[1] Operant conditioning of specific patterns of neural and muscular activity. In awake monkeys we recorded activity of single "motor" cortex cells, four contralateral arm muscles, and elbow position, while operantly reinforcing several patterns of motor activity. With the monkey's arm held semiprone in a cast hinged at the elbow, we reinforced active elbow movements and tested cell responses to passive elbow movements. With the cast immobilized we reinforced isometric contraction of each of the four muscles in isolation, and bursts of cortical cell activity with and without simultaneous suppression of muscle activity. Correlations between a precentral cell and specific arm muscles consistently appeared under several behavioral conditions, but could be dissociated by reinforcing cell activity and muscle suppression. PMID-4624487[2] Operant conditioning of isolated activity in specific muscles and precentral cells Recorded precentral units in monkeys, trained to contract 4 arm muscles in isolation, under various conditions: passive movements and cutaneous stimulation, active movements and isometric contractions. Some Ss were also reinforced for activity of cortical cells, with no contingency in muscle activity and with simultaneous suppression of all muscular activity. It is concluded that temporal correlations between activity of precentral cells and some other component of the motor response, e.g., muscle activity, force, or position, may depend as strongly on the specific response pattern which is reinforced as on any underlying physiological connection. ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-9537321[0] Somatosensory discrimination based on cortical microstimulation.
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Recently I've been working on a current-controlled microstimulator for the lab, and have not been at all satisfied with the performance - hence, I decided to redesign it. Since it is a digitally current-controlled stimulator, and the current is set with a DAC (MCP4822), we need a voltage controlled current source. Here is one design:
What I really need is a high-side regulated current source; after some fiddling, here is what I came up with:
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bibtex: Fetz-1992 Are movement parameters recognizably coded in the activity of single neurons
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IEEE-1484848 (pdf) A high-yield IC-compatible multielectrode recording array.
____References____ Najafi, K. and Wise, K.D. and Mochizuki, T. A high-yield IC-compatible multichannel recording array Electron Devices, IEEE Transactions on 32 7 1206 - 1211 (1985) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-6077726[0] The limbic system and behavioral reinforcement
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It appears that operant/feedback training of one neuron (channel 29, in SMA region) works fine (not great, but fine). In the experiment performed prior to visiting Seattle, on April 10 2007, I was not convinced that the neuron was controlling anything. Now, it is apparent that the monkey has some clue as to what he is doing. Today I made a simple change: I made the filtering function sum (all spikes) 1/12 * x*(x-1)^2, where x = time - time_of_spike. In comparison to a butterworth filter, this has no rebound oscillation & makes the estimation of firing rate much more transparent. It averages over approximately 500ms ~= lowcut of 1.5hz? I see no reason to change this filtering function much, as it works fine. Spikes were binned at 100hz as input to this function, but that should be equivalent to binning at 1khz etc. Next time, i want to do 2d, where channel 62 controls the Y-axis. really should try to determine the approximate tunings of these cells. I'm somewhat concerned as this channel seems to have a much lower mean firing rate than channel 29. According to the literature, PTNs have high firing rates and strong tuning... for reference, here is the channel used for the one-neuron BMI, recorded April 10. It has not changed much in the last 7 days. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{901} |
ref: Zacksenhouse-2007.07
tags: Zacksenhouse 2007 Odoherty Nicolelis cortical adaptation BMI
date: 01-06-2012 03:10 gmt
revision:3
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PMID-17637835[0] Cortical modulations increase in early sessions with brain-machine interface.
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{368} |
ref: thesis-0
tags: clementine 051607 operant conditioning tlh24
date: 01-06-2012 03:09 gmt
revision:1
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the cells were, basically, as usual for today. did 1-d BMI on channel 29; worked somewhat (nothing dramatic; mk is out of practice?) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{425} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
images/425_1.pdf August 2007
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{600} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Recently we bought a OCZ NIA device for our lab. Having designed similar hardware myself, I simply *had to* take the thing apart to inspect it, as others have done -- see Joe Pit's teardown (with schematic!!). Of course, I graciously let the others try it for a few hours (it doesn't work all that well) before taking the anodized, extruded, surface- ground aluminum case apart. Below is the top side of the 4-layer circuit board inside the case, as well as a key to indicate the function of the labeled devices. (some of the labels are hard to read due to the clutter of the silkscreen on the board; sorry).
Comments? | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{607} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
from the book "Neural Prostheses for Restoration of Sensory and Motor Function" edited by John Chapin and Karen Moxon. Phillip Kennedy's one-channel neurotrophic glass electrode BMI (axons apparently grew into the electrode, and he recorded from them) Pat Wolf on neural amplification / telemetry technology battery technology for powering the neural telemetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{301} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
040507. wiener pred. same deal as {262} kalman fit/pred. per-unit and channel aggregate SNR summary unit chan lag snr behav var 1.0000 69.0000 1.0000 1.1159 2.0000 1.0000 58.0000 1.0000 1.1074 6.0000 2.0000 44.0000 2.0000 1.1040 2.0000 2.0000 44.0000 1.0000 1.0953 2.0000 2.0000 93.0000 1.0000 1.0868 3.0000 2.0000 64.0000 0 1.0728 3.0000 1.0000 69.0000 2.0000 1.0698 2.0000 1.0000 32.0000 0 1.0684 3.0000 2.0000 44.0000 0 1.0634 8.0000 1.0000 58.0000 0 1.0613 6.0000 1.0000 33.0000 1.0000 1.0594 1.0000 2.0000 93.0000 3.0000 1.0523 3.0000 1.0000 63.0000 0 1.0507 3.0000 1.0000 67.0000 1.0000 1.0490 5.0000 1.0000 47.0000 0 1.0489 3.0000 1.0000 12.0000 4.0000 1.0472 3.0000 2.0000 93.0000 2.0000 1.0460 3.0000 1.0000 24.0000 0 1.0459 3.0000 1.0000 42.0000 1.0000 1.0447 6.0000 1.0000 24.0000 1.0000 1.0440 3.0000 1.0000 69.0000 3.0000 1.0431 2.0000 2.0000 60.0000 0 1.0429 5.0000 1.0000 61.0000 0 1.0410 4.0000 1.0000 12.0000 1.0000 1.0400 1.0000 1.0000 32.0000 3.0000 1.0395 3.0000 1.0000 8.0000 1.0000 1.0387 1.0000 1.0000 33.0000 0 1.0386 11.0000 1.0000 0 1.0000 1.0383 4.0000 2.0000 77.0000 2.0000 1.0383 1.0000 1.0000 47.0000 1.0000 1.0382 3.0000 2.0000 60.0000 1.0000 1.0376 10.0000 2.0000 77.0000 1.0000 1.0375 1.0000 1.0000 28.0000 1.0000 1.0374 1.0000 1.0000 69.0000 5.0000 1.0359 3.0000 1.0000 42.0000 0 1.0358 3.0000 1.0000 8.0000 0 1.0357 3.0000 1.0000 63.0000 3.0000 1.0357 3.0000 2.0000 68.0000 1.0000 1.0348 1.0000 1.0000 51.0000 0 1.0343 3.0000 1.0000 30.0000 1.0000 1.0341 1.0000 1.0000 24.0000 2.0000 1.0341 3.0000 2.0000 93.0000 5.0000 1.0340 3.0000 1.0000 63.0000 4.0000 1.0338 3.0000 1.0000 63.0000 2.0000 1.0337 3.0000 1.0000 12.0000 2.0000 1.0329 1.0000 2.0000 23.0000 1.0000 1.0325 1.0000 1.0000 46.0000 1.0000 1.0324 2.0000 1.0000 28.0000 0 1.0323 1.0000 2.0000 93.0000 4.0000 1.0321 3.0000 1.0000 58.0000 3.0000 1.0316 6.0000 1.0000 47.0000 2.0000 1.0314 6.0000 1.0000 48.0000 0 1.0311 4.0000 1.0000 12.0000 3.0000 1.0310 3.0000 1.0000 12.0000 0 1.0309 3.0000 1.0000 48.0000 1.0000 1.0303 11.0000 1.0000 28.0000 2.0000 1.0300 1.0000 2.0000 60.0000 2.0000 1.0294 10.0000 1.0000 46.0000 0 1.0293 8.0000 1.0000 49.0000 0 1.0291 3.0000 1.0000 24.0000 3.0000 1.0286 1.0000 2.0000 77.0000 3.0000 1.0282 3.0000 1.0000 8.0000 2.0000 1.0282 1.0000 2.0000 15.0000 1.0000 1.0281 3.0000 2.0000 68.0000 2.0000 1.0278 1.0000 2.0000 23.0000 0 1.0273 1.0000 1.0000 112.0000 1.0000 1.0261 7.0000 1.0000 69.0000 4.0000 1.0258 3.0000 2.0000 92.0000 3.0000 1.0244 3.0000 2.0000 42.0000 1.0000 1.0244 11.0000 1.0000 58.0000 2.0000 1.0238 3.0000 1.0000 61.0000 1.0000 1.0234 7.0000 1.0000 32.0000 4.0000 1.0232 3.0000 1.0000 33.0000 2.0000 1.0231 1.0000 1.0000 30.0000 4.0000 1.0231 3.0000 1.0000 46.0000 2.0000 1.0227 2.0000 1.0000 30.0000 3.0000 1.0226 3.0000 1.0000 45.0000 0 1.0225 3.0000 1.0000 60.0000 0 1.0225 3.0000 2.0000 84.0000 5.0000 1.0222 3.0000 1.0000 32.0000 1.0000 1.0221 1.0000 1.0000 24.0000 4.0000 1.0220 1.0000 1.0000 28.0000 3.0000 1.0219 1.0000 1.0000 64.0000 1.0000 1.0216 4.0000 2.0000 84.0000 1.0000 1.0215 3.0000 1.0000 30.0000 0 1.0212 3.0000 2.0000 77.0000 5.0000 1.0211 3.0000 1.0000 63.0000 1.0000 1.0210 3.0000 1.0000 33.0000 4.0000 1.0209 1.0000 1.0000 7.0000 1.0000 1.0209 3.0000 2.0000 35.0000 0 1.0202 3.0000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{349} |
ref: thesis-0
tags: clementine 042007 operant conditioning biofeedback tlh24
date: 01-06-2012 03:08 gmt
revision:4
[3] [2] [1] [0] [head]
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channel 29 controlled the X direction: channel 81, the Y direction (this one was very highly modulated, and the monkey could get to a high rate ~60Hz. note that both units are sorted as one -- I ought to do the same on the other channels from now on, as this was rather predictive (this is duplicating Debbie Won's results): However, when I ran a wiener filter on the binned spike rates (this is not the rates as estimated through the polynomial filter), ch 81 was most predictive for target X position; ch 29, Y target position (?). This is in agreement with population-wide predictions of target position: target X was predicted with low fidelity (1.12; cc = 0.35 or so); target Y was, apparently, unpredicted. I don't understand why this is, as I trained the monkey for 1/2 hour on just the opposite. Actually this is because the targets were not in a random sequence - they were in a CCW sequence, hence the neuronal activity was correlated to the last target, hence ch 81 to target X! for reference, here is the ouput of bmi_sql: order of columns: unit,channel, lag, snr, variable ans = 1.0000 80.0000 5.0000 1.0909 7.0000 1.0000 80.0000 4.0000 1.0705 7.0000 1.0000 80.0000 3.0000 1.0575 7.0000 1.0000 80.0000 2.0000 1.0485 7.0000 1.0000 80.0000 1.0000 1.0402 7.0000 1.0000 28.0000 4.0000 1.0318 8.0000 1.0000 76.0000 2.0000 1.0238 11.0000 1.0000 76.0000 5.0000 1.0225 11.0000 1.0000 17.0000 0 1.0209 11.0000 1.0000 63.0000 3.0000 1.0202 8.0000 movies of the performance are here: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{351} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
I tried to train Clem, once again, to do 2d BMI, this time with channel 69 for X and channel 71 for Y. X worked rather well, to a point - he realized that he could control it with left shoulder contractions, and did so (did not get a video of this). I did, however, get a video of the game, which is here:
Y training/performance was abysmal and hence did not try 2D control. Channel 71 would become silent whenever he began to pay attention; I'm not sure why. It would fire vigorously when he turned around and rested; the unit had a high firing rate at rest. I did not get a pic of the sortclient for today, but ch 29 was there as usual (though i did not use it) & channel 71 had the characteristic sharp V shape; perhaps it was an interneuron?? I don't know. anyway, the data is in SQL on hardm.ath.cx. (the real proof is in the pudding, of course). we really need to put the BMI game in his home cage, so motivation is not such a large issue | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{222} |
ref: neuro notes-0
tags: clementine thesis electrophysiology fit predictions tlh24
date: 01-06-2012 03:07 gmt
revision:4
[3] [2] [1] [0] [head]
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ok, so i fit all timestamps from clem022007001 & timarm_log_070220_173947_k.mat to clementine's behavior, and got relatively low SNR for almost everything - despite the fact that I am most likely overfitting. (bin size = 7802 x 1491) the offset is calibrated @ 2587 ms + 50 to center the juice artifact in the first bin. There are 10 lags. There are 21 sorted units. same thing, but with only the sorted units. juice prediction is, of course, worse. now, for file clem022007002 & timarm_log_070220_175636_k.mat. first the unsorted: and the sorted: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{249} |
ref: notes-0
tags: sorting SNR correlation coefficient expectation maximization tlh24
date: 01-06-2012 03:07 gmt
revision:5
[4] [3] [2] [1] [0] [head]
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Description: red is the per-channel cross-validated correlation coeifficent of prediction. Blue is the corresponding number of clusters that the unit was sorted into, divided by 10 to fit on the same axis. The variable being predicted is cartesian X position. note 32 channels were dead (from PP). The last four (most rpedictive) channels were: 71 (1 unit), 64 (5 units), 73 (6 units), 67 (1 unit). data from sql entry: clem 2007-03-08 18:59:27 timarm_log_20070308_185706.out ;Looks like this data came from PMD region. Description: same as above, but for the y-axis. Description: same as above, but for the z-axis. Conclusion: sorting seems to matter & have a non-negligible positive effect on predictive ability. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{262} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
clementine, 040207, Miguel's sorting. top 200 lags selected via bmisql.m , decent SNR on all channels but I had to z-score the state and measurement matricies. -- standard wiener -- linear kalman. -- associated behavior | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{269} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.ibva.com/Gallery/Gallery.htm
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{1034} |
ref: Towe-2007.05
tags: RF recording passive backscatter variactors
date: 01-06-2012 02:56 gmt
revision:3
[2] [1] [0] [head]
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IEEE-4227238 (pdf) Passive Backscatter Biotelemetry for Neural Interfacing
IEEE-5993487 (pdf) A Fully Passive Wireless Microsystem for Recording of Neuropotentials Using RF Backscattering Methods
____References____ Towe, B.C. Neural Engineering, 2007. CNE '07. 3rd International IEEE/EMBS Conference on 144 -147 (2007) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{992} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1634510 (pdf) Continuous shared control for stabilizing reaching and grasping with brain-machine interfaces.
____References____ Kim, H.K. and Biggs, J. and Schloerb, W. and Carmena, M. and Lebedev, M.A. and Nicolelis, M.A.L. and Srinivasan, M.A. Continuous shared control for stabilizing reaching and grasping with brain-machine interfaces Biomedical Engineering, IEEE Transactions on 53 6 1164 -1173 (2006) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1007} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-5910570 (pdf) Spiking neural network decoder for brain-machine interfaces
____References____ Dethier, J. and Gilja, V. and Nuyujukian, P. and Elassaad, S.A. and Shenoy, K.V. and Boahen, K. Neural Engineering (NER), 2011 5th International IEEE/EMBS Conference on 396 -399 (2011) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1008} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-5946801 (pdf) A low-power implantable neuroprocessor on nano-FPGA for Brain Machine interface applications
____References____ Fei Zhang and Aghagolzadeh, M. and Oweiss, K. Acoustics, Speech and Signal Processing (ICASSP), 2011 IEEE International Conference on 1593 -1596 (2011) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{929} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17694874[0] The muscle activation method: an approach to impedance control of brain-machine interfaces through a musculoskeletal model of the arm.
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{949} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-18509337[0] Cortical control of a prosthetic arm for self-feeding
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{990} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19464514[0] Three-dimensional, automated, real-time video system for tracking limb motion in brain-machine interface studies.
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{97} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
From Uncertain Spikes to Prosthetic Control a powerpoint presentation w/ good overview of all that the Brown group has done | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{210} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{309} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-10776811[0] More than a year of recording with up to 64 microelectrodes
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{1031} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17215384[0] Comparison of recordings from microelectrode arrays and single electrodes in the visual cortex.
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{995} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-936367 (pdf) Single-unit neural recording with active microelectrode arrays
____References____ Qing Bai and Wise, K.D. Single-unit neural recording with active microelectrode arrays Biomedical Engineering, IEEE Transactions on 48 8 911 -920 (2001) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{925} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-9136763[0] Reconstructing the engram: simultaneous, multisite, many single neuron recordings.
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{996} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1052646 (pdf) An implantable multielectrode array with on-chip signal processing
____References____ Najafi, K. and Wise, K.D. An implantable multielectrode array with on-chip signal processing Solid-State Circuits, IEEE Journal of 21 6 1035 - 1044 (1986) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1022} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-4121195 (pdf) A Practical 24 Channel Microelectrode for Neural Recording in Vivo ____References____ Kuperstein, Michael and Whittington, Douglas A. A Practical 24 Channel Microelectrode for Neural Recording in Vivo Biomedical Engineering, IEEE Transactions on BME-28 3 288 -293 (1981) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{330} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-13969854[0] Control and Training of Individual Motor Units
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{1021} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-4207598[0] Behavioral control of firing patterns of normal and abnormal neurons in chronic epileptic cortex.
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{219} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-6794389[0] Single neuron recording from motor cortex as a possible source of signals for control of external devices
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{1019} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-4670862[0] A sweet new multiple electrode for chronic single unit recording in moving animals.
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{1009} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-4672477[0] A miniature microelectrode array to monitor the bioelectric activity of cultured cells
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{313} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-12960378 Chronic, multisite, multielectrode recordings in macaque monkeys.
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{1011} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-4120642 (pdf) Mechanical Factors in the Design of Chronic Recording Intracortical Microelectrodes ____References____ Goldstein, Seth R. and Salcman, Michael Mechanical Factors in the Design of Chronic Recording Intracortical Microelectrodes Biomedical Engineering, IEEE Transactions on BME-20 4 260 -269 (1973) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1013} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17793797[0] Tungsten Microelectrode for Recording from Single Units.
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{940} |
ref: Fritsch-1870
tags: Fritsch Hitzig 1870 electrical stimulation
date: 01-03-2012 23:31 gmt
revision:2
[1] [0] [head]
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PMID-19457461[0] Electric excitability of the cerebrum (Uber die elektrische Erregbarkeit des Grosshirns).
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{87} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
from the Scientific American:
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{281} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-4977837[0] Activity of Pyramidal Tract neurons during postural fixation
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{288} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11240278[0] Functions of mammalian spinal interneurons during movement
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{496} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{393} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17554826[0] A fully integrated mixed-signal neural processor for implantable multichannel cortical recording.
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{902} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
bibtex:Olson-2005 Evidence of a mechanism of neural adaptation in the closed loop control of directions
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{240} |
ref: MolinaLuna-2007.03
tags: ICMS microstimulation cortical thin-film electrodes histology MEA
date: 01-03-2012 22:54 gmt
revision:2
[1] [0] [head]
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PMID-17178423[0] Cortical stimulation mapping using epidurally implanted thin-film microelectrode arrays.
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{275} |
ref: Hatsopoulos-2005.01
tags: BMI Hatsopoulos Donoghue cortex
date: 01-03-2012 22:49 gmt
revision:4
[3] [2] [1] [0] [head]
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PMID-17282055[0][] Cortically controlled brain-machine interface
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{739} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-2345003[0] Strength characterization of silicon microprobes in neurophysiological tissues.
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{941} |
ref: Penfield-1937
tags: Penfield 1937 motor cortex stimulation ICMS human neurosurgery electrodes
date: 01-03-2012 22:08 gmt
revision:3
[2] [1] [0] [head]
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No PMID / bibtex penfield-1937. Somatic motor and sensory representation in the cerebral cortex of man as studied by electrical stimulation
The account of Bartholow (1874) is interesting to say the least and may be cited. His patient was a 30-year old-domestic. As an infant this unfortunate had chanced to fall into the fire, burning her scalp so badly that " hair was never reproduced." A piece of whale bone in the wig she was forced to wear irritated the scarred scalp and, by her statement, three months before she was admitted, an ulcer appeared. When she presented herself for relief, this had eroded the skull over a space 2 in. in diameter " where the pulsations of the brain are plainly seen." Although " rather feeble-minded " Bartholow observed that Mary returned replies to all questions and no sensory or motor loss could be made out in spite of the fact that brain substance apparently had been injured in the process of evacuation of pus from the infected area. The doctor believed, therefore, that fine insulated needles could be introduced without further damage. While the electrodes were in the right side Bartholow decided to try the effect of more current. ' Her countenance exhibited great distress and she began to cry. Very soon the left hand was extended as if in the act of taking hold of some object in front of her; the arm presently was agitated with clonic spasms ; her eyes became fixed with pupils widely dilated ; the lips were blue and she frothed at the mouth ; her breathing became stertorous, she lost conscious-ness and was violently convulsed on the left side. This convulsion lasted for five minutes and was succeeded by coma. She returned to consciousness in twenty minutes from the beginning of the attack and complained of some weakness and vertigo." Three days after this stimulation, following a series of right-sided seizures, the patient died.
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{1012} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-4502738 (pdf) An Integrated-Circuit Approach to Extracellular Microelectrodes
____References____ Wise, Kensall D. and Angell, James B. and Starr, Arnold An Integrated-Circuit Approach to Extracellular Microelectrodes Biomedical Engineering, IEEE Transactions on BME-17 3 238 -247 (1970) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1014} |
ref: GULD-1964.07
tags: platinum iridium microelectrode eltrolytic etching original
date: 01-03-2012 19:05 gmt
revision:2
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PMID-14199966[0] A Glass-covered platinum microelectrode
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{961} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Beyond Boundaries: The New Neuroscience of Connecting Brains with Machines - and How It Will Change Our Lives
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PMID-20705858[0] Three-Dimensional, Flexible Nanoscale Field-Effect Transistors as Localized Bioprobes
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{1004} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1351853 (pdf) Development of integrated circuits for readout of microelectrode arrays to image neuronal activity in live retinal tissue
____References____ Dabrowski, W. and Grybos, P. and Hottowy, P. and Skoczen, A. and Swientek, K. and Bezayiff, N. and Grillo, A.A. and Kachiguine, S. and Litke, A.M. and Sher, A. Nuclear Science Symposium Conference Record, 2003 IEEE 2 956 - 960 Vol.2 (2003) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{265} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{49} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.klab.caltech.edu/news/crick-koch-05.pdf
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{212} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
properties of electrodes that are to penetrate the pia mater of a rhesus macaque:
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{972} |
ref: Bures-1968
tags: inferior colliculus stimulation classical conditioning plasticity hebb Bures
date: 01-03-2012 07:08 gmt
revision:5
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bibtex:Bures-1968 Plastic changes of unit activity based on reinforcing properties of extracellular stimulation of single neurons
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bibtex: delgado-1964 Personality, education, and electrical stimulation of the brain
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PMID-13367871[0] Conditioned reflexes established to electrical stimulation of cat cerebral cortex.
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{981} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19762428[0] Auditory midbrain implant: a review.
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{984} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-6114258 (pdf) Towards a Brain-Machine-Brain Interface:Virtual Active Touch Using Randomly Patterned Intracortical Microstimulation.
____References____ O'Doherty, J. and Lebedev, M. and Li, Z. and Nicolelis, M. Towards a Brain #x2013;Machine #x2013;Brain Interface:Virtual Active Touch Using Randomly Patterned Intracortical Microstimulation Neural Systems and Rehabilitation Engineering, IEEE Transactions on PP 99 1 (2011) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-19750199[0] A brain-machine interface instructed by direct intracortical microstimulation.
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PMID-17419757[0] Detection psychophysics of intracortical microstimulation in rat primary somatosensory cortex.
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PMID-17271187[0] Dynamic control of extracellular environment in in vitro neural recording systems.
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PMID-17271195[0] Models of stimulation artifacts applied to integrated circuit design.
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{224} |
ref: notes-0
tags: k-means clustering neurophysiology sorting
date: 01-03-2012 06:51 gmt
revision:1
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k-means is easy! % i want to do the k-means alg. v = [x y]; nc = 7; dim = cols(v); n = rows(v); cent = rand(nc,dim); d = zeros(n, nc); for k = (1:500) for s = 1:nc d(:,s) = sqrt(sum((v - rvecrep(cent(s, :), n)).^2,2)); end % select the smallest [nada, g] = min(d'); g = g'; for s = 1:nc if(numel(find(g==s)) > 0) cent(s, :) = mean(v(g==s, :)); end end end real data from clementine: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-17360898[] Relationship between Unconstrained Arm Movements and Single-Neuron Firing in the Macaque Motor Cortex
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{96} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-10561437[0] Motor cortical representation of speed and direction during reaching
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LMS-based adaptive decorrelator, xn is the noise, xs is the signal, len is the length of the signal, delay is the delay beyond which the autocorrelation function of the signal is zero but the acf of the noise is non-zero. The filter is very simple, and should be easy to implement in a DSP. function [y,e,h] = lms_test(xn, xs, len, delay) h = zeros(len, 1); x = xn + xs; for k = 1:length(x)-len-delay y(k) = x(k+delay:k+len-1+delay) * h ; e(k) = x(k) - y(k); h = h + 0.0004 * e(k) * x(k+delay:k+len-1+delay)'; endIt works well if the noise source is predictable & stable: (black = sinusoidal noise, red = output, green = error in output) Now, what if the amplitude of the corrupting sinusoid changes (e.g. due to varying electrode properties during movement), and the changes per cycle are larger than the amplitude of the signal? The signal will be swamped! The solution to this is to adapt the decorrelating filter slowly, by adding an extra (multiplicative, nonlinear) gain term to track the error in terms of the absolute values of the signals (another nonlinearity). So, if the input signal is on average larger than the output, the gain goes up and vice-versa. See the code. function [y,e,h,g] = lms_test(xn, xs, len, delay) h = zeros(len, 1); x = xn + xs; gain = 1; e = zeros(size(x)); e2 = zeros(size(x)); for k = 1:length(x)-len-delay y(k) = x(k+delay:k+len-1+delay) * h; e(k) = (x(k) - y(k)); h = h + 0.0002 * e(k) * x(k+delay:k+len-1+delay)'; % slow adaptation. y2(k) = y(k) * gain; e2(k) = abs(x(k)) - abs(y2(k)); gain = gain + 1 * e2(k) ; gain = abs(gain); if (gain > 3) gain = 3; end g(k) = gain; end If, like me, you are interested in only the abstract features of the signal, and not an accurate reconstruction of the waveform, then the gain signal (g above) reflects the signal in question (once the predictive filter has adapted). In my experiments with a length 16 filter delayed 16 samples, extracting the gain signal and filtering out out-of-band information yielded about +45db improvement in SNR. This was with a signal 1/100th the size of the disturbing amplitude-modulated noise. This is about twice as good as the human ear/auditory system in my tests.
It doesn't look like much, but it is just perfect for EMG signals corrupted by time-varying 60hz noise. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-8294972 Neuronal specification of direction and distance during reaching movements in the superior precentral premotor area and primary motor cortex of monkeys. 1993
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PMID-2340869[0] Dynamic organization of primary motor cortex output to target muscles in adult rats. II. Rapid reorganization following motor nerve lesions.
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{833} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-4358608 (pdf) An Integrated System for Simultaneous, Multichannel Neuronal Stimulation and Recording
Blum RA, Ross JD Brown EA and DeWeerth SP (2007) An Integrated System for Simultaneous, Multichannel Neuronal Stimulation and Recording IEEE Trans. Circuits Syst. I. Regular Pap 54, 2608-2618 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{934} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16859758 Brain-machine interfaces: past, present and future.
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PMID-4966614 Relation of pyramidal tract activity to force exerted during voluntary movement.
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{149} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-01258173 (pdf) Wireless implantable microsystems: high-density electronic interfaces to the nervous system - January 2004.
____References____ WISE, K.D. and ANDERSON, D.J. and HETKE, J.F. and KIPKE, D.R. and NAJAFI, K. Wireless implantable microsystems: high-density electronic interfaces to the nervous system Proceedings of the IEEE 92 1 76 - 97 (2004) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-12904510[0] Csicsvari 2003 Massively parallel recording of unit and local field potentials with silicon-based electrodes
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PMID-5683678[0] Intracerebral radio stimulation and recording in completely free patients.
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{150} |
ref: Otto-2006.02
tags: electrophysiology recording rejuvenation stimulation MEA
date: 01-03-2012 03:21 gmt
revision:3
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PMID-16485763[0] Voltage pulses change neural interface properties and improve unit recordings with chronically implanted microelectrodes.
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{928} |
ref: Kennedy-1989.09
tags: Kennedy neurotrophic electrode recording fabrication 1989 electrophysiology
date: 01-03-2012 03:21 gmt
revision:2
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PMID-2796391[0] The cone electrode: a long-term electrode that records from neurites grown onto its recording surface.
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PMID-10592339[0] Long term neural recording characteristics of wire microelectrode arrays implanted in cerebral cortex
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PMID-19668698[0] A low-cost multielectrode system for data acquisition enabling real-time closed-loop processing with rapid recovery from stimulation artifacts
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{788} |
ref: -0
tags: reinforcement learning basis function policy specialization
date: 01-03-2012 02:37 gmt
revision:1
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{760} |
ref: -0
tags: LDA myopen linear discriminant analysis classification
date: 01-03-2012 02:36 gmt
revision:2
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How does LDA (Linear discriminant analysis) work? It works by projecting data points onto a series of planes, one per class of output, and then deciding based which projection plane is the largest. Below, to the left is a top-view of this projection with 9 different classes of 2D data each in a different color. Right is a size 3D view of the projection - note the surfaces seem to form a parabola. Here is the matlab code that computes the LDA (from myopen's ceven % TrainData and TrainClass are inputs, column major here. % (observations on columns) N = size(TrainData,1); Ptrain = size(TrainData,2); Ptest = size(TestData,2); % add a bit of interpolating noise to the data. sc = std(TrainData(:)); TrainData = TrainData + sc./1000.*randn(size(TrainData)); K = max(TrainClass); % number of classes. %%-- Compute the means and the pooled covariance matrix --%% C = zeros(N,N); for l = 1:K; idx = find(TrainClass==l); % measure the mean per class Mi(:,l) = mean(TrainData(:,idx)')'; % sum all covariance matrices per class C = C + cov((TrainData(:,idx)-Mi(:,l)*ones(1,length(idx)))'); end C = C./K; % turn sum into average covariance matrix Pphi = 1/K; Cinv = inv(C); %%-- Compute the LDA weights --%% for i = 1:K Wg(:,i) = Cinv*Mi(:,i); % this is the slope of the plane Cg(:,i) = -1/2*Mi(:,i)'*Cinv*Mi(:,i) + log(Pphi)'; % and this, the origin-intersect. end %%-- Compute the decision functions --%% Atr = TrainData'*Wg + ones(Ptrain,1)*Cg; % see - just a simple linear function! Ate = TestData'*Wg + ones(Ptest,1)*Cg; errtr = 0; AAtr = compet(Atr'); % this compet function returns a sparse matrix with a 1 % in the position of the largest element per row. % convert to indices with vec2ind, below. TrainPredict = vec2ind(AAtr); errtr = errtr + sum(sum(abs(AAtr-ind2vec(TrainClass))))/2; netr = errtr/Ptrain; PeTrain = 1-netr; | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{771} |
ref: -0
tags: procreation babies commentary demography
date: 01-03-2012 02:36 gmt
revision:2
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Demography: Babies make a comeback
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PMID-16543459[0] Reward Timing in the Primary Visual Cortex
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PMID-18229536[0] Effect of mental imagery on the development of skilled motor actions.
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PMID-9307146[0] Systematic changes in directional tuning of motor cortex cell activity with hand location in the workspace during generation of static isometric forces in constant spatial directions.
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Reinforcement learning in the cortex (a web scour/crawl):
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PMID-6253605[0] Functional classes of primate corticomotoneuronal cells and their relation to active force
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PMID-7760138[0] Temporal encoding of movement kinematics in the discharge of primate primary motor and premotor neurons
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IEEE-1419566 (pdf) A Portable Wireless DSP System for a Brain Machine Interface
____References____ Darmanjian, S. and Morrison, S. and Dang, B. and Gugel, K. and Principe, J. Neural Engineering, 2005. Conference Proceedings. 2nd International IEEE EMBS Conference on 112 -115 (2005) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-15132510[0] A fully Integrated Neural Recording Amplifier with DC Input Stabilization
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PMID-17260864[0] An integrated system for multichannel neuronal recording with spike/LFP separation, integrated A/D conversion and threshold detection.
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{744} |
ref: Merletti-2009.02
tags: surface EMG multielectrode recording technology italy
date: 01-03-2012 01:07 gmt
revision:2
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PMID-19042063[0] Technology and instrumentation for detection and conditioning of the surface electromyographic signal: state of the art
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PMID-21880826[0] http://cshprotocols.cshlp.org/content/2011/9/pdb.prot065474.full?rss=1
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IEEE-5619710 (pdf) A Multi-Channel Low-Power IC for Neural Spike Recording with Data Compression and Narrowband 400-MHz MC-FSK Wireless Transmission
____References____ Bonfanti, A. and Ceravolo, M. and Zambra, G. and Gusmeroli, R. and Borghi, T. and Spinelli, A.S. and Lacaita, A.L. ESSCIRC, 2010 Proceedings of the 330 -333 (2010) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-11491[0] Afferent input to movement-related precentral neurones in conscious monkeys.
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{665} |
ref: Cho-2007.03
tags: SOM self organizing maps Prinicpe neural signal reconstruction recording compression
date: 01-03-2012 00:59 gmt
revision:2
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PMID-17234384[0] Self-organizing maps with dynamic learning for signal reconstruction.
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PMID-19255459[0] A fully implantable 96-channel neural data acquisition system.
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PMID-6492861[0] A simple method for the construction of electrode arrays.
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PMID-12367642[0] Multielectrode recordings: the next steps.
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PMID-8351520[0] Dynamics of the hippocampal ensemble code for space.
PMID-8036517[1] Reactivation of hippocampal ensemble memories during sleep.
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IEEE-4463150 (pdf) A neural signal processor for an implantable multi-channel cortical recording microsystem
____References____ Sodagar, A.M. and Wise, K.D. and Najafi, K. Engineering in Medicine and Biology Society, 2006. EMBS '06. 28th Annual International Conference of the IEEE 5900 -5903 (2006) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1001} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-5335132 (pdf) Low-cost wireless neural recording system and software
____References____ Gregory, J.A. and Borna, A. and Roy, S. and Xiaoqin Wang and Lewandowski, B. and Schmidt, M. and Najafi, K. Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE 3833 -3836 (2009) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-21240274[0] A wireless multi-channel neural amplifier for freely moving animals.
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{1002} |
ref: Fan-2011.01
tags: TBSI wireless recordings system FM modulation multiplexing poland
date: 01-03-2012 00:55 gmt
revision:5
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PMID-21765934[0] A wireless multi-channel recording system for freely behaving mice and rats.
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{1003} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-5333227 (pdf) In vivo testing of a low noise 32-channel wireless neural recording system
____References____ Ming Yin and Seung Bae Lee and Ghovanloo, M. Engineering in Medicine and Biology Society, 2009. EMBC 2009. Annual International Conference of the IEEE 1608 -1611 (2009) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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IEEE-5471737 (pdf) HermesD: A High-Rate Long-Range Wireless Transmission System for Simultaneous Multichannel Neural Recording Applications
____References____ Miranda, H. and Gilja, V. and Chestek, C.A. and Shenoy, K.V. and Meng, T.H. HermesD: A High-Rate Long-Range Wireless Transmission System for Simultaneous Multichannel Neural Recording Applications Biomedical Circuits and Systems, IEEE Transactions on 4 3 181 -191 (2010) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1006} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-5061585 (pdf) Wireless Neural Recording With Single Low-Power Integrated Circuit
____References____ Harrison, R.R. and Kier, R.J. and Chestek, C.A. and Gilja, V. and Nuyujukian, P. and Ryu, S. and Greger, B. and Solzbacher, F. and Shenoy, K.V. Wireless Neural Recording With Single Low-Power Integrated Circuit Neural Systems and Rehabilitation Engineering, IEEE Transactions on 17 4 322 -329 (2009) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{738} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15651568[0] A compact large voltage-compliance high output-impedance programmable current source for implantable microstimulators.
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{998} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
The Coming War on General Computation "M.P.s and Congressmen and so on are elected to represent districts and people, not disciplines and issues. We don't have a Member of Parliament for biochemistry, and we don't have a Senator from the great state of urban planning, and we don't have an M.E.P. from child welfare. " | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{365} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-717081 (pdf) An Implantable Multichannel Digital neural recording system for a micromachined sieve electrode
____References____ Akin, T. and Najafi, K. and Bradley, R.M. Solid-State Sensors and Actuators, 1995 and Eurosensors IX.. Transducers '95. The 8th International Conference on 1 51 -54 (1995) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-19162894[0] Implementation of a telemetry system for neurophysiological signals.
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{993} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-1439548 (pdf) Interpreting spatial and temporal neural activity through a recurrent neural network brain-machine interface
____References____ Sanchez, J.C. and Erdogmus, D. and Nicolelis, M.A.L. and Wessberg, J. and Principe, J.C. Interpreting spatial and temporal neural activity through a recurrent neural network brain-machine interface Neural Systems and Rehabilitation Engineering, IEEE Transactions on 13 2 213 -219 (2005) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{983} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21976021[0] Active tactile exploration using a brain-machine-brain interface.
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PMID-16291944[0] Stable ensemble performance with single-neuron variability during reaching movements in primates.
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{974} |
ref: Fitzsimmons-2007.05
tags: Fitzsimmons nicolelis stimluation ICMS owl monkeys
date: 01-01-2012 00:12 gmt
revision:2
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PMID-17522304[0] Primate reaching cued by multichannel spatiotemporal cortical microstimulation.
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PMID-11986657 Rat navigation guided by remote control.
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{5} |
ref: bookmark-0
tags: machine_learning research_blog parallel_computing bayes active_learning information_theory reinforcement_learning
date: 12-31-2011 19:30 gmt
revision:3
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hunch.net interesting posts:
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PMID-17187065[0] Separate neural substrates for skill learning and performance in the ventral and dorsal striatum.
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PMID-14757341[1] A low power multichannel analog front end for portable neural signal recordings.
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{917} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-4888623[0] Electrical stimulation of the brain in behavioral context.
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{973} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-14090522[0] The Brains record of auditory and visual experience -- A final summary and discussion
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{962} |
ref: Harris-2009.06
tags: Bartholow 1874 Mary experiment stimulation ICMS
date: 12-29-2011 05:13 gmt
revision:2
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PMID-19286295[0] Probing the human brain with stimulating electrodes: The story of Roberts Bartholow’s (1874) experiment on Mary Rafferty
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{963} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-4598035[0] Operant conditioning of single-unit response patterns in visual cortex.
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{60} |
ref: Douglas-1991.01
tags: functional microcircuit cat visual cortex microstimulation
date: 12-29-2011 05:12 gmt
revision:3
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PMID-1666655[0] A functional microcircuit for cat visual cortex
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PMID-8815302[0] Electrical stimulation of neural tissue to evoke behavioral responses
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{964} |
ref: OLDS-1954.12
tags: Olds Milner operant conditioning electrical reinforcement wireheading BMI
date: 12-29-2011 05:09 gmt
revision:5
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PMID-13233369[0] Positive reinforcement produced by electrical stimulation of septal area and other regions of rat brain.
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{621} |
ref: Ativanichayaphong-2008.05
tags: wireless neural recording stimulation
date: 12-28-2011 21:15 gmt
revision:3
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PMID-18262282[0] A combined wireless neural stimulating and recording system for study of pain processing
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{719} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
I was looking over the NIH's omnibus document (181 pages!) for the Challenge Grants due April 27, and happened upon a few interesting & relevant ones - and made some observations along the way.
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PMID-5941514[0] Feeding induced in cats by electrical stimulation of the brain stem.
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{834} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-4464125 (pdf) Stimulus-Artifact Elimination in a Multi-Electrode System
Brown EA, Ross JD, Blum RA, Yoonkey N, Wheeler BC, and DeWeerth SP (2008) Stimulus-Artifact Elimination in a Multi-Electrode System. IEEE TRans. Biomed. Circuit Sys. 2. 10-21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-20404313[0] Spinal cord stimulation failed to relieve akinesia or restore locomotion in Parkinson disease.
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PMID-10196571[0] Simultaneous encoding of tactile information by three primate cortical areas
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{968} |
ref: Bassett-2009.07
tags: Weinberger congnitive efficiency beta band neuroimagaing EEG task performance optimization network size effort
date: 12-28-2011 20:39 gmt
revision:1
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PMID-19564605[0] Cognitive fitness of cost-efficient brain functional networks.
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{960} |
ref: -0
tags: M1 Evarts PTN conduction velocity monkey electrophysiology spinal cord
date: 12-25-2011 04:25 gmt
revision:0
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PMID-14283057 Relation of Discharge Frequency to conduction velocity in pyramidal tract neurons
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PMID-11017158 One motor cortex, two different views
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PMID-11017160 Reply to One motor cortex, two different views | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-19923243 Complex Spatiotemporal Tuning in Human Upper-Limb Muscles
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PMID-10725914 Population vectors and motor cortex: neural coding or epiphenomenon?
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{953} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11017157 One motor cortex, two different views.
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PMID-10725930 Direct cortical control of muscle activation in voluntary arm movements: a model.
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{948} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-6396456[0] Computer separation of multi-unit neuroelectric data: a review
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{945} |
ref: -0
tags: Georgopoulos population vector arm motor control
date: 12-20-2011 22:26 gmt
revision:1
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PMID-3139485 Neural integration of movement: role of motor cortex in reaching.
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IEEE-4352820 (pdf) Constant-Current Adjustable-Waveform Microstimulator for an Implantable Hybrid Neural Prosthesis
____References____ Hassell, T.J. and Jedlicka, S.S. and Rickus, J.L. and Irazoqui, P.P. Engineering in Medicine and Biology Society, 2007. EMBS 2007. 29th Annual International Conference of the IEEE 2436 -2439 (2007) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{622} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16835359[0] Direct and indirect activation of cortical neurons by electrical microstimulation.
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{939} |
ref: -0
tags: Georgopoulos 1988 population vector tuning
date: 12-20-2011 01:13 gmt
revision:1
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PMID-3411362[0] Primate motor cortex and free arm movements to visual targets in three-dimensional space. II. Coding of the direction of movement by a neuronal population.
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{938} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-3411363[0] Primate motor cortex and free arm movements to visual targets in three-dimensional space. III. Positional gradients and population coding of movement direction from various movement origins.
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{936} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-3411361[0] Primate motor cortex and free arm movements to visual targets in three-dimensional space. I. Relations between single cell discharge and direction of movement.
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{935} |
ref: Georgopoulos-1982.11
tags: Georgopoulos 1982 motor tuning cortex M1 population vector
date: 12-19-2011 23:52 gmt
revision:1
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PMID-7143039 On the relations between the direction of two-dimensional arm movements and cell discharge in primate motor cortex.
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{922} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-20011034[0] A Wireless Brain-Machine Interface for Real-Time Speech Synthesis
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{200} |
ref: Nicolelis-1997.04
tags: nicolelis kralik electrodes electrophysiology 1997
date: 12-17-2011 01:41 gmt
revision:3
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PMID-11812202[0] Techniques for long-term multisite neuronal ensemble recordings in behaving animals.
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{832} |
ref: Jimbo-2003.02
tags: MEA microstimulation artifact supression
date: 12-17-2011 01:41 gmt
revision:2
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PMID-12665038[0] A system for MEA-based multisite stimulation.
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{267} |
ref: Kennedy-1992.08
tags: BMI Kennedy cone electrode electrophysiology recording neurotrophic
date: 12-17-2011 01:00 gmt
revision:1
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PMID-1407726[] The cone electrode: ultrastructural studies following long-term recording in rat and monkey cortex
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{65} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
follow up paper: http://spikelab.jbpierce.org/Publications/LaubachEMBS2003.pdf
____References____ Laubach, M. and Arieh, Y. and Luczak, A. and Oh, J. and Xu, Y. Bioengineering Conference, 2003 IEEE 29th Annual, Proceedings of 17 - 18 (2003.03) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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quote: All the loose speculation provoked by roborats is ironic considering that the experiment is just a small-scale replay of a major media event that is 40 years old. In 1964, José Delgado, a neuroscientist from Yale University, stood in a Spanish bullring as a bull with a radio-equipped array of electrodes, or "stimoceiver," implanted in its brain charged toward him. When Delgado pushed a button on a radio transmitter he was holding, the bull stopped in its tracks. Delgado pushed another button, and the bull obediently turned to the right and trotted away. The New York Times hailed the event as "probably the most spectacular demonstration ever performed of the deliberate modification of animal behavior through external control of the brain." | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-19386759[0] Wireless neural stimulation in freely behaving small animals.
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PMID-16102841[0] An autonomous implantable computer for neural recording and stimulation in unrestrained primates.
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{69} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17057705 Long-term motor cortex plasticity induced by an electronic neural implant.
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{56} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15214971[0] Ensemble recordings of human subcortical neurons as a source of motor control signals for a brain-machine interface
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{916} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
To stream a webcam directly -- no transcoding (this is useful in the case that you have a direct, fast connection between the source and sink), do the following: cvlc v4l2:///dev/video0 --sout '#standard{access=http,mux=ts,dst=:1234}' To see this on a webpage, make a file localstream.asx and put in it: <ASX version ="3.0"> <TITLE>Stream1234</TITLE> <ENTRY> <REF HREF="http://lovely.local:1234" /> </ENTRY> </ASX> (where lovely.local is replaced by your machine name). Then link to it or embed this file in a webpage! Note: I have been unable to stream more than one camera, but perhaps this is because they are both on the same USB hub. Could also be that they are both cheap ($7) pieces of shit, but that's why I bought 2. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-9658025[0] Predictive reward signal of dopamine neurons.
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{156} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-12040201[0] Anterior cingulate: single neuronal signals related to degree of reward expectancy
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{154} |
ref: OReilly-2006.02
tags: computational model prefrontal_cortex basal_ganglia
date: 12-07-2011 04:11 gmt
revision:1
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PMID-16378516[0] Making Working Memory Work: A Computational Model of Learning in the Prefrontal Cortex and Basal Ganglia found via: http://www.citeulike.org/tag/basal-ganglia ____References____
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{135} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16212764[0] Incremental online learning in high dimensions ideas:
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{119} |
ref: Hallworth-2005.07
tags: globus pallidus subthalamic nucelus parkinsons
date: 12-07-2011 04:04 gmt
revision:1
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PMID-16000620[0] Globus Pallidus Neurons Dynamically Regulate the Activity Pattern of Subthalamic Nucleus Neurons through the Frequency-Dependent Activation of Postsynaptic GABAA and GABAB Receptors
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{24} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15537672[0] On the Benefits of not Trying: Brain Activity and Connectivity Reflecting the Interactions of Explicit and Implicit Sequence Learning quote: ünder certain curcumstances, automatic learning may be attenuated by explicit memory processes" : expicit attemps to learn a difficult sequence (compared to a control) produces a failure in implicit learning, and this failure is caused by the supression of learning rather than the expression. There is a deleterious effect of explicit search on implicit learning.
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{199} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16928796[0] Fast modulation of prefrontal cortex activity by basal forebrain noncholinergic neuronal ensembles in the author's own words:
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{323} |
ref: Loewenstein-2006.1
tags: reinforcement learning operant conditioning neural networks theory
date: 12-07-2011 03:36 gmt
revision:4
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PMID-17008410[0] Operant matching is a generic outcome of synaptic plasticity based on the covariance between reward and neural activity
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{638} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{698} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
From Scott MacKenzie:
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{699} |
ref: Harris-2008.03
tags: retroaxonal retrosynaptic Harris learning cortex backprop
date: 12-07-2011 02:34 gmt
revision:2
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PMID-18255165[0] Stability of the fittest: organizing learning through retroaxonal signals
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{702} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-8670641[0] The hippocampo-neocortical dialogue.
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{714} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-12433288[0] Real-time computing without stable states: a new framework for neural computation based on perturbations.
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{718} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Timetable / Plan:
Contingency Plan:
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{723} |
ref: notes-0
tags: data effectiveness Norvig google statistics machine learning
date: 12-06-2011 07:15 gmt
revision:1
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The unreasonable effectiveness of data.
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PMID-6772272 Operant control of precentral neurons: bilateral single unit conditioning.
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PMID-4041789 Synchrony between cortical neurons during operant conditioning.
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{912} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-6457106 Processing visual feedback information for movement control.
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{915} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
-- So cool! How do you come up with something like this? | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-10681435 Cortical correlates of learning in monkey adapting to a new dynamical environment. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-7140894 Short-term changes in cell activity of areas 4 and 5 during operant conditioning.
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PMID-12929922 Training in cortical control of neuroprosthetic devices improves signal extraction from small neuronal ensembles.
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{899} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-4598035 Operant conditioning of single-unit response patterns in visual cortex
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{896} |
ref: Friston-2002.1
tags: neuroscience philosophy feedback top-down sensory integration inference
date: 10-25-2011 23:24 gmt
revision:0
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PMID-12450490 Functional integration and inference in the brain
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{892} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Open letter proposing some ideas on how to automate programming: simulate a human! Rather from a neuro background, and rather sketchy (as in vague, not as in the present slang usage). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{890} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
I'm an avid open-water swimmer, and other than the quarry and beach, I spend many fridays hoping the water in Falls lake is not too choppy. If it's glassy and smooth (and even sometimes when it's not), I can fall into the hypnotic 4/4 chug of stroke-stroke-stroke-breathe, stroke-str ... not hard, since the brown water is featureless, and the above-water scenery doesn't change much either. Several years ago I was out on Falls lake doing my thing, comfortably clear in the middle of the lake, heading back to the beach. In my unawareness I failed to notice that a thunderstorm had grown in the hot summer afternoon. Normally I'm rather debonaire about these things, but have been in places just before they were struck by lightning, and this felt a little like that. So, SOL Tim starts considering the rather limited options (god) (hold breath for as long as possible) (are they the same?). Just then, some Mexican guy on a kayak comes paddling out of ... nowhere ... and asks me if I need help. I bearhug the back of his boat and we get back to shore before the storm breaks. .... Another friday, another season and I set off with a friend clear across Falls lake, which is far, like 3mi round trip. I chat with a Mexican dude before we launch the ships; i guess he seems a bit familiar, but I'm too nervous, eager, and worrying about the thoughts/abilities of my friend to think much. That swim goes fine, minus all the damned speadboats and the ravenous hunger that sets in afterward. Yesterday I had intended to swim at a pool, but some toddling kid chose to contaminate it, and so back to Falls Lake. It's choppy and hard to swim, and I don't make it as far as intended; again before launching, I meet a Mexican dude, and he asks me if I'm crossing the lake again. I tell him no, not enough time; the water envelops, and I'm back in the swim coma, gone to the point when I get back the sun is down and the moon has risen. Surprisingly, when I get back the Mexican guy and his family are still there, slowly cleaning up BBQ debris by the light of highbeams and one crappy flashlight. It's cool and peaceful on the lake, but they probably should have left half an hour ago; as I go to the restroom to change, I wave to the guy and realize two things simultaneously: (1) fuck, it's been the same guy, (2) he may have delayed departure, gracefully and surreptitiously, until I was back. Curiosity makes me want to ask if he had, to see if coincidence licked me again, but that's not right; I did't. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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I love this short story. It tastes like the complexity and frustrating richness of an examined life. It smells like the disparity between being able to understand things and being able to affect things in our incidental, stratified, limited world. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{886} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Just got back from a trek through the volcanic mountains of Iceland. The landscape is extremely dramatic; though it’s not nearly the scale of Alaska or the Rockies, it presents itself as such, as the largest plant is thick moss or stubble grass (in places); everything is bare, the vistas unobstructed. (What do you do if you get lost in an Icelandic forest? Stand up.). There are no trees for size reference, indeed it seemed so alien for a bit that I was amazed that I could still breathe the air. The first day of exploring I had a pretty serious scare. Was walking, very light and fast as usual, with just enough to protect against rain, just enough food to keep me from eating moss. I elected to take the less-popular route back, which lead across a high muddy (no plants) gray (all the snow is ashen) scree-filled plain, to a hunchback of a mountain, and down into the river valley where I was camped. The first part was fine, though searingly desolate and wind-shorn. The problem came when I rounded the final peak and discovered that the trail was covered by a gray wind-sculpted snowmass. It was at an angle too steep for my shit shoes and lack of ice-tools, and the slopes everywhere else were critical: free a rock and it will tumble 100‘. Free a Tim and he will also tumble 100 feet .. or more. I didn’t want to hike the 17km back the way I came without an attempt at re-finding the trail, so I set off, gingerly, over the ice and gravel, alone. The ash actually saved me, as it coated the snowfields, and made them passable in the late late afternoon warmth (the sun ‘sets’ around midnight and rises at 2.). This lead to a pinnacle from which I could *see* the campsite! But there was only slide-to-death venues for descent, until I noticed a set of footprints heading up a steep snowbank to my left. I was elated - a trace of humanity! I set off with renewed vigor, and did a semi-controlled fall down the ice; the foot-holes kept me under control. But they were not foot holes. I noticed quickly that the holes were irregular in spacing and shape, and shortly after I passed the steepest wind sculpted section of snowbank, realized that they were made by a large rock falling off the mountain, picking up speed as it dented the ice shell. I kept going, mostly because I could not stop, though eventually it leveled off. Had that rock not fallen, I don’t think I would have had the psychological wherewithal to try the slope, nevermind foot purchase to slow my descent. As a stream gets broader its slope generally decreases, given constant resistance from the rock / earth, so as I descended the valleys broadened and became less treacherous. I made the remainder of the way back on a riverbed, albeit with wet feet. It was exciting, and i felt fully in the world as i was trying to get off that trail-less mountain, but I’m not sure if I want to do it again; the following day while hiking up neighboring peaks I felt a heightened sense of caution, vertigo. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{885} |
ref: -0
tags: entropy life proteonomics transcription factors
date: 07-08-2011 22:42 gmt
revision:0
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Reduction in Structural Disorder and Functional Complexity in the Thermal Adaptation of Prokaryotes -- read the article. These are my disordered, mesothermophylic notes.
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{883} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Response to Jonah Lehrer's The Web and the Wisdom of Crowds: Lehrer is right on one thing: culture. We're all consuming similar things (e.g. Rebecca Black) via the strong positive feedback of sharing things that you like, liking things that you share, and becoming more like the things that are shared with you. Will this lead to a cultural convergence, or stable n-ary system? To early to tell, but probably not: likely this is nothing new. Would you expect music to collapse to a single genre? No way. Sure, there will be pop culture via the mechanisms Lehrer suggests, but meanwhile there is too much to explore, and we like novelty too much. Regarding decision making through stochastic averaging as implemented in democracy, I have to agree with John Hawk here. The growing availability of knowledge, news, and other opinions should be a good thing. This ought to be more than enough to counteract the problem of everyone reading say the NYTimes instead of many varied local newspapers; there should be no impoverishment of opinion. Furthermore, we read blogs (like Lehrer's) which have to compete increasingly honestly in the attention economy. The cost of redirecting our attention has gone from that of a subscription to free. Plus, this attention economy ties communication to reality at more points - each reader, as opposed to each publisher, is partially responsible for information amplification and dissemination. (I mean I just published this damn thing and almost zero cost - is that not a great thing?) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Conjecture: the entropic cost of simulating a system (complex evolved or not) in a system (e.g. machine) versus physical reality is proportional to the information content of original system * energy per bit of simulation * time to simulate / KL divergence between simulation and reality, where information content KL divergence are calculated within the space of measured dimensions. Am I missing terms? Or rather: what terms am I missing? :-) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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to remove lines beginning with a question mark (e.g. from subversion) svn status | perl -nle 'print if !/^?/' here's another example, for cleaning up the output of ldd: ldd kicadocaml.opt | perl -nle '$_ =~ /^(.*?)=>/; print $1 ;' and one for counting the lines of non-blank source code: cat *.ml | perl -e '$n = 0; while ($k = <STDIN>) {if($k =~ /\w+/){$n++;}} print $n . "\n";' By that metric, kicadocaml (check it out!), which I wrote in the course of learning Ocaml, has about 7500 lines of code. Here is one for resizing a number of .jpg files in a directory into a thumb/ subdirectory: ls -lah | perl -nle 'if( $_ =~ /(\w+)\.jpg/){ `convert $1.jpg -resize 25% thumb/$1.jpg`;}'or, even simpler: ls *.JPG | perl -nle '`convert $_ -resize 25% thumb/$_`;' Note that -e command line flag tells perl to evaluate the expression, -n causes the expression to be evaluated once per input line from standard input, and -l puts a line break after every print statement. reference For replacing charaters in a file, do something like: cat something | perl -nle '$_ =~ s/,/\t/g; print $_' | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{877} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.chapel.duke.edu/documents/Feb13ChoosingLifeandLivingwithChoices.pdf This is a good sermon with a lot of good points (gasp! did an atheist just say that?), and is making me think hard -- or at least hard enough to write down how I feel on abortion. I agree with the pastor that the community does seem at fault for not helping women whose 'unwanted' pregnancies might be wanted if there was more social support. I guess, atheist that I am, that religion has a strong and good role here by providing the impetus to make people be more cohesive and behave morally better. IMHO Thoreau-inspired mental integrity and thoughtful examination are another (better?) way to get there, but perhaps religion is a cultural shortcut to the same end, hence valuable. (As an aside, I'm irked by the repeated phrase that 'they need the church'. Seems like the church is the needy one here - if what it offers is valuable, it need not insist. A second irritation is that the church sometimes misappropriates credit/importance: things that a community of good people create (e.g. support for single mothers) the church assumes primary credit for. You preach humility, show some.) I doubt women abort have children out of shame, as he suggests. More likely the mother understands the complex economies and timing of raising a child; presumably, in situations where an abortion is considered the mother could hope to have another child later, when she could support and raise he/she better - give he/she a happier life with more love to share to others. Are lives exchangeable in this way? You make these choices implicitly every time you choose not to have unprotected sex with someone - exchanging the possibility of creating a life presently with the possibility of creating an even better life later. This is normal and good, the point of decision has just been moved albeit utilitarian ... and of course utilitarianism is limited, because things aren't linear or monotonic. If we treat even unwanted pregnancy with 'mischievous joy' (i like that) as he suggests, perhaps the attitude of sacred life itself guarantees a happier existence than the attitude of exchangeable life. More basically: despite the logic above I intuitively and instinctively find the thought of killing anything remotely human horrific. But, we kill things all the time. We kill (are killing..) solders in war. We kill a lot of pigs, which (this is a very iffy argument here) have as much if not more capability for suffering and pleasure than a very young fetus. And then we eat them. We, loosely and implicitly, kill people by not sending an section of our income to buy medicine, food - this to grown people with families, friends and standing importance. Is their death worse than the death of a fetus? My brain tells me that there is a continuum of existence and meaning, and in this messy realistic world, we have to admit ordering and make compromises; my soul still hates this fact. Ultimately, human happiness and suffering, life and death, cannot be completely reduced to a utilitarian calculus. In such a calculus we should aim to optimize the total joy in the world, minus the pain and dread, integrated over lifetimes and people. To a rough and imperfect scale that is what we do, in our personal lives and more broadly. Treating all human lives as equal is an idea of both democracy and religion that makes the calculus balanced and fair, and allows us to derive usable laws and stable societies (integrated joy...), but it seems to break down in the case of abortion. This is why I think the oft myopic and special-interest swayed government should have no say in a woman's choice; if I can't come up with a solid reason either way, why should the government? | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{857} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.nvnews.net/vbulletin/showthread.php?t=141845 -- when running multiple nvidia cards on one linux computer with a 32-bit kernel, you may run out of kernel memory while loading the video drivers. To fix this, pass vmaloc=256M to the kernel prior boot - e.g. by editing /boot/grub/menu.lst (grub 1) or /boot/grub/grub.cfg (grub 2) If you want to make the change permanent with all kernels, edit /etc/grub.d/10_linux and add vmalloc=256M to the end of linux ${rel_dirname}/${basename} root=${linux_root_device_thisversion} ro ${args} see also the Nvidia driver release notes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{876} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Excellent hike with So-- and Vi-- today. We somehow completely overshot the original southward path toward the car @ ~ 5:30-5:45 (marked with 'oops' on the map). In our race against the falling sun we continued too far west, ultimately all the way to Uzzle Rd; hence we had to return for a good number of miles on the road under the cooling night sky. Gorgeous country; the hill in that area is even 'large' (740') for Piedmont standards, and affords a view of the farms. for S & V: the hill we saw from the top is right by Pyrophyllite Lake 3 miles south of the lookout point. Total hike distance was 9.5 miles. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{874} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Email received January 30 2011 - I've tried to understand the story, but all i get a sense of is strange injured exaggerations, statements which try to draw ire. The below-linked report is one of the most bizarre cases we have reported in quite a while. A high-paid, prestigious professor at the Catholic Duke University, who was recently appointed to the Vatican's Academy of Sciences, mind you, is not only pro abortion and in favor of gay marriage, but he also is threatening to call the police on people who disagree with him on these issues -- specifically, one pastor (Julio Severo, a friend of ours) who works with troubled homosexuals desiring to quit the lifestyle, and another Christian who has spoken only in the mildest terms of this professor. Now picture this if you will: Here we have a homeless Pastor, Julio Severo, who has been banned from his homeland for sincerely practicing his life work of helping homosexuals cope with unwanted desires. These are poor men who are terrified of contracting AIDS and dying. Some already have tested HIV positive. They come to Julio out of desperation for psychological and spiritual assistance, guidance from the Word of God. And now, for the crime of heeding God's call to help them, Pastor Severo is forced to leave his country or be jailed for the "crime" of helping homosexuals desirous of raising themselves out of a situation they deplore and fear. Because Brazil is in the hands of leftist elitists who have outlawed any public speech unfavorable to homosexuality. Meanwhile, the desolate Pastor Severo is living in poverty with a wife and children, desperately trying to fend for himself and find work to buy food for his family. All for the crime of lending people a helping hand as he felt called to do by his Savior. And now comes an elitist, high-paid, pampered professor from a prestigious university surrounded by luxury, enjoying all the finer things of life and going to the finest restaurants, working ridiculously easy hours, with lots of leisure, time and money to travel. And what does this wealthy, influential professor do? Does he offer to help the poor man who has been persecuted unjustly by a godless, heartless government for the "crime" of helping others? Why no, the professor simpers and whimpers that he is afraid of the homeless pastor who is out of work and has a hungry family with nowhere to go and no one to help them. And in an interview with a like-minded elitist blogger, this rich, comfortable professor who has all the comforts one can imagine -- things the poor pastor never even has dreamed of, brags of the high security at his lab and says that if he ever feels 'threatened' by this unfortunate penniless, harmless pastor, living in poverty and hiding somewhere in an unknown part of the world, why he will just call the police from the comfort of his luxurious home or his multi-million dollar fully equipped lab and they will arrest the homeless man so that he, the rich, pampered, powerful professor, can be even more comfortable surrounded by his art collection, his latest model car, his designer clothes, his plasma TV and his well-stocked wine cellar. Here are the details: http://laiglesforum.com/pro-abort-pro-gay-marriage-duke-u-prof-threatens-to-sic-cops-on-detractors/2091.htm Please take the time to call or email Dr. Nicolelis and ask him why he is threatening a homeless pastor for adhering to the Bible in his beliefs? And why does he think that homosexuals should be obliged to remain in their dangerous lifestyle? Does he not know that many want to quit this lifestyle for health and safety reasons? You may also ask the good doctor whether he would like to report me too for the "crime" of speaking out against this outrage. Thank you and God bless. Don Hank | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Excellent hike in Bynum NC starting at the old homestead down there, crossed a number of random properties, entered and left Haw river state park, saw a good number of decomposing farmhouses, all on a gorgeous day. Route was taken clockwise; jog at the end away from main trail was to avoid a hunter in the main fields. This forced us to do a good bit of bushwacking and gave the opportunity to meet some local horses, goats, and runners. Total distance about 9 miles.
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http://www.autonlab.org/tutorials/ -- excellent http://energyfirefox.blogspot.com/2010/12/data-mining-with-ubuntu.html -- apt-get! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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The goal is to make a system that is capable of automatic debugging / design. It seems to me that a good bit of the work of designing and debugging such a program - which I imagine to be basically a set of heuristics triggered by certain situations - is mechanical, and hence could be automated. First, debugging: Say your program doesn't compile. You look at the error message + location, look at the code, and change variables either there or in causally-connected code to fix the error. The knowledge of what to change basically involves a forward model of how the computer runs the program and experiential knowledge of what worked in the past. The former need not be encoded - the computer can simply run slightly different versions of the program and see what happens itself (aka 'taking the partial derivatives of a program'). The latter can be stored in a well-designed database. Then your program crashes. Usually, you look at the code and run it on a model of the computer in your mind, checking at every point if the given data-path and code-path to see if it diverges from acceptable behavior. Maybe you instrument the code with printfs. Then, you look at the causally-connected code to see what can be changed to alleviated the error condition, or to make the code/datapath align with well-known programming patterns. Again, the computer does not need a model of itself - the computer can simply running the code as an interpreted language; everything is then instrumented. The well-known patterns can be entered by a human, or learned via experimentation (analogous to 'school' and 'hacking' to a person). Now your program runs and compiles. But, it doesn't do what you want it to do - you see in one particular case there is an error. So, you look at the program, run it in your mind, and look at all the variables and codepaths that are causally related to producing that case, imagining what changes to each will do to the error. Possibly this involves changing the AST, adding an if-statement, etc. You poke around; eventually something works, if partially. The computer can do the same thing, via the well-instrumented interpreted language. Eventually this produces spaghetti code (unless you're really smart, and predicted all this case-programming), and small tweaks break more things than they fix. Time to refactor - apply well-known invariant code transformations, or more generally look for simpler codepaths with the same effective datapaths. Perhaps you avoided it by using good initial programming patterns, found mostly through analogy with the real world (object-orientation, MVC etc). Again this is where a good memory of programming-patterns will serve well. That's the gist. There is much more - namely, the importance of finding transforms that render problems and sub-problems linear, and the practical consideration that the end goal in much computer programming is itself found through iteration - but this email is long enough. What I've outlined probably doesn't look close to GA / EA, but in practice will most likely involve intense and random experimentation within each of the steps above, something that GA does a lot of. What should make it faster is that individual random experimentation is more constrained - smaller space to explore - and when possible memory can replace expending time and power on experimentation. To look at it another way, the project should move a feedback loop (write compile observe) from the human to the computer; this is OK as all the needed info is within the computer already; no outside interaction is needed (unlike, say physical evolution). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Commentary on Why Caltech Is in a Class by Itself (I do not go to Caltech, but this is not the reason the article rubbed me): This is a good argument, especially given the real need to educate students in STEM subjects. However I would like to make four counterpoints: 1. Only accepting students based on test scores - as your article suggests - strikes me as a rather narrow criteria. There are many forms of intelligence, and the variety of problems is much broader than those posed within a SAT - surely there should be some leeway in accepting individuals? Any single criteria would seem to impoverish the student body. 2. Maybe affirmative action will not heal wounds; I have not read your book (obviously). But what would happen if all universities stopped accepting minority students? Our society is already stratified, and this would make it worse. (The counterargument would be that by making the criteria equal, minorities would be forced to rise up - yes, eventually, but slow enough to not set off a positive feedback loop) 3. I don't watch sports myself, but a lot of my friends do. Sure, there may be an excess now of section-9 type stuff, but is there anything wrong with cultivating athletic excellence? Is it not inspiring to be on campus with these people as well as to watch them? More importantly, people *really enjoy* athletics, which seems a good enough reason to me. 4. Where's your soul, man? My criteria would be: "Caltech is great because the students there are motivated and happy, and when they graduate they go on to contribute to and greatly enjoy the f- out of life." which is true, btw. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{867} |
ref: -0
tags: evolutionary psychology human mating sexuality discrimination wedlock
date: 01-09-2011 18:22 gmt
revision:1
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From Why Beautiful people have more daughters: "Abuse, degradation, and intimidation are all part of men's unfortunate repertoire of tactics employed in competitive situations. In other words, men are not harassing women because they are treating them differently than men (which is the definition of discrimination under which harassment legally falls), but the exact opposite: men harass women because they are not discriminating between men and women." Interesting argument. But in sexual discrimination cases, the women are not being treated the way they want to be treated - this is more a problem than the inequality. The author then goes on to pose that current sexual discrimination law and policy in US corporations actually inhibits welcome sexual/romantic interest/advances. Many people do find partners at work. Again, I beg to differ: if there is passion between people, things will fall as they should; if policy and culture serves to make this more civilized (provided it's not completely inhibited, as the author suggests), then all the better. In related news: An Analysis of Out-Of-Wedlock Births in the United States Central hypothesis: Contraceptive technology shifted the balance of power between the sexes: prior the pill, women could force the men into promising to marry; in the case of preganancy, cultural standards forced marriage - shotgun marriage. Men accepted these terms because they were uniform across all women - sex implies pregnancy implies child rearing. When contraception became available, this was decoupled, as sex did not beget pregnancy; those women who negotiated on the old terms were likely to lose their mate, hence shotgun marriages (the result of such negotiations) gradually disappeared from culture. The author generally approves of the idea of shotgun marriage, and suggests that a governmental body should enforce a form of it through child support payments. Presently about 40% of children in the US are born out of wedlock. Finally, Serial monogamy increases reproductive success in men but not in women. It rests upon data, only recently gathered, that supports that having multiple partners increases reproductive success more strongly in male than in female humans. This implies that the variance of the fertility of men should be higher than that of women - again, which is borne out in the data, but only weakly: men have 10% higher variance in # of offspring than women. This effect is correlated to serial monogamy - "Compared with men with 1 spouse, men with 3 or more spouses had 19% more children in the total sample". This did not hold with women, nor did varying spouse number in men change the survival rate of their offspring. Irregardless, this reading was spurred by someone mentioning that a genetic analysis of human populations reveals that while 80% of women reached reproductive success, only 40% of men did - implying that historically a few more successful men fathered a large fraction of children. I was unable to find evidence to support this on the internet (and indeed the Behavioral Ecology article gives much less dramatic figures), but it makes intuitive sense, especially in light of some patterns of male behavior. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{866} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Remembered fragment of a dream, letter never sent. Probably it was ill-fated to ---. Eh. That didn't distract me from having a batshit insane dream last night, feat three army goons, myself, and the vivacious ---. The goons and I were soldiers in charge of some truck-mounted machine gun in a logged and dried-mud hillcountry - probably Serbia - but whenever we tried to get it ready, the part in question would instantly transform into crochet. When the ammunition roll was finally in the yarn gun, all the bullets would fall on the ground; look away and it would resume metallic reality. On cue to amplify our disorganization a officer sped in to harass us in a Honda S2000. Annoyed, I threw gravel at him; it transformed into a lamborghini, then a porsche, a tesla, a toyota. (I've seen a lot of fancy cars this past week). Given the frustrated Daliesque nature of the battlefield, we retreated, I as a restrained but irked soldier. Montage in, montage out, you enter to this scene as an bit-played angry estranged woman, pissed at my lack of caring / perceived neglect. Bitch complain threaten whine, I guilt but look outside and the vegetation is gorgeous, lush, the sky a mild hazy blue. I am a little thirsty. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{864} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Interesting ideas from __This Will Change Everything__
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{865} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
This evening, on the drive back from wacky (and difficult) Russian-style yoga, I got a chance to explain to my brother what I really want to be working on, the thing that really tickles my fancy. My brother and I, so much as genetic commonality and common upbringing seem to effect, have very similar styles of thinking, which made explaining things a bit easier. For you, dear readier, I'll expand a bit. I'd like to write a program that writes other programs, iteratively, given some objective function / problem statement / environment in which to interact. The present concrete goal is to have a said program make a program that is able to lay out PCBs with quality similar to that of humans. The overarching framework that I'm planning on using is genetic/evolutionary algorithms (the latter does not have crossover, fyi), but no one has applied GA to the problem in this way: most people use GA to solve a particular instance of a problem. Rubbish, i say, this is energy wasteful! Rubbish, you may return: the stated problem requires a degree of generalization and disconnect from the 'real world' (the PCB) that makes GAs extremely unlikely to come up with any solutions. Expressed another way: the space to be explored is too large (program begets program begets solution). This is a very sensible critique; there is no way in hell a GA can solve this problem. They are notably pathetic at exploring space in a energy-efficient way (to conclude a paragraph again with energy... ). There are known solutions for this: memory -- cache the results, in terms of algorithm & behavior, of all 'hypotheses' or individuals tried out by a GA. This is what humans do -- they remember the results of their experiment, and substitute the result rather than running a test again. But humans do something far more sophisticated and interesting than just memory - they engineer systems; engineering is an iterative process that often goes down wrong design paths, yet it nonetheless delivers awesome things like Saabs and such. As I described to K--, engineering is not magic and can be (has been?) described mechanistically. First of all, most engineering artifacts start off from established, well-characterized components, aggregated through the panoply of history. Some of these components describe how other components are put together, things that are either learned in school or by taking things apart. Every engineer, ala Newton, stands on the vast shoulders of the designers before; hence any program must also have these shoulders available. The components are assembled into a system in a seemingly ad-hoc and iterative procedure: sometimes you don't know what you want, so you play with the parts sorta randomly, and see what interesting stuff comes out. Other times you know damn well what you / your boss / the evil warlord who holds you captive wants. Both modes are interesting (and the dichotomy is artificial), but the latter is more computer-like, hence to be modeled. Often the full details of the objective function or desired goal is very unclear in the hands of the boss / evil warlord (1), despite how reluctant they may be to admit this. Such an effect is well documented in Fred Brooks' book, __The Design of Design__. Likewise, how to get to a solution is unclear in the mind of an engineer, so he/she shuffles things around in the mind (2),
This search is applied iteratively, apparently a good bit of the time subconsciously. A component exists in our mind as a predictive model of how the thing behaves, so we simulate it on input, observe output, and check to see if anything there is correlated / decorrelated with target features. (One would imagine that our general purpose modeling ability grew from needing to model and predict the world and all the yummy food/dangerous animals/warlords in it). The bigger the number of internal models in the engineers mind, the bigger the engineers passion for the project, the more components can be simulated and selected for. Eventually progress is made, and a new subproblem is attacked in the same way, with a shorter path and different input/output to model/regress against. This is very non-magical, which may appall the more intuitive designers among us. It is also a real issue, because it doesn't (or poorly) explains really interesting engineering: e.g. the creation of the Fourier transform, the creation of the expectation-maximization algorithm, all the statistical and mathematical hardware that lends beauty and power to our design lives. When humans create these things, they are at the height of their creative ability, and thus it's probably a bit ridiculous to propose having a computer program do the same. That does not prevent me from poking at the mystery here, though: perhaps it is something akin to random component assembly (and these must be well known components (highly accurate, fast internal models); most all innovations were done by people exceptionally familiar with their territory), with verification against similarly intimately known data (hence, all things in memory - fast 'iteration cycles'). This is not dissimilar to evolutionary approaches to deriving laws. A Cornell physicist / computer scientist was able to generate natural laws via a calculus-infused GA {842}, and other programs were able to derive Copernicus' laws from planetary data. Most interesting scientific formulae are short, which makes them accessible to GAs (and also aesthetically pleasurable, and/or memelike, but hey!). In contrast engineering has many important design patterns that are borrowed by analogy from real-world phenomena, such as the watermark algorithm, sorting, simulated annealing, the MVC framework, object-oriented programming, WIMP interface, verb/noun interface, programming language, even GAs themselves! Douglas Hofstadter has much more to say about analogies, so I defer to him here. Irregardless, as K-- pointed out, without some model for creativity (even one as soulless as the one above), any proposed program-creating program will never come up with anything really new. To use a real-world analogy, at his work the boss is extremely crazy - namely, he mistook a circuit breaker for an elevator (in a one-story factory!). But, this boss also comes up with interminable and enthusiastic ideas, which he throws against the wall of his underlings a few dozen times a day. Usually these ideas are crap, but sometimes they are really good, and they stick. According to K--, the way his mind works is basically opaque and illogical (I've met a few of these myself), yet he performs an essential job in the company - he spontaneously creates new ideas. Without such a boss, he claimed, the creations of a program-creating-program will impoverished. And perhaps hence this should be the first step. Tonight I also learned that at the company (a large medical devices firm) they try to start projects at the most difficult step. That way, projects that are unlikely to succeed are killed as soon as possible. The alternate strategy, which I have previously followed, is to start with the easiest things first, so you get some motivation to continue. Hmm... The quandary to shuffle your internal models over tonight then, dear readers, is this: is creativity actually (or accurately modeled by) random component-combination creation (boss), followed by a selection/rejection (internal auditing, or colleague auditing)? (3)
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Whether Software Engineering Needs to Be Artiï¬cially Intelligent By Herbert Simon, author of __The Sciences of the Artificial__
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Automatic Programming: Myths and Prospects by Charles Rich and Richard C Waters, 1988
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Short script for copying & tagging files from a playlist to a flat target. #!/usr/bin/perl # sub rand_pass { my @chars = ('a'..'k','m','n','p'..'z','2'..'9'); my $length = 8; my $password = ''; for (0..$length) { $password .= $chars[int rand @chars]; } return $password; } open FH, "playedlst.txt"; my $targ = "/media/usb0"; while($k = <FH>){ #print "$k\n"; $k =~ s/^\.//; $k =~ s/\n//; my $dest = $k; my $suffix = ".mp3"; if($dest =~ /\.(\w+)$/){ $suffix = $1; } #print(" suffix $suffix \n"); if($dest =~ /\/([^\/]+)\.[^\.]+/){ #remove any suffix $dest = "/$1"; } if(-e "$targ/$dest.$suffix") { #test to see if the target exists $dest = rand_pass(); } my $src = "\"/mnt/crackle/hanson/music$k\""; my $fdest = "\"$targ$dest.$suffix\""; print("$dest.$suffix\n"); `cp $src $fdest`; `id3v2 -r \"COMM\" $fdest`; `id3v2 -c \"$k\" $fdest`; } close FH; | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{862} |
ref: -0
tags: backpropagation cascade correlation neural networks
date: 12-20-2010 06:28 gmt
revision:1
[0] [head]
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The Cascade-Correlation Learning Architecture
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{860} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
"The Truth Wears Off" by Jonah Lehrer, the New Yorker.
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What does technology want? An interview with Steven Johnson and Kevin Kelly at the New York Public Library, usefully condensed to a half-hour segment for the RadioLab podcast.
This blog is probably failing in the attention economy. Again, oops ;-) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{859} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Learning by Playing: Video Games in the Classroom
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Notes & responses to evolutionary psychologists John Toobey and Leda Cosmides' - authors of The Adapted Mind - essay in This Will change Everything
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http://www.gamedev.net/community/forums/topic.asp?topic_id=432583 -- bump, it helped me solve a problem with cgGLGetLatestProfile() failing!! (the class I was using to examine openGL extensions was writing to the openGL supplied string) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{855} |
ref: -0
tags: sciences artificial Simon organizations economic rationality
date: 12-01-2010 07:33 gmt
revision:2
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These are notes from reading Herbert A. Simon’s The Sciences of the Artificial, third edition, 1996 (though most of the material seems from the 70s). They are half quoted / half paraphrased (as needed when the original phrasing was clunky). I’ve added a few of my own observations, and reordered the ideas from the book. “A large body of evidence shows that human choices are not consistent and transitive, as they would be if a utility function existed ... In general a large gain along one axis is required to compensate for a small loss along another.†HA Simon. Companies within a capitalist economy make almost negligible use of markets in their internal functioning†- HA Simon. Eg. they are internally command economies. (later, p 40...) We take the frequent movability and indefiniteness of organizational boundaries as evidence that there is often a near balance between the advantages of markets and organizationsâ€
That said: organizations are not highly centralized structures in which all the important decisions are made at the center; this would exceed the limits of procedural rationality and lose many of the advantages attainable from the use of hierarchical authority. Business organizations, like markets, are vast distributed computers whose decision processes are substantially decentralized. In fact, the work of the head of a corporation is a market-like activity: allocating capital to promising or desirable projects. In organizations, uncertainty is often a good reason to shift from markets to hierarchies in making decisions. If two different arms of a corporation - production and marketing - make different decisions on the uncertain number of units to be sold next year, there will be a problem. It is better for the management to share assumptions. “Left to the market, this kind of uncertainty leads directly to the dilemmas of rationality that we described earlier in terms of game theory and rational expectations†I retain vivid memories of the astonishment and disbelief expressed by the architecture students to whom I taught urban land economics many years ago when I pointed to medieval cities as marveluosly patterned systems that had mostly just ‘grown’ in response to myriads of individual human decisions. To my students a pattern implied a planner in whose mind it had been conceived and whose hand it had been implemented. The idea that a city could acquire its patter as naturally as a snowflake was foreign to them ... they reacted to it as many christian fundamentalists responded to Darwin: no design without a Designer! Markets appear to conserve information and calculation by assigning decisions to actors who can make them on the basis of information that is available to them locally. von Hayek: “The most significant fact about this system is the economy of knowledge with which it operates, o how little the individual participants need to know in order to make the right actionâ€. To maintain actual Pareto optimality in the markets would require information and computational requirements that are exceedingly burdensome and unrealistic (from The New Palgrave: A dictionary of Economics) Nelson and winter observe that in economic evolution, in contract to biological evolution, sucessful algorithms (business practices) may be borrowed from one firm to the other. The hypothesized system is Lamarkian, because any new idea can be incorporated in opearting procedures as soon as its success is observed" . Also, it's good as corporations don't have secual reproduction / crossover. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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http://www.xbdev.net/directx3dx/specialX/Fur/index.php -- for future reference. Simple algorithm that seems to work quite well. Can be done almost entirely in vertex shader... | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{844} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
"Stage 6" part selection:
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{839} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
(I'm posting this here as it's easier than putting a image & text in subversion) I'm building a wireless headstage for neural recording. Hence, it has sensitive, high-gain amplifiers (RHA2116) pretty close to a wireless transmitter + serial lines. The transmitter operates intermittently to save power, only sending samples from one continuous channel + threshold crossings for all the other channels. 27 byte-wide samples + channel identifier + 4 bytes threshold crossing are sent in one radio packet; as the radio takes some 130us to start up the PLL, 8 of these packets are chunked together into one frame; one frame is transmitted every 144hz (actually, 1e6/(32*27*8)Hz. At the conclusion of each frame, the continuous channel to be transmitted is incremented. It seems that radio transmission is interfering with the input amplfifiers, as the beginning samples from a frame are corrupted - this is when the previous frame is going out over the air. It could also be noise from the SPI lines, which run under and close to the amplifiers. This may also not be a problem in vivo - it could only be an issue when the input to the amplifiers are floating. Above, a plot of the raw data coming off the headstage radio. Red trace indicates the channel currently being transmitted; blue are the samples. Note that some chanels do not have the artifact - I presume this is because their input is grounded. This will be very tricky to debug, as if we turn off the radio, we'll get no data. Checking if it is a SPI problem is possible by writing the bus at a specified time. Tested with radio PA disabled, it is definitely the SPI bus - routing problem! Stupid. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{838} |
ref: -0
tags: meta learning Artificial intelligence competent evolutionary programming Moshe Looks MOSES
date: 08-07-2010 16:30 gmt
revision:6
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{815} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Jacques Pitrat seems to have many of the same ideas that I've had (only better, and he's implemented them!)-- A Step toward and Artificial Scientist
Artificial beings - his book. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{837} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Hutter's Theorem: for all problems asymptotically large enough, there exists one algorithm that is within a factor of 5 as fast as the fastest algorithm for a particular problem. http://www.hutter1.net/ai/pfastprg.htm | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{836} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{826} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Studies in astronomical time series analysis. II - Statistical aspects of spectral analysis of unevenly spaced data Scargle, J. D.
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{825} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{583} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
From this and the USB 2.0 spec, I made this quick (totally incomprehensible?) key for understanding the output of commands like # mount -t debugfs none_debugs /sys/kernel/debug # modprobe usbmon # cat /sys/kernel/debug/usbmon/2u To be used with the tables from the (free) USB 2.0 spec: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{821} |
ref: work-0
tags: differential evolution function optimization
date: 07-09-2010 14:46 gmt
revision:3
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Differential evolution (DE) is an optimization method, somewhat like Neidler-Mead or simulated annealing (SA). Much like genetic algorithms, it utilizes a population of solutions and selection to explore and optimize the objective function. However, it instead of perturbing vectors randomly or greedily descending the objective function gradient, it uses the difference between individual population vectors to update hypothetical solutions. See below for an illustration. At my rather cursory reading, this serves to adapt the distribution of hypothetical solutions (or population of solutions, to use the evolutionary term) to the structure of the underlying function to be optimized. Judging from images/821_1.pdf Price and Storn (the inventors), DE works in situations where simulated annealing (which I am using presently, in the robot vision system) fails, and is applicable to higher-dimensional problems than simplex methods or SA. The paper tests DE on 100 dimensional problems, and it is able to solve these with on the order of 50k function evaluations. Furthermore, they show that it finds function extrema quicker than stochastic differential equations (SDE, alas from 85) which uses the gradient of the function to be optimized. I'm surprised that this method slipped under my radar for so long - why hasn't anyone mentioned this? Is it because it has no proofs of convergence? has it more recently been superseded? (the paper is from 1997). Yet, I'm pleased because it means that there are also many other algorithms equally clever and novel (and simple?), out their in the literature or waiting to be discovered. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{820} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Another excellent post from Steinberg regarding treating people as predictable nonlinear fluids. "The system works far better when a column is introduced off-center in front of the door,as demonstrated Mr. Torrens. "It's counterintuitive, but the column sends shock waves through the crowds to break up the congestion patterns." (...) Most traffic jams are emergent phenomena that begin with mistakes from just one or two drivers. According to Horvitz's models, they can actually "un-jam" traffic by calling drivers at a particular location, and giving them very specific instructions: "Move to the left-most lane, and then speed-up to 65." | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{813} |
ref: work-0
tags: kicadocaml zbuffer comparison picture screenshot
date: 03-03-2010 16:38 gmt
revision:4
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Simple illustration of Kicadocaml with Z buffering enabled: and disabled: I normally use it with Z buffering enabled, but turn it off if, say, I want to clearly see all the track intersections, especially co-linear tracks or zero length tracks. (Probably I should write something to merge and remove these automatically.) Note that in either case, tracks and modules are rendered back-to-front, which effects a Z-sorting of sorts; it is the GPUs Z buffer that is enabled/disabled here. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{812} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Aint she pretty? More shots of the completed board (click for full resolution image):
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{810} |
ref: -0
tags: circular polarized antenna microstrip ultrawideband
date: 02-03-2010 21:30 gmt
revision:1
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excellent! Ultra-wideband circular polarized microstrip archimedean spiral | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{808} |
ref: Inzlicht-2009.03
tags: uncertainty religion conviction decision science
date: 02-02-2010 20:39 gmt
revision:3
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The Neural Markers of Religious Conviction PMID-19291205 Recently a friend pointed this article out to me, and while I found the scientific results interesting though slightly questionable - that religious people have less anterior cingulate cortex activation upon error - the introduction and discussion were stimulating. What follows are a few quotes and my interpretation and implications of the authors' viewpoint. "The absence of a cognitive map providing clear standards and goals is uncomfortable and leads people to search for and assert belief systems that quell their anxiety by allowing for clearer goal pursuit (McGregor, Zanna, Holmes, & Spencer, 2001)." I would argue that uncertainty itself is highly uncomfortable - whether it is uncertainty as to how much food you will have in the future, or uncertainty as to the best behavior. In this sense, of course religion decreases anxiety - it provides a structured way to think about this disordered and highly undecidable world, a filter to remove or explain away many of the random parts of our lives. In my personal experience, conviction is usually easier than trying to hold accurate probabalistic models in your mind - conviction is pleasurable, even if it is wrong. I find their short review of cognitive science in the introduction interesting - they claim that the septo-hippocampal system is concerned with the detection and correction of errors associated with concrete behaviors and goals, while in humans (and other primates?) the ACC allows error and feedback based operations on concepts and higher-order goals. The need for a higher-level error detection circuit makes sense in humans, as we are able to bootstrap our behavior to very complicated limits, but it also begs to question - what trains the ACC? To some degree, it must train itself in the via the typical loopy feedback-based brain way, but this only goes so far, as (at least in the modern world) the space of all possible behaviors, longterm and short term, given stochastic feedback is too large to be either decidable or fully parseable/generalizable into an accurate global model, even given a lifetime of experience. Religion, as this paper and many others posits, provides this global model against which behaviors and perceptions can be measured. But why does a uncertainty challenge causes a compensatory increase in the strength of convictions, almost to the point of zealousness (how is this adaptive? just as a means of reducing anxiety?); I've seen it happen, but why. From a Bayesian point of view, increased uncertainty necessitates decreased certainty, or fewer convictions. From a pragmatic point of view, increased uncertainty requires increased convictions purely because the convictions have to make up for the lack of environmental information from which to make a decision. Any theory must include the cost of not making a decision, the cost of delaying a decision, and the principle of sunk costs. There are other solutions to the 'undecidable' problems of life than religion - literary culture and science come to mind. The principle behind all may be that, while individual experience and intellect is possibly insufficient for generating global rules to guide behavior, the condensed experience of thousands/millions/billions of people is. This assumes that experience, as a random variable/signal, scales according to the laws of large numbers - noise decreases monotonically as sample size increases. This may not actually be true, it depends on the structure of the distributions, and the extent to which people's decisions/behaviors are orthogonal, and the fidelity of the communication / aggregation channels which operate on the data. I think the dimensionality increase afforded by larger sample size is slower than the concomitant noise decrease, hence (valid) global rules guiding behavior can be extracted from large populations of people. Regarding the communication channels, it seems there were always high fidelity channels of experience - e.g. Homer, Benjamin Franklin's transatlatic trips, the royal Society of London, (forgive my western pov) - and now, there are even more (the internet)! The latter invention should, at least within the framework here, allow larger groups of people to make 'harder' or 'more undecidable' decisions by virtue of greater information. Fairly standard rhetoric to the internet crowd (c.f. forums), I know. I would argue that this is better than using convictions... but the result of communication / aggregation is convictions anyway, so eh. Getting back to the uncertainty issue, the authors point out that conservative cultures there is usually greater uncertainty (which way is the arrow of causality?), and increasing uncertainty bolsters support zealous action, e.g. war. "For example, contemporary social psychological research indicates that uncertainty threats can cause people to become more extreme in their opinions, so that they exaggerate their religious convictions and become more willing to support a war to defend those convictions (McGregor, Haji, Nash, & Teper, 2008). In fact, even nonbelievers bolster their personal convictions to near-religious levels in order to reduce uncertainty-related distress (McGregor et al., 2001). Thus, in terms of feedback-loop models, the standards and predictions provided by religious convictions are strong enough that they can resist any discrepant feedback that might alert the comparator system." This, I believe, is fairly accurate, and it implies several dramatic things: if a despot or leader wishes to engender support for a war, particularly a religious war, then he should make the lives of his constituents uncertain. If their lives are stable and certain sans ideology, then they will be less likely to have the convictions ('the other side is bad!') to fight certain wars. (It of course depends on who/what the other side is!). Take Europe vs. America as an example - America has far fewer social support systems and greater uncertainty in life than in Europe. The Economist frequently phrases American businesses' penchant for hiring and firing people quickly and seemingly at whim, as it encourages creative reuse, economic flexibility, and better allocation of capital, but it has a clear downside - increased anxiety, uncertainty. We (well, not me, but many Americans) deal with this via religion, the article would argue (that said, I should guess that there are a great many other reasons people are religious). Still, in western Europe has less uncertainty in life, is more secular, and less tolerant of ideological wars. Hence the antidote for war is to give people stable, significant lives. More common-sense rhetoric. On to another suggestive point made by the article: "In terms of feedback-loop models, this explanation suggests that the standards and predictions provided by religion are inadequate and should, in fact, result in prediction errors; however, because religious beliefs are rigid, inconsistent information is reinterpreted in such a way that it becomes assimilated to preexisting convictions, further sustaining beliefs (Park, 2005)." I would be interested in an actual test of this hypothesis - if it is possible without bias (perhaps another EEG study? perhaps it has been already done?) The authors actually prove the opposite point, that religions people are more likely to answer correctly on the Stroop test. They take more time, but seem to be more careful. This reminds me of Matteo Ricci, who allegedly used his Jesuit training in sustained concentration and memorization to master the Chinese language; clearly religion is far more than just a means of reducing perceived uncertainty about the world. To loop the argument back on its tail - this is the 'meta' blog, afterall - one may question if the theory (looking at behavior in terms of the unpleasantness of uncertainty and the need for decidability) is a good way of looking at things, just as we questioned if religion is a good theory of the world. I think it generalizes; for example, Solaiman mentioned that the European children of the revolution of 1968 had parents who notably applied very little guidance to their lives; they were like the American hippies. These people grew up disliking their parents, and sought far more structure in their lives and in parenting their own children. One may imagine that they disliked the vast uncertainty their parents bluntly exposed them to, and paucity of guiding principles - something that the parents, after years of living in the world, probably had. Secondly, Solaiman recalled that all his favorite teachers were those that were strictest, strongest in their conviction, and most structured in their pedagogy. People seek to make decisions decidable whether through parents, teachers, religion, science or even art and literature. To summarize, uncertainty engenders convictions by the pragmatic principle. Best thing we can do is to either reduce uncertainty or found those convictions on aggregate data(*) (*) Google publication. The principle of data is our zeitgist, but history suggests that independent of what we think now it will not be the last. comments? edit this, write below. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{807} |
ref: -0
tags: reynolds number microorganisms engineering math fluid mechanics
date: 01-25-2010 19:17 gmt
revision:0
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http://jilawww.colorado.edu/perkinsgroup/Purcell_life_at_low_reynolds_number.pdf - great! Never thought about this before.
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{805} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://silentlistening.wordpress.com/2008/05/09/dispersion-of-sound-waves-in-ice-sheets/ -- amazing! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{804} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
I find this particular study of how things fail fascinating - http://foreignaffairs.us/solutions.php | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{803} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
This morning i checked my bank account, and was throughly offended with what was in there. To figure out where I was spending my money, I exported a csv from the bank's website, and read it into open office to label each expense. Since I couldn't easily figure out how to sum along each label, I wrote an ocaml program to do this -- ocaml let gitline ic = ( try input_line ic, false with _ -> "", true ) ;; let fos = float_of_string let ios = int_of_string let soi = string_of_int let sof = string_of_float let foi = float_of_int let iof = int_of_float let fabs = abs_float let read fname = let eof = ref false in let out = ref [] in let ic = open_in fname in let tab = Str.regexp "," in while not !eof do ( let line, eoff = gitline ic in let ar = Array.of_list (Str.split tab line) in if Array.length ar = 7 then ( let debit = fos ar.(3) in let credit = fos ar.(4) in let wha = ar.(6) in out := (debit,credit,wha) :: !out ; ); eof := eoff; ) done; close_in_noerr ic ; !out ;; let _ = let sumht = Hashtbl.create 50 in List.iter (fun a -> let debit,credit,wha = a in let m = try Hashtbl.find sumht wha with _ -> 0.0 in let m2 = m -. credit +. debit in Hashtbl.replace sumht wha m2 ) ( read "/home/tlh24/Desktop/Suntrust_History.csv"); Hashtbl.iter (fun wha valu -> print_endline( wha^","^(sof valu)); ) sumht ;The first half of this file is 'stock' - just helper functions for reading in the CSV file (you can copy-paste to use on your own files). After that, it's just assigning fields to variables and summing along the labels with a hash table - easy as it should be. Certainly it could be accomplished in far fewer lines with perl, but perl is not at the tip of my tongue as ocaml is now :-) For the curious, here is the result (bar charts >> pie charts): I spend a lot of money on food and 'parts'. Food is pretty self-explanatory; 'parts' includes electronic parts, bike parts (a fender, bike clips, new lights), a new cell phone, stuff from home depot. Tools was mostly for a cylinder of welding gas - you have to buy the cylinder; the gas is relatively cheap. The labels are sort-of amorphous, since all are directed toward the goal of fixing my (*&^%) car, which has a rusted-out crack in the frame from where the (*&^%) previous owner attached an aftermarket brace. Finally, the gas was from a 1300 mile road trip over Thanksgiving (in my other POS car, whose drivers side front wheel bearing is loose on the strut mount, oh my). Normally I don't spend that much on gas. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{798} |
ref: notes-0
tags: Gladwell talent narcissism management structure business
date: 11-19-2009 06:02 gmt
revision:1
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http://www.gladwell.com/pdf/talent.pdf -- From 2002. Old but excellent. Structure is required to achieve broad, slow to ROI projects. (It's almost common sense when expressed this way!) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{796} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
An interesting field in ML is nonlinear dimensionality reduction - data may appear to be in a high-dimensional space, but mostly lies along a nonlinear lower-dimensional subspace or manifold. (Linear subspaces are easily discovered with PCA or SVD(*)). Dimensionality reduction projects high-dimensional data into a low-dimensional space with minimum information loss -> maximal reconstruction accuracy; nonlinear dim reduction does this (surprise!) using nonlinear mappings. These techniques set out to find the manifold(s):
(*) SVD maps into 'concept space', an interesting interpretation as per Leskovec's lecture presentation. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{795} |
ref: work-0
tags: machine learning reinforcement genetic algorithms
date: 10-26-2009 04:49 gmt
revision:1
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I just had dinner with Jesse, and the we had a good/productive discussion/brainstorm about algorithms, learning, and neurobio. Two things worth repeating, one simpler than the other: 1. Gradient descent / Newton-Rhapson like techniques should be tried with genetic algorithms. As of my current understanding, genetic algorithms perform an semi-directed search, randomly exploring the space of solutions with natural selection exerting a pressure to improve. What if you took the partial derivative of each of the organism's genes, and used that to direct mutation, rather than random selection of the mutated element? What if you looked before mating and crossover? Seems like this would speed up the algorithm greatly (though it might get it stuck in local minima, too). Not sure if this has been done before - if it has, edit this to indicate where! 2. Most supervised machine learning algorithms seem to rely on one single, externally applied objective function which they then attempt to optimize. (Rather this is what convex programming is. Unsupervised learning of course exists, like PCA, ICA, and other means of learning correlative structure) There are a great many ways to do optimization, but all are exactly that - optimization, search through a space for some set of weights / set of rules / decision tree that maximizes or minimizes an objective function. What Jesse and I have arrived at is that there is no real utility function in the world, (Corollary #1: life is not an optimization problem (**)) -- we generate these utility functions, just as we generate our own behavior. What would happen if an algorithm iteratively estimated, checked, cross-validated its utility function based on the small rewards actually found in the world / its synthetic environment? Would we get generative behavior greater than the complexity of the inputs? (Jesse and I also had an in-depth talk about information generation / destruction in non-linear systems.) Put another way, perhaps part of learning is to structure internal valuation / utility functions to set up reinforcement learning problems where the reinforcement signal comes according to satisfaction of sub-goals (= local utility functions). Or, the gradient signal comes by evaluating partial derivatives of actions wrt Creating these goals is natural but not always easy, which is why one reason (of very many!) sports are so great - the utility function is clean, external, and immutable. The recursive, introspective creation of valuation / utility functions is what drives a lot of my internal monologues, mixed with a hefty dose of taking partial derivatives (see {780}) based on models of the world. (Stated this way, they seem so similar that perhaps they are the same thing?) To my limited knowledge, there has been some work as of recent in the creation of sub-goals in reinforcement learning. One paper I read used a system to look for states that had a high ratio of ultimately rewarded paths to unrewarded paths, and selected these as subgoals (e.g. rewarded the agent when this state was reached.) I'm not talking about these sorts of sub-goals. In these systems, there is an ultimate goal that the researcher wants the agent to achieve, and it is the algorithm's (or s') task to make a policy for generating/selecting behavior. Rather, I'm interested in even more unstructured tasks - make a utility function, and a behavioral policy, based on small continuous (possibly irrelevant?) rewards in the environment. Why would I want to do this? The pet project I have in mind is a 'cognitive' PCB part placement / layout / routing algorithm to add to my pet project, kicadocaml, to finally get some people to use it (the attention economy :-) In the course of thinking about how to do this, I've realized that a substantial problem is simply determining what board layouts are good, and what are not. I have a rough aesthetic idea + some heuristics that I learned from my dad + some heuristics I've learned through practice of what is good layout and what is not - but, how to code these up? And what if these aren't the best rules, anyway? If i just code up the rules I've internalized as utility functions, then the board layout will be pretty much as I do it - boring! Well, I've stated my sub-goal in the form of a problem statement and some criteria to meet. Now, to go and search for a decent solution to it. (Have to keep this blog m8ta!) (Or, realistically, to go back and see if the problem statement is sensible). (**) Corollary #2 - There is no god. nod, Dawkins. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{780} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
A Self-learning Evolutionary Chess Program
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{793} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Andrew Ng's notes on learning theory
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http://www.cs.cmu.edu/~wcohen/slipper/
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{789} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
I've been reading Computational Explorations in Cognitive Neuroscience, and decided to try the code that comes with / is associated with the book. This used to be called "PDP+", but was re-written, and is now called Emergent. It's a rather large program - links to Qt, GSL, Coin3D, Quarter, Open Dynamics Library, and others. The GUI itself seems obtuse and too heavy; it's not clear why they need to make this so customized / panneled / tabbed. Also, it depends on relatively recent versions of each of these libraries - which made the install on my Debian Lenny system a bit of a chore (kinda like windows). A really strange thing is that programs are stored in tree lists - woah - a natural folding editor built in! I've never seen a programming language that doesn't rely on simple text files. Not a bad idea, but still foreign to me. (But I guess programs are inherently hierarchal anyway.) Below, a screenshot of the whole program - note they use a Coin3D window to graph things / interact with the model. The colored boxes in each network layer indicate local activations, and they update as the network is trained. I don't mind this interface, but again it seems a bit too 'heavy' for things that are inherently 2D (like 2D network activations and the output plot). It's good for seeing hierarchies, though, like the network model. All in all looks like something that could be more easily accomplished with some python (or ocaml), where the language itself is used for customization, and not a GUI. With this approach, you spend more time learning about how networks work, and less time programming GUIs. On the other hand, if you use this program for teaching, the gui is essential for debugging your neural networks, or other people use it a lot, maybe then it is worth it ... In any case, the book is very good. I've learned about GeneRec, which uses different activation phases to compute local errors for the purposes of error-minimization, as well as the virtues of using both Hebbian and error-based learning (like GeneRec). Specifically, the authors show that error-based learning can be rather 'lazy', purely moving down the error gradient, whereas Hebbian learning can internalize some of the correlational structure of the input space. You can look at this internalization as 'weight constraint' which limits the space that error-based learning has to search. Cool idea! Inhibition also is a constraint - one which constrains the network to be sparse. To use his/their own words: ... given the explanation above about the network's poor generalization, it should be clear why both Hebbian learning and kWTA (k winner take all) inhibitory competition can improve generalization performance. At the most general level, they constitute additional biases that place important constraints on the learning and the development of representations. Mroe specifically, Hebbian learning constrains the weights to represent the correlational structure of the inputs to a given unit, producing systematic weight patterns (e.g. cleanly separated clusters of strong correlations). Inhibitory competition helps in two ways. First, it encourages individual units to specialize in representing a subset of items, thus parcelling up the task in a much cleaner and more systematic way than would occur in an otherwise unconstrained network. Second, inhibition greatly restricts the settling dynamics of the network, greatly constraining the number of states the network can settle into, and thus eliminating a large proportion of the attractors that can hijack generalization.." | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{790} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.carolinamtnclub.com/%5CHiking%5Cgoogle%5C511.htm awesome place! but watch out for the cows! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{791} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Our ancestor, a proton powered rock?-- great article, wish i knew more of the biochemistry behind this research. linked from that, something of a less pure science: Future women, shorter, plumper, more fertile --read the comments, some of them are insane (but provocative?)! Viz:
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{783} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19435684[0] A 128-channel 6 mW wireless neural recording IC with spike feature extraction and UWB transmitter.
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{787} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
My theory on the Flynn effect - human intelligence IS increasing, and this is NOT stopping. Look at it from a ML perspective: there is more free time to get data, the data (and world) has almost unlimited complexity, the data is much higher quality and much easier to get (the vast internet & world!(travel)), there is (hopefully) more fuel to process that data (food!). Therefore, we are getting more complex, sophisticated, and intelligent. Also, the idea that less-intelligent people having more kids will somehow 'dilute' our genetic IQ is bullshit - intelligence is mostly a product of environment and education, and is tailored to the tasks we need to do; it is not (or only very weakly, except at the extremes) tied to the wetware. Besides, things are changing far too fast for genetics to follow. Regarding this social media, like facebook and others, you could posit that social intelligence is increasing, along similar arguments to above: social data is seemingly more prevalent, more available, and people spend more time examining it. Yet this feels to be a weaker argument, as people have always been socializing, talking, etc., and I'm not sure if any of these social media have really increased it. Irregardless, people enjoy it - that's the important part. My utopia for today :-) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{786} |
ref: -0
tags: linux keyboard international characters symbols
date: 10-01-2009 14:09 gmt
revision:1
[0] [head]
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Need to type international symbols and characters on your keyboard, e.g. for writing in another language? Do this: cp /usr/share/X11/locale/en_US.UTF-8/Compose ~/.XCompose xmodmap -e 'keycode 115 = Multi_key Multi_key Multi_key Multi_key' xmodmap -e 'keycode 116 = Multi_key Multi_key Multi_key Multi_key' Where 115 and 116 are the windows keys on my keyboard. (You can find this out for your keyboard by running 'xev'); Then:
yay! And now for something completely unrelated but highly amusing, at least in title: Optimal Brain Damage | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{785} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Recently I got an audiobook in m4b format, but I wanted to play it on my mp3 (only!) device. So, had to convert it. To do this, on my Debian Lenny box I first: apt-get install ffmpeg libmp3lame30 libfaad0 libavcodec51 The last one seems to be the most important, nothing works even though libavcodec51 wold seem to have nothing to do with mp3 encoding... Then used a bash script: #!/bin/bash for i in *.m4b; do ffmpeg -i "$i" -acodec libmp3lame "${i%m4b}mp3"; done to convert all the m4b files in a directory. Later, I used easytag to add tags to the mp3s so they would show up properly on the device {770}. Simplest way to get this to work was to just change the name of the containing folder to Artist - Title; didn't want to manually change the tags on all the mp3's, and I didn't find a 'apply all' button. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{770} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
During the GOSH! summit there was an intensive talk about making a open-hardware USBkey-to-television converter/computer/mp4 player, an idea (patented!) by Joshua Kauffman and Gwendolyn Floyd. Since this was a very hands-on workshop, I decided to get an mp4 player in downtown Banff and take it apart to see how it works. The selected device, a RCA Lyra MC4202-A portable media player, is, in accordance with its low price, electrically simple on the inside. What follows is a rough teardown of the internals. -- View of the Lya with the back plastic panel removed.
-- View underneath the main PCB, showing the keypad PCB.
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{690} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-10404201 Real-time control of a robot arm using simultaneously recorded neurons in the motor cortex.
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{776} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.willamette.edu/~gorr/classes/cs449/intro.html -- descent resource, good explanation of the equations associated with artificial neural networks. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{774} |
ref: work-0
tags: functional programming compilation ocaml
date: 08-24-2009 14:33 gmt
revision:0
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The implementation of functional programming languages - book! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{772} |
ref: -0
tags: xmos microcontroller microporcessor threading
date: 08-11-2009 16:15 gmt
revision:0
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{769} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Marian Bantjes - kickass designer. Just see her business card! or Saks snowflake theme | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{768} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://mlpost.lri.fr/ -- allows drawing Latex or postscript figures programmatically. Interesting. Included in Debian. source | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{767} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
to read!
to think!
to make!
to program!
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{765} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
shows that I'd like to watch:
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{766} |
ref: life-0
tags: enfranchised mind blog population wealth future
date: 07-06-2009 21:43 gmt
revision:0
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http://enfranchisedmind.com/blog/posts/the-fermi-paradox/
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{764} |
ref: work-0
tags: ocaml mysql programming functional
date: 07-03-2009 19:16 gmt
revision:2
[1] [0] [head]
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Foe my work I store a lot of analyzed data in SQL databases. In one of these, I have stored the anatomical target that the data was recorded from - namely, STN or VIM thalamus. After updating the analysis programs, I needed to copy the anatomical target data over to the new SQL tables. Where perl may have been my previous go-to language for this task, I've had enuogh of its strange quiks, hence decided to try it in Ruby (worked, but was not so elegant, as I don't actually know Ruby!) and then Ocaml. ocaml #use "topfind" #require "mysql" (* this function takes a query and a function that converts entries in a row to Ocaml tuples *) let read_table db query rowfunc = let r = Mysql.exec db query in let col = Mysql.column r in let rec loop = function | None -> [] | Some x -> rowfunc col x :: loop (Mysql.fetch r) in loop (Mysql.fetch r) ;; let _ = let db = Mysql.quick_connect ~host:"crispy" ~database:"turner" ~password:"" ~user:"" () in let nn = Mysql.not_null in (* this function builds a table of files (recording sessions) from a given target, then uses the mysql UPDATE command to propagate to the new SQL database. *) let propagate targ = let t = read_table db ("SELECT file, COUNT(file) FROM `xcor2` WHERE target='"^targ^"' GROUP BY file") (fun col row -> ( nn Mysql.str2ml (col ~key:"file" ~row), nn Mysql.int2ml (col ~key:"COUNT(file)" ~row) ) ) in List.iter (fun (fname,_) -> let query = "UPDATE `xcor3` SET `target`='"^targ^ "' WHERE STRCMP(`file`,'"^fname^"')=0" in print_endline query ; ignore( Mysql.exec db query ) ) t ; in propagate "STN" ; propagate "VIM" ; propagate "CTX" ; Mysql.disconnect db ;; Interacting with MySQL is quite easy with Ocaml - though the type system adds a certain overhead, it's not too bad. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{762} |
ref: work-0
tags: covariance matrix adaptation learning evolution continuous function normal gaussian statistics
date: 06-30-2009 15:07 gmt
revision:0
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http://www.lri.fr/~hansen/cmatutorial.pdf
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{758} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Ocaml has an interactive top level, but in order to make this useful (e.g. for inspecting the types of variables, trying out code before compiling it), you need to import libraries and modules. If you have ocamlfind on your system (I think this is the requirement..), do this with: #use "topfind";; at the ocaml prompt, then #require"package names" . e.g: tlh24@chimera:~/svn/m8ta/yushin$ ledit | ocaml Objective Caml version 3.10.2 # #use "topfind";; - : unit = () Findlib has been successfully loaded. Additional directives: #require "package";; to load a package #list;; to list the available packages #camlp4o;; to load camlp4 (standard syntax) #camlp4r;; to load camlp4 (revised syntax) #predicates "p,q,...";; to set these predicates Topfind.reset();; to force that packages will be reloaded #thread;; to enable threads - : unit = () # #require "bigarray,gsl";; /usr/lib/ocaml/3.10.2/bigarray.cma: loaded /usr/lib/ocaml/3.10.2/gsl: added to search path /usr/lib/ocaml/3.10.2/gsl/gsl.cma: loaded # #require "pcre,unix,str";; /usr/lib/ocaml/3.10.2/pcre: added to search path /usr/lib/ocaml/3.10.2/pcre/pcre.cma: loaded /usr/lib/ocaml/3.10.2/unix.cma: loaded /usr/lib/ocaml/3.10.2/str.cma: loaded # Pcre.pmatch ;; - : ?iflags:Pcre.irflag -> ?flags:Pcre.rflag list -> ?rex:Pcre.regexp -> ?pat:string -> ?pos:int -> ?callout:Pcre.callout -> string -> bool = <fun> # let m = Gsl_matrix.create 3 3;; val m : Gsl_matrix.matrix = <abstr> # m;; - : Gsl_matrix.matrix = <abstr> # m.{1,1};; - : float = 6.94305623882282e-310 # m.{0,0};; - : float = 6.94305568087725e-310 # m.{1,1} <- 1.0 ;; - : unit = () # m.{2,2} <- 2.0 ;; - : unit = () # let mstr = Marshal.to_string m [] ;; Nice! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{756} |
ref: life-0
tags: education wikinomics internet age college university pedagogy
date: 06-11-2009 12:52 gmt
revision:0
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Will universities stay relevant? and the rest of the wikinomics blog
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{755} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gleaned from the Economist (June 6-12 2009) "
Italy imports 86% of it's electricity (!) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{754} |
ref: Gilbert-2009.03
tags: human prediction estimation social situation neighbor advice affective forecasting
date: 06-10-2009 15:13 gmt
revision:2
[1] [0] [head]
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PMID-19299622[0] The Surprising Power of Neighborly Advice.
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{752} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.theatlantic.com/doc/200501/kirn -- goood.
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{666} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15286181[0] Providing explicit information disrupts implicit motor learning after basal ganglia stroke.
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{742} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17873433[0] A single-chip signal processing and telemetry engine for an implantable 96-channel neural data acquisition system.
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{456} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
"One shot of [Lee Freidlander's], from 1969, traps an entire landscape of feeling: a boundless American sky, salted with high clouds, plus Freidlander's wife, Maria, with her slightly smiling face - inside the cab of a single truck, layering what we see through the side window with what is reflected in it. I know of long novels that tell you less " (not the shot above, but just the same - ) some more - http://www.nga.gov.au/SurfaceBeauty/IMAGES/LRG/Fiedlander-1981.954.jpg | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{735} |
ref: -0
tags: processing javascript vector graphics web
date: 05-03-2009 18:20 gmt
revision:0
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http://www.mattryall.net/blog/2008/11/wiki-visualisations-with-javascript -- way cool!! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{734} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Rethinking the American Dream by David Kamp
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{733} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Moral Saints by Susan Wolf
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{730} |
ref: -0
tags: recroding biopotential MOS-bipolar pseudoresistor
date: 04-15-2009 22:03 gmt
revision:0
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Linear transconductor with rail-to-rail input swing for very large time constanct applications
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{664} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17946962[0] A reconfigurable neural signal processor (NSP) for brain machine interfaces.
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{364} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17946450[0] An Autonomous, broadband, multi-channel neural recording system for freely behaving primates
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{727} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
quote: For a given amount of 10kHz rejection, a 1ksps ADC (a) is equivalent to a 1Msps SAR ADC (b). Filtering determines the ADC's effective throughput, not the sampling rate (c). exactly! (click to see full res version. from an excellent article, "Managing high-voltage lithium-ion batteries in HEVs" by Michael Kultgen. more notes:
other stuff in that issue:
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{715} |
ref: Legenstein-2008.1
tags: Maass STDP reinforcement learning biofeedback Fetz synapse
date: 04-09-2009 17:13 gmt
revision:5
[4] [3] [2] [1] [0] [head]
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PMID-18846203[0] A Learning Theory for Reward-Modulated Spike-Timing-Dependent Plasticity with Application to Biofeedback
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{724} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{722} |
ref: notes-0
tags: programming excellence norvig 10 years
date: 04-07-2009 20:26 gmt
revision:0
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Teach yourself programming in 10 years
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{720} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.the-scientist.com/2009/04/1/34/1/ -- good layperson-level review of the present research on sleep. Includes interviews with Strickgold and other prominents. References:
http://www.the-scientist.com/2009/04/1/15/1/ -- points out that Western sleep style is a relative outlier compared to sleeping in other cultures. More 'primitive' cultures have polyphasic sleep, with different stages of alertness, dozing, napping, disengaged, vigilance, etc.
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{717} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
For the Instructions for use:
For the assembly instructions:
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{716} |
ref: Ribeiro-2004.12
tags: Sidarta Ribeiro reverberation sleep consolidation integration replay REM SWS
date: 03-26-2009 03:19 gmt
revision:2
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PMID-15576886[0] Reverberation, storage, and postsynaptic propagation of memories during sleep
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{706} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-8987766[0] Functional Stages in the Formation of Human Long-Term Motor Memory
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{712} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19245368[0] The influence of learning on sleep slow oscillations and associated spindles and ripples in humans and rats
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{685} |
ref: BrashersKrug-1996.07
tags: motor learning sleep offline consolidation Bizzi Shadmehr
date: 03-24-2009 15:39 gmt
revision:1
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PMID-8717039[0] Consolidation in human motor memory.
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{691} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-18835655[0] Sleep-related improvements in motor learning following mental practice.
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{701} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-18836440[0] Pharmacological REM sleep suppression paradoxically improves rather than impairs skill memory
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{710} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19233172[0] Synchronisation in the beta frequency-band - The bad boy of parkinsonism or an innocent bystander?
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{708} |
ref: Wagner-2004.01
tags: sleep insight mental restructure integration synthesis consolidation
date: 03-20-2009 21:31 gmt
revision:1
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PMID-14737168[0] Sleep Inspires Insight.
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{297} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17182912[0] Skill Representation in the Primary Motor Cortex After Long-Term Practice
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{705} |
ref: Tononi-2006.02
tags: sleep synaptic homeostasis plasticity
date: 03-20-2009 15:45 gmt
revision:1
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PMID-16376591[0] Sleep function and synaptic homeostasis.
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{704} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17978020[0] The Upshot of Up States in the Neocortex: From Slow Oscillations to Memory Formation
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{594} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{287} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
the organization of the human triphasic EMG control sequence:
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{462} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Defense Advanced Research Projects Agency's Alan Rudolph:
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Alopex: A Correlation-Based Learning Algorithm for Feed-Forward and Recurrent Neural Networks (1994)
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{694} |
ref: Diedrichsen-2005.1
tags: Shadmehr error learning basal ganglia cerebellum motor cortex
date: 03-09-2009 19:26 gmt
revision:0
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PMID-16251440[0] Neural correlates of reach errors.
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PMID-17189946[0] Cortico-hippocampal interaction during up-down states and memory consolidation.
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PMID-17173043[0] Coordinated memory replay in the visual cortex and hippocampus during sleep.
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PMID-14983183[0] Off-line replay maintains declarative memories in a model of hippocampal-neocortical interactions
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PMID-16474382[0] Reverse replay of behavioral sequences in hippocampal place cells during the awake state.
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PMID-18958234 Endocannabinoid Signaling is Critical for Habit Formation.
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PMID-17855611 Motor Force Field Learning Influences Visual Processing of Target Motion
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PMID-8922425 Primary Motor and Sensory Cortex Activation during Motor Performance and Motor Imagery: A Functional Magnetic Resonance Imaging Study.
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PMID-18951924[0] Consciousness and the consolidation of motor learning
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{678} |
ref: Rasch-2009.06
tags: sleep cholinergic acetylcholine REM motor consolidation
date: 02-18-2009 17:27 gmt
revision:0
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PMID-19194375[0] "Impaired Off-Line Consolidation of Motor Memories After Combined Blockade of Cholinergic Receptors During REM Sleep-Rich Sleep."
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PMID-18482830[0] Reinforcement learning of motor skills with policy gradients
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PMID-18578851 Overconfidence in an objective anticipatory motor task.
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{674} |
ref: notes-0
tags: Barto Hierarchal Reinforcement Learning
date: 02-17-2009 05:38 gmt
revision:1
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Recent Advancements in Hierarchal Reinforcement Learning
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{673} |
ref: Vasilaki-2009.02
tags: associative learning prefrontal cortex model hebbian
date: 02-17-2009 03:37 gmt
revision:2
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PMID-19153762 Learning flexible sensori-motor mappings in a complex network.
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In the process of installing compiz - which I decided I didn't like - I removed Xfce4's window manager, xfwm4, and was stuck with metacity. Metacity probably allows focus-follows-mouse, but this cannot be configured with Xfce's control panel, hence I had to figure out how to change it back. For this, I wrote a command to look for all files, opening each, and seeing if there are any lines that match "metacity". It's a brute force approach, but one that does not require much thinking or googling. find . -print | grep -v mnt | \ perl -e 'while($k = <STDIN>){open(FH,"< $k");while($j=<FH>){if($j=~/metacity/){print "found $k";}}close FH;}'This led me to discover ~/.cache/sessions/xfce4-session-loco:0 (the name of the computer is loco). I changed all references of 'metacity' to 'xfwm4', and got the proper window manager back. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{668} |
ref: notes-0
tags: triangulation kicadocaml
date: 02-04-2009 21:40 gmt
revision:7
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PCB copper zones using triangle meshes Abstract: Many tasks in computer-assisted design involve the removal of polygons from other polygons. Particularly, this problem is found when filling a region of a printed circuit board (PCB) with a polygonal zone or 'pour' of copper. This zone is attached to a net, perhaps ground, and hence other tracks, vias, and segments of copper not on the same net but within its region must be avoided by a clearance distance. This clearance can be observed by subtraction of expanded polygons from the original zone's outline polygon, as is done in two open-source PCB design softwares, Kicad and gEDA. Here we present a fast and scalable algorithm that works with triangles instead of polygons. The algorithm is able to mesh, add edges, and remove conflicting triangles within a few seconds for problems involving 10,000 points. Introduction: I have contributed, infrequently, to the open-source electronic design automation (EDA) suite Kicad for the past year or so. November/December of 2007 I added duplicated hierarchal support to Kicad's schematic editor, eeschema, which allows, like many commercial packages, duplicate instances of sub-schematics. This feature is used when a segment of circuitry is duplicated multiple times in a design, perhaps when there are multiple identical channels, e.g. in an audio mixer. However pcbnew (the layout editor in Kicad) is unaware of the duplication, hence for each sub-schematic the layout had to be duplicated. This involved a lot of work for the 8-channel microstimulator board that I was working on at the time, so I decided to implement a small application to help layout an array of duplicated circuitry. Ocaml was chosen to implement the software, as I wanted to learn the language. In the course of working on PCBs, learning Ocaml, and basically scratching a series of itches, the software, tentatively named "Kicadocaml", has become progressively more feature-rich, useful, and tested. It has ratsnest, DRC online and offline checking, push routing, schematic hierarchy comprehension (of course), connectivity testing, bill-of-materials generation, and a responsive OpenGL-based GUI. In my last board, pcbnew failed to fill all the zones; I'm not sure why. I tried to fix the bug, but got lazy/overwhelmed after a while, and decided to just write a zone-filling algorithm from scratch myself (to scratch the itch, so to speak). Sure it's reinventing the wheel, but reinventing is fun. In the interest of documenting the algorithm a bit for posterity, the algorithm is described below. Algorithm: A list is made of all points and segments that may be involved in the zone-fill. This includes, of course, the edges of the zone, as well as the outline of any track/via/pad cutout within the zone (and not of the same net number), expanded to allow for zone clearance and zone-edge stroking. The list of points also must include any intersections between segments. For efficiency, the lists of points and segments are culled by checking each polygon to be subtracted to make sure that at least one of it's points is within the zone polygon; this is done via the standard inside/outside polygon test. The list of points is then incrementally inserted into a linked triangle mesh via a very simple, very effective method of triangle splitting and edge-flipping. Linked triangle mesh means that each triangle stores a index (or pointer) to the triangle off each of its three edges. This is to facilitate the insertion of points: to find the triangle that a point is in, you walk over the linked mesh, crossing the edge between triangles that intersects a ray from the center of the present triangle to the target point. (Given the ordering of points within the list, this can be nearly a constant-time operation). See below.
Once a triangle is found, it is split into three triangles by the addition of the point. Then, each pair of triangles, one new and one old (bordering the triangle that was split) is checked to see if flipping the interior segment would increase the smallest angle. Remarkably, this reliably takes care of edge insertion - no specialized edge insertion routine was required (however, loops in the find triangle algorithm (figure 1) must be eliminated for a triangle to be found when a point is on an edge). I decided to simply maximize the minimum angle in each triangle, rather than observe the Delaunay criteria which doesn't matter for this application.
This algorithm only deals with finding containing triangles and inserting points; hence, it must be seeded with at least one triangle which will contain all others. I chose to use two triangles defined by a slightly-enlarged bounding box of all points to be inserted. The algorithm does not insure that all polygon segments are in the list of edges of a mesh; hence, after all points are inserted, every edge is checked to make sure if it is in the mesh -- see figure 3.
Once all points and all edges from the original list are in the mesh, then each triangle may be tested to see if it should be kept or removed. In kicadocaml this is done with DRC (design rule check) testing.
Afterword: The algorithm runs well; it takes ~ 2 seconds to mesh, edge check, and filter 10,000 points on my Core2 2.4Ghz desktop computer. Though it was written in a higher-level language (about 600 lines of Ocaml), I do not think that it would be hard to port to C++ for inclusion in other PCB layout packages. Great effort was not necessarily put into the design of the algorithm, but rather the numerical stability of it's sub-components, such as the triangle inside-outside check (computed with the cross product), and the segment intersection test. For these, please see the source, or {661}. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{661} |
ref: -0
tags: computational geometry triangulation ocaml kicadocaml zone fill edge
date: 01-26-2009 01:47 gmt
revision:3
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I have been working hard to add zone support to kicadocaml since the implementation in kicad's PCBnew is somewhat borken (at least for my boards). It is not a very easy task! Roughly, the task is this: given a zone of copper pour, perhaps attached to the ground net, and a series of tracks, vias, and pads also on that layer of the PCB but not on the same net, form cutouts in the zone so that there is an even spacing between the tracks/vias and zone. Currently I'm attacking the problem using triangles (not polygons like the other PCB softwares). I chose triangles since I'm using OpenGL to display the PCB, and triangles are a very native mode of drawing in OpenGL. Points are added to the triangle mesh with an incremental algorithm, where the triangles are stored as a linked-mesh : each triangle has a pointer (index#) to the triangle off edge ab,bc,ca. This allows finding the containing triangle when inserting a point a matter of jumping between triangles; since many of the points to be inserted are close to eachother, this is a relatively efficient algorithm. Once the triangle containing a point to be inserted is found, the triangle is split into three, the pointers are updated appropriately, and each triangle is tested to see if flipping with it's pair would result in a net larger smallest interior angle between the two. (This is not the same as Delaunay's criteria, but it is simpler, and it produces equally beautiful pictures.) The problem is when two triangles are allowed to overlap or a gap is allowed - this makes the search algorithm die or get into a loop, and is a major major problem of the approach. In Guibas and Stolfi's paper, "Primitives for the manipulation of general subdivisions and the computation of Voronoi diagrams", they use an edge data structure, rather than a triangle data structure, which I suppose avoids this problem. I was lazy when starting this project, and chose the more obvious triangle-centric way of storing the data. The insertion of points is actually not so hard; the big problem is making sure the edges in the original list of polygons are represented in the list of edges in the triangle mesh. Otherwise, triangles will span edges, which will result in DRC violations (e.g.g copper too close to vias). My inefficient way of doing this is to calculate, for all triangles, their intersections with the polygon segments, then adding this to the mesh until all segments are represented in the list. This process, too, is prone to numerical instability. Perhaps the solution is to move back to an edge-centric data representation, so that certain edges can be 'pinned' or frozen, and hence they are guaranteed to be in the triangle mesh's edge list. I don't know; need to think about this more. Update: I got most of it working; at least the triangulation & making sure the edges are in the triangle mesh are working. Mostly there were issues with numerical precision with narrow / small triangles; I rewrote the inside triangle function to use the cross product, which helped (this seems like the simplest way, and it avoids divisions!): ocaml let insidetri a b c d = cross (sub b a) (sub d a) > 0.0 && cross (sub c b) (sub d b) > 0.0 && cross (sub a c) (sub d c) > 0.0 ;; as well as the segment-segment intersection algorithm: ocaml let intersect a b c d = (* see if two line segments intersect *) (* return the point of intersection too *) let ab = sub b a in (* a prime is the origin *) let bp = length ab in let xx = norm ab in let yy = (-1.) *. (snd xx) , (fst xx) in let project e = (dot (sub e a) xx) , (dot (sub e a) yy) in let cp = project c in let dp = project d in let cd = sub dp cp in let m = (fst cd) /. (snd cd) in let o = (fst cp) -. m *. (snd cp) in let e = add (scl ab (o /. bp)) a in (* cp and dp must span the x-axis *) if ((snd cp) <= 0. && (snd dp) >= 0.) || ((snd cp) >= 0. && (snd dp) <= 0.) then ( if o >= 0. && o <= bp then ( true, e ) else ( false, e ) ) else ( false, e ) ;; Everything was very sensitive to ">" vs. ">=" -- all must be correct. All triangles must be CCW, too, for the inside algorithm to work - this requires that points to be inserted close to a triangle edge must be snapped to that edge to avoid any possible CW triangles. (Determining if a triangle is CW or CCW is as simple as measuring the sign of the smallest cross product between two segments). I tried, for a day or so, to include a specialized function to insert points along a triangle's edge, but that turned out not to matter; the normal flipping routine works fine. I also tried inserting auxiliary points to try to break up very small triangles, but that really didn't affect the stability of the algorithm much. It is either correct, or it is not, and my large board was a good test suite. I have, however, seeded the triangularization with a grid of (up to) 20x20 points (this depends on the aspect ratio of the region to be filled - the points are equally spaced in x and y). This adds (max) 800 triangles, but it makes the algorithm more stable - fewer very narrow triangles - and we are working with sets of 10,000 triangles anyway for the large zones of copper. Some corrections remain to be done regarding removing triangles based on DRC violation and using the linked-mesh of triangles when calculating edge-triangle edge intersection, but that should be relatively minor. Now I have to figure out how to store it in Kicad's ".brd" file format. Kicad uses "Kbool" library for intersection polygons - much faster than my triangle methods (well, it's in C not ocaml) - and generates concave polygons not triangles. Would prefer to do this so that I don't have to re-implement gerber export. (Of course, look at how much I have re-implemented! This was originally a project just to learn ocaml - Well, gotta have some fun :-) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-11411161[0] The anterior cingulate cortex. The evolution of an interface between emotion and cognition
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{656} |
ref: Schicknick-2008.11
tags: dopamine plasticity auditory cortex
date: 12-15-2008 04:13 gmt
revision:1
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PMID-18321872[0] Dopaminergic Modulation of Auditory Cortex-Dependent Memory Consolidation through mTOR.
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PMID-12371511[0] Dopamine: generalization and bonuses
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PMID-16855102[0] Complex spike activity of purkinje cells in the oculomotor vermis during behavioral adaptation of monkey saccades.
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{652} |
ref: notes-0
tags: policy gradient reinforcement learning aibo walk optimization
date: 12-09-2008 17:46 gmt
revision:0
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Policy Gradient Reinforcement Learning for Fast Quadrupedal Locomotion
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{178} |
ref: Churchland-2006.12
tags: motor_noise CNS Churchland execution variance motor_planning 2006
date: 12-08-2008 22:50 gmt
revision:2
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PMID-17178410[0] A central source of movement variability.
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ME 270 Final Project - Optical Power Transfer The purpose of this project was to develop a means for delivering optical power to the top of monkey unconstrained within his cage. This power will ultimately be used to recharge the batteries on a small neural telemetry device that we are developing. To deliver the power, we decided to use a moving-mirror DJ light controlled through a microcontroller in turn controlled via a video tracking computer. Hence, out report will be broken into three sections: the light, microcontroller, and video tracking. Section 1 : Reverse-engineering the light, part selectionRather than engineering our own articulated spotlight, we elected to buy a moving-mirror DJ light; creating our own light source would simply have taken too much time, and demanded optical experience that we lack. After a brief survey, we bought an Elekralite mm150 (moving mirror, 150W bulb) DJ light, one of the cheapest on the market ($650); despite this, it is very well constructed, as you will see below. The light was originally controlled through the stage-specific DMX bus, but the possibility of directly controlling the light through this was discarded after we learned that the resolution on each axis is only 8 bits (+- 127); given the large range of the pan mirror, this is insufficient for tracking. Hence we decided to reverse engineer the light to determine the best way to directly control the mirror and shutter.
Section 2: Microcontroller & microsteppingAs mentioned before, we chose MSP430F5438 100-pin 16 bit microcontroller because it offers sufficient timers and speed for our problem and because we were both familiar with the architecture. Four 16-bit timers are used to control microstepping mirror tilt and pan, since the stepper motors have two phases. The microcontroller only needs to provide digital signals; current is provided through H-bridge drivers in the control board of the mm-150 - the DIPs with heat sinks below.Opposite sides of the H-bridge are driven via hex inverters; hence, we only have to supply two PWM signals per motor, one per phase. Setting the PWM duty cycle to 50% will set the motor phase current to zero; by vectoring the duty cycle proportional to the sine and cosine of theta, where theta is the orientation of the motor * number of poles of the stepper, you can control microstepping. That, of course, is simplified; in practice, there are many details to contend with, namely:
We approximated sine and cosine, needed to vector the stepper motor phase currents, in fixed-point arithmetic first in C on linux - where the results could be plotted in matlab - before converting to MSP430 code. Since the trigonometric functions are repeating, we only need a polynomial approximation of sine from 0 to pi/2. The taylor series for sine is sin(x) = x - x^3/3! + x^5/5! - x^7/7! ...; a quick check in matlab showed that the first three terms are enough to get an accurate approximation in the domain of interest. The MSP430 does not have division, however, so we approximated 1/3! = 1/6 as (1/8 + 1/32 + 1/128) and 1/5! = 1/120 as 1/128; division by powers of two is possible with right bit-shift operations. We chose base 11 (5 bits whole, 11 bits fractional) representation to avoid overflow: if 2^11 -> 1, we need to represent (pi/2)^5 -> 9.5 ; ceil(log_2(9.5)) = 4 (plus one bit for safety). The C program below shows this test. #include <stdio.h> char qsin(short i){ //i goes from 0 pi/2 base 11 or... // 0 to 3217 unsigned int cube, fifth, result; cube = (i*i) >> 11; cube = (cube*i) >> 11; //max = 7937 fifth = (cube*i) >> 11; fifth = (fifth*i) >> 11; // max = 19585 //our approximation to sine based on taylor series: //original: sin(x) = x - x^3/3! + x^5/5! //sin(x) = x - x^3*(1/8+1/32+1/128) + x^5*(1/128) result = (unsigned int)i - ((cube >> 3) + (cube >> 5) + (cube >> 7)) + (fifth >> 7); //result is base 11. need it to be base 7. result = result >> 4; if(result > 127) result = 127; return (char)result; } //this is tricky, as it involves shifts, x-inversions, and y-inversions. //but it all makes sense if you plot out the respective functions. char isin(short i){ // i is base 2^11 //but we accept 0 to 2*pi or 12867 if(i >= 0 && i < 3217) return qsin(i); else if(i >= 3217 && i < 6434) return qsin(6434 - i); else if(i >= 6434 && i < 9651) return -1*qsin(i - 6434); else if(i >= 9651 && i < 12867) return -1*qsin(12867 - i); else return 0; } char icos(short i){ // i is base 2^11 //but we accept 0 to 2*pi or 12867 if(i >= 0 && i < 3217) return qsin(3217 - i); else if(i >= 3217 && i < 6434) return -1*qsin(i - 3217); else if(i >= 6434 && i < 9651) return -1*qsin(9651 - i); else if(i >= 9651 && i < 12867) return qsin(i - 9651); else return 0; } int main(void){ short i; for(i=0; i<12867; i++){ printf("%d\t%f\t%d\t%d\n", i, ((float)i)/2048.0, (int)(isin(i)), (int)(icos(i))); } return 0; } We compiled and ran this program on the command line: gcc integer_trig.c ./a.out > test.txt Then we imported the data into matlab and plotted (Actual double floating-point sine and cosine are plotted on the same axis as thin black and magenta lines, respectively) Later, we had to change the naive standard implementation of multiply to assembly to properly implement the fixed-point arithmetic - the MSP430's standard library did not implement the 16x16 multiply followed by shift correctly (it only keeps the bottom 16 bits). Note: this assembly function is for use with Code-Composer Studio, available from the Texas Instruments website. It seems that the IAR compiler uses different assembly syntax. ;******************************************************************************* .cdecls C,LIST,"msp430x54x.h" ; Include device header file ;------------------------------------------------------------------------------- .text ; Progam Start ;------------------------------------------------------------------------------- ;;.sect "mply_11" ;;.asmfunc "mply_11" .global mply_11 ;; this MUST BE PRECEDED BY TABS !!!!! mply_11: PUSH SR ; DINT ; turn off interrupts here. NOP ; required after DINT MOV.W R12, &MPY ; load the first operand. MOV.W R13, &OP2 ; load the second operand & start multiplication. MOV.W &RESLO, R12 ; low to R12 (this is the return value) MOV.W &RESHI, R13 ; high to R13 RRA.W R12 ; 1 RRA.W R12 ; 2 RRA.W R12 ; 3 RRA.W R12 ; 4 RRA.W R12 ; 5 RRA.W R12 ; 6 RRA.W R12 ; 7 RRA.W R12 ; 8 RRA.W R12 ; 9 RRA.W R12 ; 10 RRA.W R12 ; 11 RLA.W R13 ; 1 RLA.W R13 ; 2 RLA.W R13 ; 3 RLA.W R13 ; 4 RLA.W R13 ; 5 ;; r14 can be clobbered across a function call, according to the msp430 ABI MOV.W #0x001f, R14 AND.W R14, R12 ; mask off all but the bottom 5 bits from RESLO ADD.W R13, R12 ; add (logical OR) the results. R12 is the 11-bit fixed point result. POP.W SR ; RETA ; return from subroutine. .end Note the MSP430 does not have an opcode for multiple arithmetic shifts, nor does it have code for logical shifts - hence the need for repeated shifts and bitmasks! #include <msp430x54x.h> #define INCR 1 #define PI2 (12868) //we use a 11 bit fixed-point representationf of motor angles. // 12867 = 2*pi*2^11. #define TIMER_SCL 128 #define SHUTTER_CLOSED 0 //defines used in the state-machine control of the shutter. #define SHUTTER_OPEN 1 #define SHUTTER_SMALL 2 //Start of Stepper Motor Program //ME270 Project short theta1 = 0; //the MSP430 is a 16-bit processor. short theta2 = 0; //hence, most datatypes should be 'short' for efficiency. short theta1_v = 0; //we cannot control the poition of the stepper motors directly, short theta2_v = 0; // since we only have 3 bits of control from the parallel port. // also, direct position control of postion would cause the stepper to miss steps // smooth position change and limited acceleration is guaranteed by controlling the velocity. short shutter_state = 0; // none of the steppers have encoders, // so we keep track of the shutter position here. short shutter_cmd ; //this is set in ISR (interupt service routine) // and read, and acted upon, in the main loop. short qsin(short i){ //i goes from 0 pi/2 base 11 or... // 0 to 3217 short cube, fifth, result; cube = mply_11(i,i); cube = mply_11(cube, i); fifth = cube; fifth = mply_11(fifth, i); fifth = mply_11(fifth, i); //our approximation to sine based on taylor series: //original: sin(x) = x - x^3/3! + x^5/5! //sin(x) = x - x^3/(8+32+128) + x^5/128 result = i - ((cube >> 3) + (cube >> 5) + (cube >> 7)) + (fifth >> 7); //result is base 11. need it to be base 7. (0 to 127) result = result >> 4; if(result > TIMER_SCL) result = TIMER_SCL; return (short)result; } // this is an even more simplified version of sin - // made in an attempt to make the microstepping smoother. // it turned out to not matter very much. to get very smooth stepping , // may have to develop an inverse model of the nonlinear stepper motors // ** quantitatively ** short qsin2(short i){ //i goes from 0 pi/2 base 11 or... // 0 to 3217 short cube, result; cube = mply_11(i,i); cube = mply_11(cube, i); //our approximation to sine based on taylor series: //original: sin(x) = x - x^3/3! + x^5/5! //sin(x) = x - x^3/(8+32+128) + x^5/128 result = i - (cube >> 3) ; //result is base 11. need it to be base 7. result = result >> 4; if(result > TIMER_SCL) result = TIMER_SCL; //maximum.. return (short)result; } short isin(short i){ // i is base 2^11 //but we accept 0 to 2*pi or 12867 if(i >= 0 && i < 3217) return qsin(i); else if(i >= 3217 && i < 6434) return qsin(6434 - i); else if(i >= 6434 && i < 9651) return -1*qsin(i - 6434); else if(i >= 9651 && i < 12867) return -1*qsin(12867 - i); else return 0; } short icos(short i){ // i is base 2^11 //but we accept 0 to 2*pi or 12867 if(i >= 0 && i < 3217) return qsin(3217 - i); else if(i >= 3217 && i < 6434) return -1*qsin(i - 3217); else if(i >= 6434 && i < 9651) return -1*qsin(9651 - i); else if(i >= 9651 && i < 12867) return qsin(i - 9651); else return 0; } //this interrupt is triggered by the parallel port. //because we only have 3 lines and need 8 commands, //after triggering (0 to 1 transition on PORT2.0 ), //the control program on the PC will either hold the pin up // (indicating a velocity step command) or drop it (indicating shutter/stop cmd). #pragma vector=PORT2_VECTOR __interrupt void port2_ISR (void) { //need to read the two pins to figure out which axis to change. short k; for(k=0; k<8; k++){ P9OUT ^= 0x4; } switch(P2IN & 0x7){ case 1: theta1_v += INCR; break; case 3: theta1_v -= INCR; break; case 5: theta2_v += INCR; break; case 7: theta2_v -= INCR; break; case 0: shutter_cmd = SHUTTER_CLOSED; break; case 2: shutter_cmd = SHUTTER_SMALL; break; case 6: shutter_cmd = SHUTTER_OPEN; break; case 4: theta1_v = 0; theta2_v = 0; break; } P2IFG = 0; //clear the interupt. } #pragma vector=TIMER1_A0_VECTOR __interrupt void timera1_ISR (void) { return; //if this vector is not here and the interupt is enabled, then the proc will crash! } // have to integrate the velocity at a consistent rate, // hence we pushed integration as well as the sine/cosine computation // into this timer interrupt. #pragma vector=TIMER1_A1_VECTOR __interrupt void timera11_ISR (void) { short ps, pc; P1OUT ^= 0xFF; //toggle P1 to indicate the update rate. (the led is there) TA1CTL = 0x0004; //reset counter TA1CTL = 0x0112; //turn back in interrupts. theta1 += theta1_v; theta2 += theta2_v; if(theta1 > PI2) theta1 -= PI2; if(theta1 < 0) theta1 += PI2; if(theta2 > PI2) theta2 -= PI2; if(theta2 < 0) theta2 += PI2; ps = isin(theta1)+TIMER_SCL; pc = icos(theta1)+TIMER_SCL; TA0CCR1 = ps; //update the counter (PWM output) registers. TA0CCR4 = pc; ps = isin(theta2)+TIMER_SCL; pc = icos(theta2)+TIMER_SCL; TA0CCR2 = ps; TA0CCR3 = pc; P1OUT ^= 0xFF; //toggle P1 to indicate the update rate. (the led is there) return; } //delay is used in moving the shutter. // too short, and the stepper motor controlling the shutter will skip steps! void delay(short time){ short k; short j = 0; for(k=0; k<time; k++){ j++; j++; } } void delay_long(short time){ short k,j,f; for(k=0; k<time; k++){ f = 0; for(j=0; j<100; j++){ f++; } } } // ideally, we would ramp the shutter velocity up and down to maximize speed // and minimize time - constant velocity works fine and fast. #define SHUTDLY 1600 void shutter_ccw(void){ P9OUT = 0x1; delay(SHUTDLY); P9OUT = 0x3; delay(SHUTDLY); P9OUT = 0x2; delay(SHUTDLY); P9OUT = 0x0; delay(SHUTDLY); } void shutter_cw(void){ P9OUT = 0x2; delay(SHUTDLY); P9OUT = 0x3; delay(SHUTDLY); P9OUT = 0x1; delay(SHUTDLY); P9OUT = 0x0; delay(SHUTDLY); } void shutter_open(void){ short i; if(shutter_state == SHUTTER_CLOSED){ //I was quite pleased to discover that the three shutters states // are exactly 5 full steps apart! for(i=0; i<5; i++){ shutter_ccw(); } } if(shutter_state == SHUTTER_SMALL){ for(i=0; i<5; i++){ shutter_cw(); } } shutter_state = SHUTTER_OPEN; } void shutter_close(void){ short i; if(shutter_state == SHUTTER_OPEN){ for(i=0; i<5; i++){ shutter_cw(); } } if(shutter_state == SHUTTER_SMALL){ for(i=0; i<10; i++){ shutter_cw(); } } shutter_state = SHUTTER_CLOSED; } void shutter_small(void){ short i; if(shutter_state == SHUTTER_OPEN){ for(i=0; i<5; i++){ shutter_ccw(); } } if(shutter_state == SHUTTER_CLOSED){ for(i=0; i<10; i++){ shutter_ccw(); } } shutter_state = SHUTTER_SMALL; } void main (void){ //SR = 0x02; short t1, t2, ps, pc; short k; WDTCTL = WDTPW + WDTHOLD; //stop the watchdog timer. // UCSCTL = Universal clock system control (registers). // sets the core clock of the device. _bis_SR_register(SCG0); //SR = SR | 0x40 ; // setup the digitally controlled oscillator. UCSCTL0 = 0x0700; //DCO = 5, MOD = 0 UCSCTL1 = 0x0060; //DCORSEL = 3, middle freq. UCSCTL2 = 0x101F; //FLL (frequency locked loop); doesnt matter here. UCSCTL4 = 0x0333; //select DCOCLK for all clock sources UCSCTL0 = 0x0900; //DCO = 9, MOD = 0 // DCO = internal high-frequency oscillator). //UCSCTL5 = 0x0000; // setup timer A (for controlling PWM outputs) TA0CCR0 = TIMER_SCL*2+1; //Timer A end pulse TA0CCR1 = TIMER_SCL; //Timer A start pulse TA0CCR2 = TIMER_SCL; //Timer A start pulse TA0CCR3 = TIMER_SCL; //Timer A start pulse TA0CCR4 = TIMER_SCL; //Timer A start pulse TA0CTL = 0x0110; //TASSEL = ACLK; input divider=1; MCx = count up mode; TA0CCTL0 = 0x0040; //sets the mode of the output: here=2, toggle/reset. // (produces pulses at 8Khz). TA0CCTL1 = 0x00C0; //output mode: toggle/set. TA0CCTL2 = 0x00C0; // same TA0CCTL3 = 0x00C0; // same TA0CCTL4 = 0x00C0; // same //setup timer B (for controlling theta & velocity updates). TA1CCR0 = 10000; //Timer A end pulse TA1CCR1 = 5000; //Timer A start pulse TA1CCR2 = 5000; //Timer A start pulse TA1CTL = 0x0004; TA1CTL = 0x0112; //TASSEL = ACLK; input divider=1; MCx = count up mode; TA1CCTL0 = 0x0050; //sets the mode of the output: here=2, toggle/reset. // (produces pulses at 8Khz). TA1CCTL1 = 0x00C0; //output mode: toggle/set. TA1CCTL2 = 0x00C0; // same P1DIR = 0x03; //P1.0 and P1.1 to output. (the LED) P1SEL = 0x00; P1OUT = 0; P8DIR = 0xFF; //for some reason Port 1 does not work for the dev board -- P8SEL = 0x7F; //hence, we switched over to Port 8, which also is connected // to the timers. // the P8SEL register selects the timer output as opposed to general purpose IO. //setup port2 (computer command via parallel port) interrupt. P2DIR = 0; //all inputs. P2IFG = 0; P2IE = 0x01; //enable interupts on P2.0 P2IES = 0; // low to high edge detect. _bis_SR_register(GIE | SCG0 ); //enable interrupts, dont go to sleep. P9DIR = 0x07; //test the shutter. first move all the way to the limit. // since we do not know the initial position. for(k=0; k<30; k++){ shutter_cw(); } shutter_ccw(); //step one out so we don't hit the limits later. shutter_state = SHUTTER_CLOSED; //this is where the init will leave it while(1){ //now just sit here waiting for a shutter command from the // parallel port ISR. if(shutter_state != shutter_cmd){ switch(shutter_cmd){ case SHUTTER_OPEN: shutter_open(); break; case SHUTTER_CLOSED: shutter_close(); break; case SHUTTER_SMALL: shutter_small(); break; } } } } We has some problem getting Port1 to work, hence had to use Port8 to get the PWM signals out -- see below. Note the shutter does not need to be microstepped and instead can be controlled as per a conventional stepper motor. The pins used are marked in yellow; pin 57 is a simple pulse output. Note that each PWM signal is generated from the same timer counter, hence they are synchronous (this is of course not necessary). Below are some examples of two phases of one motor output; in real life, of course, the PWM ratio continually changes. Below is the development board being probed to produce the plots above. We then used the pinouts of the NXP microcontrollers, intuited last time by probing their on-line function (specifically the auto-calibration sequence upon startup), to wire up a harness for external control of the H-bridges. Below is a picture of that (we removed the original microcontrollers to prevent contention), and the associated wiring labels.
The next task was to make a 5V to 3.2V regulator (the MSP430 only runs at 3.2V, max), nothing major just a LM317. See below. Finally, everything was wired together. The 3.2 V supply was jumpered, as the MSP430 USB programmer provided its own power. (Amazingly, the ultra low power MSP430 could run on power from the parallel port, too!) A level translator is needed to properly interface the 3.2V MSP430 to the 5V parallel port - we canibalized a spare JTAG adapter for this purpose. It was this that limited us to only 3 bits of control. And that, minus the difficulty we had getting the compiler working properly, is the entirety of the microcontroller part of the project. Section 3 - Video tracking and host computer controlWith the microcontroller done, we then moved to controlling it via a video-tracking computer. At this point, we had created a simple program for testing out parallel port control of the light's three axes using the keyboard (tilt, pan, and shutter). This program was split into two files, a main, and a set of subroutines that could then be called and compiled into the full video tracking program. It uses libparapin to abstract interaction with the parallel port in userspace.First, the main loop, which is very simple: #include "parallelout.h" #include <stdio.h> #include <stdlib.h> #include <unistd.h> char g_main_loop ; int main(int argc, char *argv[]) { g_main_loop = 1; char c; parallel_setup(); while(1){ c = fgetc(stdin); interpret_cmd(c); } } Second, the parallel port controller. This uses a thread and circular queue to provide asynchronous, non-blocking control of the communications channel. Non-blocking is critical, as the program waits a small period between low-high transition of the interrupt pin (pin 4) for the MSP430 to read the status of the three lines. #include <stdio.h> #include <stdlib.h> #include <unistd.h> #include <parapin.h> #include <pthread.h> #include "parallelout.h" char g_q[1024]; //queue for the commands. int g_q_rptr; //where to read the next command from. int g_q_wptr; //where to put the next command double g_velPan; double g_velTilt; void stepstep(void){ int i = 0; for(i=0; i<20000; i++){ set_pin(LP_PIN[4]); clear_pin(LP_PIN[4]); set_pin(LP_PIN[5]); clear_pin(LP_PIN[5]); set_pin(LP_PIN[5]); clear_pin(LP_PIN[5]); } } void velstep(int n){ //printf("velstep %d\n", n); clear_pin(LP_PIN[4]); if(n&0x1) set_pin(LP_PIN[2]) ; else clear_pin(LP_PIN[2]); if(n&0x2) set_pin(LP_PIN[3]) ; else clear_pin(LP_PIN[3]); set_pin(LP_PIN[4]); //leave it up, so the msp430 knows it is a velocity command. } void openShutter(){ printf("opening shutter\n"); clear_pin(LP_PIN[4]); set_pin(LP_PIN[2]); set_pin(LP_PIN[3]); set_pin(LP_PIN[4]); clear_pin(LP_PIN[4]); //clear the trigger to indicate a shutter command. } void closeShutter(){ printf("closing shutter\n"); clear_pin(LP_PIN[4]); clear_pin(LP_PIN[2]); clear_pin(LP_PIN[3]); set_pin(LP_PIN[4]); clear_pin(LP_PIN[4]); //clear the trigger to indicate a shutter command. } void smallShutter(){ printf("small shutter\n"); clear_pin(LP_PIN[4]); clear_pin(LP_PIN[2]); set_pin(LP_PIN[3]); set_pin(LP_PIN[4]); clear_pin(LP_PIN[4]); //clear the trigger to indicate a shutter command. } void stopMirror(){ printf("stop mirror\n"); clear_pin(LP_PIN[4]); set_pin(LP_PIN[2]); clear_pin(LP_PIN[3]); set_pin(LP_PIN[4]); clear_pin(LP_PIN[4]); //clear the trigger to indicate a shutter command. } void parallel_setup(){ if (pin_init_user(LPT1) < 0) exit(0); pin_output_mode(LP_DATA_PINS | LP_SWITCHABLE_PINS); clear_pin(LP_PIN[2]); clear_pin(LP_PIN[3]); clear_pin(LP_PIN[4]); pthread_t thread1; //start the queue-servicing thread. pthread_create ( &thread1, NULL, pq_thread, NULL ); } void interpret_cmd(char cmd){ //these codes don't make much sense unless you are //controlling from a keyboard. switch(cmd){ case 'w': velstep(0); g_velPan-=1.0; break; //pan to right (looking at but of light) case 'a': velstep(1); g_velTilt+=1.0; break; //tilt toward. case 's': velstep(2); g_velPan+=1.0; break; //pan to left case 'd': velstep(3); g_velTilt-=1.0; break; //tilt away case 'o': openShutter(); break; case 'c': closeShutter(); break; case 'x': smallShutter(); break; case ' ': stopMirror(); g_velPan=0; g_velTilt=0; break; } } void usleep(int us){ timespec ts; ts.tv_sec = 0; ts.tv_nsec = us * 1000; nanosleep(&ts, NULL); } extern int g_main_loop ; void* pq_thread(void* a){ while(g_main_loop){ if(g_q_wptr > g_q_rptr){ char cmd = g_q[g_q_rptr % sizeof(g_q)]; g_q_rptr++; interpret_cmd(cmd); } usleep( 200 ); // run at max 500hz update. // the msp430 takes about 125us to service the parallel port irq. } return (void*)0; } void enqueue(char cmd){ //this should be sufficiently atomic so there is no thread contention. g_q[g_q_wptr % sizeof(g_q)] = cmd; g_q_wptr++; } Then, we worked on the video tracking program. I will omit the some of the noncritical sections involving the firewire (ieee1394), Xv (video display) and X11 (window manager) calls, as the whole program is long, ~1000 lines. Below is 'main' -- see the comments for a detailed description. int main(int arc, char *argv[]){ int i; double t1, t2, t3, t4; t1 = t2 = t3 = t4 = 0.0; signal(SIGINT, cleanup); //trap cntrl c signal(SIGPIPE, cleanup); //turn off output buffering for ttcp! //setvbuf(stdout,(char*)NULL,_IONBF,0); //init buffers for old tracking... for(int i=0; i<4; i++){ g_buffer[i] = (short*)malloc(640*480*sizeof(short)); } g_averagefb = (int*)malloc(640*480*sizeof(int)); g_velfb = (int*)malloc(640*480*sizeof(int)); g_lastfb = (unsigned char*)malloc(640*480); g_trackedfb = (unsigned char*)malloc(640*480); for(i=0; i < 640*480; i++){ g_averagefb[i] = 0; } //Step -2: set up threads (the display runs on a seperate thread // to keep from blocking the iscochronous recieve channel // and hence causing the frame rate to drop. pthread_mutex_init(&g_dispthread_mutex, NULL); pthread_cond_init(&g_dispthread_cond, NULL); //STEP -1: init the parallel port for control of mirror (this also starts that thread) parallel_setup(); //Step 0: small shutter so we can track the light easily. smallShutter(); //Step 0.5: move the mirror to the close left (from but of light) for calibration //for reference (from the viewpoint of the cord end of the light): // pan left : s // pan right: w // tilt toward: a // tilt away: s // small shutter: x // open shutter: o // closed shutter: c // stop mirrors : <space> for(i=0; i<10; i++){ enqueue('s'); //to the left if you are looking at the but of the light. enqueue('a'); //the tilt axis has far fewer steps for full range than enqueue('s'); // the pan axis hence requires a much higher velocity - enqueue('s'); // so enqueue more 's'. enqueue('s'); enqueue('s'); } //Step 1: Open ohci and assign a handle to it. //================================================================================================================== init_cards(); //Step 2: Get the camera nodes and describe them as we find them. //================================================================================================================== init_cams(); //Step 3: Setup Capture //================================================================================================================== setup_cams(); //Step 4: Start sending data //================================================================================================================== start_iso_transmission(); //start the other thread. pthread_t thread1; pthread_attr_t attr; pthread_attr_init(&attr); pthread_create( &thread1, &attr, display_thread, 0 ); //Main event loop while(g_main_loop==true){ for( i=0; i<numCameras; i++){ if(dc1394_dma_single_capture(&camera[i]) != DC1394_SUCCESS){ fprintf(stderr, "dma1394: Failed to capture from cameras\n"); cleanup(0); } } t2=get_time(); for( i=0; i<numCameras; i++){ //display_frames_old(i); display_frames(i); /*if((g_frame%60) < 15){ velstep(0); }else if((g_frame%60) < 45){ velstep(2); }else { velstep(0); } */ if(dc1394_dma_done_with_buffer(&camera[i]) != DC1394_SUCCESS){ fprintf(stderr, "dma1394: Can't release dma bufer\n"); } } if(g_frame % 60 == 0){ printf("frame dt: %f (%f) track time %f (%f)\n", t2-t4, 1/(t2-t4), tracktime, 1/(tracktime)); } //start with the state machine for the calibration -- if(g_frame == CALIB_0){ enqueue(' '); //stop it printf("!!assuming that the mirror reached it's limit!!\n"); for( i=0; i<3; i++){ //now that we have put the mirror into a corner, give it velocity // to move to the center of the FOV so that we may turn on // feedback-based tracking. enqueue('w'); //to the left if you are looking at the but of the light. enqueue('d'); enqueue('w'); //again, pan motor has many more steps/range than tilt enqueue('w'); enqueue('w'); enqueue('w'); enqueue('w'); enqueue('w'); enqueue('w'); } } if(g_frame == CALIB_1){ enqueue(' '); //stop it printf("!!assuming light is centered now!!\n"); } if(g_frame == CALIB_2){ enqueue('x'); } t4 = t2; g_frame++; } cleanup(0); return 0; } Our tracking algorithm periodically opens and closes the shutter on the light. It is impossible to track a target based on brightness or even pattern detection, since the light is so bright it is impossible to image what it hits and what it does not with our cameras of limited dynamic range. (The human eye, of course, has far better dynamic range.) During the period when the light is off, we wait for the camera shutter speed to stabilize, then average the brightest spot over 10 consecutive frames to obtain a target position. Then, the shutter is opened, and visual feedback is used with a simple PD controller to guide the light to the target. When the device is deployed, we will make the update non-periodic and purely contingent on the detection of motion or of decreased solar cell output. See below for the thread that implements this logic, as well as blits the image onto the screen. void* display_thread(void* ptr ){ make_window(); while(g_main_loop){ if(pthread_cond_wait(&g_dispthread_cond, &g_dispthread_mutex) == 0){ pthread_mutex_unlock(&g_dispthread_mutex); double t1 = get_time(); g_first_frame=false; //convert into the XV format (this seems very inefficient to me...) for(unsigned int i=0; i< g_framewidth*g_frameheight; i++){ g_fb[i] = g_trackedfb[i]+ 0x8000; } double c_r, c_c; new_track(0, &tcam[0], g_trackedfb, g_framewidth, g_frameheight, CONTRAST_MIN, SEARCHR, GAUSSDROPOFF, NUMBER_OF_MARKERS, &c_r, &c_c); xv_image=XvCreateImage(display, info[adaptor].base_id, format_disp, (char*)g_fb, g_framewidth, g_frameheight*numCameras); XvPutImage(display, info[adaptor].base_id, window, gc, xv_image, 0, 0, g_framewidth, g_frameheight*numCameras, 0, 0, g_windowwidth, g_windowheight); free(xv_image); //do some dumb control (finally!) // initially, guide the light to the center of the screen. if(g_frame > CALIB_1 && g_frame <= CALIB_2){ g_target_c = 320.0; g_target_r = 240.0; servo_mirror(c_c, c_r); //get it stuck on the center! } int time = g_frame - CALIB_2; // below is the *main loop* for cycling the shutter open/close if(g_frame > CALIB_2){ if(time % 300 < 240){ servo_mirror(c_c, c_r); } if(time % 300 == 240){ enqueue('c'); enqueue(' '); } if(time % 300 >= 260 && time % 300 < 280 ){ g_target_c += c_c; g_target_r += c_r; } if(time % 300 == 280){ enqueue('x'); g_target_c /= 20.0; g_target_r /= 20.0; } } double t2 = get_time(); tracktime = t2 - t1 ; } //normalize_com(NUMBER_OF_MARKERS); XFlush(display); while(XPending(display)>0){ XNextEvent(display,&xev); switch(xev.type){ case ConfigureNotify: g_windowwidth=xev.xconfigure.width; g_windowheight=xev.xconfigure.height; break; case KeyPress: switch(XKeycodeToKeysym(display,xev.xkey.keycode,0)){ case XK_q: case XK_Q: g_main_loop = false; //cleanup(0); break; } break; } } //XPending } if ((void *)window != NULL){ XUnmapWindow(display,window); } fprintf(stderr,"dma1394: Unmapped Window.\n"); if (display != NULL){ XFlush(display); } return (void*) 0; } The PD controller uses very pessimistic values for the coefficients, as we discovered that the timing resolution on out older linux computer is low - about 5ms. This means that if too many velocity step commands are sent to the parallel port thread at one time, it will get backlogged, which will induce a phase-shift between control and actuation of velocity. Hence, the light must move rather slowly, on the order of one velocity step on each axis per frame. Again, below. void servo_mirror(double c_c, double c_r ){ double dc = c_c - g_target_c; //for now assume that we want to stabilize in double dr = c_r - g_target_r; // the center. double vgain = 8.0 ; double pgain = 1.0/80.0; int lim = 1; double c = dc + g_velPan*vgain ; int ccmd = 0; int rcmd = 0; if(c > 0){ for(int i=0; i<c*pgain && i < lim; i++){ enqueue('w'); ccmd --; } } if(c < 0){ for(int i=0; i<c*-1.0*pgain && i < lim; i++){ enqueue('s'); ccmd ++; } } vgain *= 1.5; //tilt mirror moves quicker! double r = dr + g_velTilt*vgain; if(r>0){ for(int i=0; i<r*pgain && i < lim; i++){ enqueue('d'); rcmd--; } } if(r<0){ for(int i=0; i<r*-1.0*pgain && i < lim; i++){ enqueue('a'); rcmd++; } } //this for debugging loop stability problems in matlab. //printf("%f %f %d %f %f %d\n", dc, g_velPan*vgain, ccmd, dr, g_velTilt*vgain, rcmd); //if(dr + g_velTilt*vgain > 0) enqueue('d'); OLD //if(dr + g_velTilt*vgain < 0) enqueue('a'); } Our video tracking algorithm first uses a tree-like algorithm to quickly and robustly search for the brightest region in the scene; we presume, somewhat simplistically, that this will be the target. When the device is put into use with an actual monkey cage, we'll surround the camera with high-intensity infrared LEDs to effectively illuminate a retroreflector placed on the monkey's head. Below is the code which performs this computation. //make a blur matrix //void blur(frame_info* frame, unsigned char * fb, int framewidth, int downsamp, int downsamp_w, int downsamp_h){ void blur(int camno, track_cam* tcam, unsigned char* fb, int framewidth, int downsamp_r, int downsamp_c, int downsamp_w, int downsamp_h){ //initialize contrasts for(int m=0; m<downsamp_r * downsamp_c; m++){ tcam[camno].frame.sum[m]=0; tcam[camno].frame.contr_min[m]=255; tcam[camno].frame.contr_max[m]=0; } for(int k=0; k<downsamp_r; k++){ for(int row=k*downsamp_h; row<k*downsamp_h+downsamp_h; row++){ for(int j=0; j<downsamp_c; j++){ for(int col=j*downsamp_w; col<j*downsamp_w+downsamp_w; col++){ tcam[camno].frame.sum[j+(k*downsamp_c)]+=int(fb[row*framewidth+col]); if(int(fb[row*framewidth+col])>tcam[camno].frame.contr_max[j+(k*downsamp_c)]){ tcam[camno].frame.contr_max[j+(k*downsamp_c)]=int(fb[row*framewidth+col]); //introducing a contrast check. } if(int(fb[row*framewidth+col])<tcam[camno].frame.contr_min[j+(k*downsamp_c)]){ tcam[camno].frame.contr_min[j+(k*downsamp_c)]=int(fb[row*framewidth+col]); //introducing a contrast check } } } } } } //blob_search function //search through the sum matrix and find the brightest sums //void blob_search(frame_info* frame, marker* marker, int num_markers, int contrast_min){ void blob_search(int camno, track_cam* tcam, int num_markers, int contrast_min, int downsamp_r, int downsamp_c){ //frame->num_blobs=0; //innocent until proven guilty for(int i=0; i<num_markers; i++){ int blob_val=0; for(int m=0; m<downsamp_r*downsamp_c; m++){ if(tcam[camno].frame.sum[m]>blob_val && tcam[camno].frame.contr_max[m]-tcam[camno].frame.contr_min[m]>contrast_min){ //has to have a big contrast to be a blob (CONTRAST is user defined macro) blob_val=tcam[camno].frame.sum[m]; //the new max' tcam[camno].marker[i].downsamp_loc=m; //the sum integer (0-255) //frame->num_blobs++; } } tcam[camno].frame.sum[tcam[camno].marker[i].downsamp_loc]=0; //kill the one we just found so we can find the next biggest one. } } //brightest_pix_search function //search through the blobs for the brightest pixel //void brightest_pix_search(unsigned char * fb, frame_info* frame, marker* marker, int num_markers, int framewidth, int downsamp, int downsamp_w, int downsamp_h){ void brightest_pix_search(unsigned char * fb, int camno, track_cam* tcam, int num_markers, int framewidth, int downsamp_r, int downsamp_c, int downsamp_w, int downsamp_h){ //br_pix_info[0] is the row //br_pix_info[1] is the col //br_pix_info[2] is the value for(int i=0; i<num_markers; i++){ tcam[camno].marker[i].br_pix_val=0; //always has to start low for(int row=int(floor(tcam[camno].marker[i].downsamp_loc/downsamp_c))*downsamp_h; row<int(floor(tcam[camno].marker[i].downsamp_loc/downsamp_c))*downsamp_h+downsamp_h; row++){ for(int col=tcam[camno].marker[i].downsamp_loc%downsamp_c*downsamp_w; col<tcam[camno].marker[i].downsamp_loc%downsamp_c*downsamp_w+downsamp_w; col++){ if(int(fb[row*framewidth+col])>tcam[camno].marker[i].br_pix_val){ //if it is greater than the brightest pixel then store its info tcam[camno].marker[i].br_pix_row=row; //save the row tcam[camno].marker[i].br_pix_col=col; //save the column tcam[camno].marker[i].br_pix_val=int(fb[row*framewidth+col]); //save the value } } } } } The blocking (or blobbing) and search algorithm yields the estimated location of the brightest pixel in the image. This is passed to a specialized array-growth region growing algorithm which dynamically expands a region around the suggested brightest pixel to include all pixels that are within a threshold of brightness to the brightest. The region growing algorithm then computes the center of mass from the list of pixel coordinates, which are then passed to the PD and target location routines. void region_grow(unsigned char * src, unsigned short* dest, int w, int h, int b_r, int b_c, double* c_r, double* c_c){ //need to do an expansion from the brightest point. //this is sorta a random-access op - which is bad. unsigned short fill = 0xff00; int n = 0; short r, c; int i, p; unsigned char thresh = 20 ; unsigned char brightest = src[w*b_r + b_c]; g_rows[n] = b_r; g_cols[n] = b_c; n++; int sta = 0; int end = 0; int lim = sizeof(g_rows)/sizeof(int); while(n < lim && n > sta){ //loop through all the new points, adding to the set as we go. end = n; for(i=sta; i < end; i++){ r = g_rows[i]; c = g_cols[i]; r++; //down if(r >= 0 && r < h && c >= 0 && c < w && n < lim){ p = r*w +c; if(brightest - src[p] < thresh){ src[p] = 0; dest[p] = fill; g_rows[n] = r; g_cols[n] = c; n++; } } r -= 2; //up. if(r >= 0 && r < h && c >= 0 && c < w && n < lim){ p = r*w +c; if(brightest - src[p] < thresh){ src[p] = 0; dest[p] = fill; g_rows[n] = r; g_cols[n] = c; n++; } } r++; //center c++; //to the right. if(r >= 0 && r < h && c >= 0 && c < w && n < lim){ p = r*w +c; if(brightest - src[p] < thresh){ src[p] = 0; dest[p] = fill; g_rows[n] = r; g_cols[n] = c; n++; } } c-=2; //to the left. if(r >= 0 && r < h && c >= 0 && c < w && n < lim){ p = r*w +c; if(brightest - src[p] < thresh){ src[p] = 0; dest[p] = fill; g_rows[n] = r; g_cols[n] = c; n++; } } }//end loop over past points. sta = end; } //calculate the center of mass. double cm_r = 0; double cm_c = 0; for(i=0; i<n; i++){ cm_r += g_rows[i]; cm_c += g_cols[i]; } cm_r /= n; cm_c /= n; *c_r = cm_r; *c_c = cm_c; //printf("point: %f %f %d \n", cm_r, cm_c, g_frame++); int cm_r_i, cm_c_i; cm_r_i = (int)cm_r; cm_c_i = (int)cm_c; if(cm_c_i >= 0 && cm_c_i < w && cm_r_i >= 0 && cm_r_i < h) dest[cm_r_i*w + cm_c_i] = 0xffff; } And that is, roughly, the entirety of the video tracking program! (Most of the rest of the code deals with the firewire bus and other less interesting details.) We conclude with a picture of the whole setup in the office. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{648} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Section 3 - Video tracking and host computer controlWith the microcontroller done, we then moved to controlling it via a video-tracking computer. At this point, we had created a simple program for testing out parallel port control of the light's three axes using the keyboard (tilt, pan, and shutter). This program was split into two files, a main, and a set of subroutines that could then be called and compiled into the full video tracking program. It uses libparapin to abstract interaction with the parallel port in userspace.First, the main loop, which is very simple: #include "parallelout.h" #include <stdio.h> #include <stdlib.h> #include <unistd.h> char g_main_loop ; int main(int argc, char *argv[]) { g_main_loop = 1; char c; parallel_setup(); while(1){ c = fgetc(stdin); interpret_cmd(c); } } Second, the parallel port controller. This uses a thread and circular queue to provide asynchronous, non-blocking control of the communications channel. Non-blocking is critical, as the program waits a small period between low-high transition of the interrupt pin (pin 4) for the MSP430 to read the status of the three lines. #include <stdio.h> #include <stdlib.h> #include <unistd.h> #include <parapin.h> #include <pthread.h> #include "parallelout.h" char g_q[1024]; //queue for the commands. int g_q_rptr; //where to read the next command from. int g_q_wptr; //where to put the next command double g_velPan; double g_velTilt; void stepstep(void){ int i = 0; for(i=0; i<20000; i++){ set_pin(LP_PIN[4]); clear_pin(LP_PIN[4]); set_pin(LP_PIN[5]); clear_pin(LP_PIN[5]); set_pin(LP_PIN[5]); clear_pin(LP_PIN[5]); } } void velstep(int n){ //printf("velstep %d\n", n); clear_pin(LP_PIN[4]); if(n&0x1) set_pin(LP_PIN[2]) ; else clear_pin(LP_PIN[2]); if(n&0x2) set_pin(LP_PIN[3]) ; else clear_pin(LP_PIN[3]); set_pin(LP_PIN[4]); //leave it up, so the msp430 knows it is a velocity command. } void openShutter(){ printf("opening shutter\n"); clear_pin(LP_PIN[4]); set_pin(LP_PIN[2]); set_pin(LP_PIN[3]); set_pin(LP_PIN[4]); clear_pin(LP_PIN[4]); //clear the trigger to indicate a shutter command. } void closeShutter(){ printf("closing shutter\n"); clear_pin(LP_PIN[4]); clear_pin(LP_PIN[2]); clear_pin(LP_PIN[3]); set_pin(LP_PIN[4]); clear_pin(LP_PIN[4]); //clear the trigger to indicate a shutter command. } void smallShutter(){ printf("small shutter\n"); clear_pin(LP_PIN[4]); clear_pin(LP_PIN[2]); set_pin(LP_PIN[3]); set_pin(LP_PIN[4]); clear_pin(LP_PIN[4]); //clear the trigger to indicate a shutter command. } void stopMirror(){ printf("stop mirror\n"); clear_pin(LP_PIN[4]); set_pin(LP_PIN[2]); clear_pin(LP_PIN[3]); set_pin(LP_PIN[4]); clear_pin(LP_PIN[4]); //clear the trigger to indicate a shutter command. } void parallel_setup(){ if (pin_init_user(LPT1) < 0) exit(0); pin_output_mode(LP_DATA_PINS | LP_SWITCHABLE_PINS); clear_pin(LP_PIN[2]); clear_pin(LP_PIN[3]); clear_pin(LP_PIN[4]); pthread_t thread1; //start the queue-servicing thread. pthread_create ( &thread1, NULL, pq_thread, NULL ); } void interpret_cmd(char cmd){ //these codes don't make much sense unless you are //controlling from a keyboard. switch(cmd){ case 'w': velstep(0); g_velPan-=1.0; break; //pan to right (looking at but of light) case 'a': velstep(1); g_velTilt+=1.0; break; //tilt toward. case 's': velstep(2); g_velPan+=1.0; break; //pan to left case 'd': velstep(3); g_velTilt-=1.0; break; //tilt away case 'o': openShutter(); break; case 'c': closeShutter(); break; case 'x': smallShutter(); break; case ' ': stopMirror(); g_velPan=0; g_velTilt=0; break; } } void usleep(int us){ timespec ts; ts.tv_sec = 0; ts.tv_nsec = us * 1000; nanosleep(&ts, NULL); } extern int g_main_loop ; void* pq_thread(void* a){ while(g_main_loop){ if(g_q_wptr > g_q_rptr){ char cmd = g_q[g_q_rptr % sizeof(g_q)]; g_q_rptr++; interpret_cmd(cmd); } usleep( 200 ); // run at max 500hz update. // the msp430 takes about 125us to service the parallel port irq. } return (void*)0; } void enqueue(char cmd){ //this should be sufficiently atomic so there is no thread contention. g_q[g_q_wptr % sizeof(g_q)] = cmd; g_q_wptr++; } Then, we worked on the video tracking program. I will omit the some of the noncritical sections involving the firewire (ieee1394), Xv (video display) and X11 (window manager) calls, as the whole program is long, ~1000 lines. Below is 'main' -- see the comments for a detailed description. int main(int arc, char *argv[]){ int i; double t1, t2, t3, t4; t1 = t2 = t3 = t4 = 0.0; signal(SIGINT, cleanup); //trap cntrl c signal(SIGPIPE, cleanup); //turn off output buffering for ttcp! //setvbuf(stdout,(char*)NULL,_IONBF,0); //init buffers for old tracking... for(int i=0; i<4; i++){ g_buffer[i] = (short*)malloc(640*480*sizeof(short)); } g_averagefb = (int*)malloc(640*480*sizeof(int)); g_velfb = (int*)malloc(640*480*sizeof(int)); g_lastfb = (unsigned char*)malloc(640*480); g_trackedfb = (unsigned char*)malloc(640*480); for(i=0; i < 640*480; i++){ g_averagefb[i] = 0; } //Step -2: set up threads (the display runs on a seperate thread // to keep from blocking the iscochronous recieve channel // and hence causing the frame rate to drop. pthread_mutex_init(&g_dispthread_mutex, NULL); pthread_cond_init(&g_dispthread_cond, NULL); //STEP -1: init the parallel port for control of mirror (this also starts that thread) parallel_setup(); //Step 0: small shutter so we can track the light easily. smallShutter(); //Step 0.5: move the mirror to the close left (from but of light) for calibration //for reference (from the viewpoint of the cord end of the light): // pan left : s // pan right: w // tilt toward: a // tilt away: s // small shutter: x // open shutter: o // closed shutter: c // stop mirrors : <space> for(i=0; i<10; i++){ enqueue('s'); //to the left if you are looking at the but of the light. enqueue('a'); //the tilt axis has far fewer steps for full range than enqueue('s'); // the pan axis hence requires a much higher velocity - enqueue('s'); // so enqueue more 's'. enqueue('s'); enqueue('s'); } //Step 1: Open ohci and assign a handle to it. //================================================================================================================== init_cards(); //Step 2: Get the camera nodes and describe them as we find them. //================================================================================================================== init_cams(); //Step 3: Setup Capture //================================================================================================================== setup_cams(); //Step 4: Start sending data //================================================================================================================== start_iso_transmission(); //start the other thread. pthread_t thread1; pthread_attr_t attr; pthread_attr_init(&attr); pthread_create( &thread1, &attr, display_thread, 0 ); //Main event loop while(g_main_loop==true){ for( i=0; i<numCameras; i++){ if(dc1394_dma_single_capture(&camera[i]) != DC1394_SUCCESS){ fprintf(stderr, "dma1394: Failed to capture from cameras\n"); cleanup(0); } } t2=get_time(); for( i=0; i<numCameras; i++){ //display_frames_old(i); display_frames(i); /*if((g_frame%60) < 15){ velstep(0); }else if((g_frame%60) < 45){ velstep(2); }else { velstep(0); } */ if(dc1394_dma_done_with_buffer(&camera[i]) != DC1394_SUCCESS){ fprintf(stderr, "dma1394: Can't release dma bufer\n"); } } if(g_frame % 60 == 0){ printf("frame dt: %f (%f) track time %f (%f)\n", t2-t4, 1/(t2-t4), tracktime, 1/(tracktime)); } //start with the state machine for the calibration -- if(g_frame == CALIB_0){ enqueue(' '); //stop it printf("!!assuming that the mirror reached it's limit!!\n"); for( i=0; i<3; i++){ //now that we have put the mirror into a corner, give it velocity // to move to the center of the FOV so that we may turn on // feedback-based tracking. enqueue('w'); //to the left if you are looking at the but of the light. enqueue('d'); enqueue('w'); //again, pan motor has many more steps/range than tilt enqueue('w'); enqueue('w'); enqueue('w'); enqueue('w'); enqueue('w'); enqueue('w'); } } if(g_frame == CALIB_1){ enqueue(' '); //stop it printf("!!assuming light is centered now!!\n"); } if(g_frame == CALIB_2){ enqueue('x'); } t4 = t2; g_frame++; } cleanup(0); return 0; } Our tracking algorithm periodically opens and closes the shutter on the light. It is impossible to track a target based on brightness or even pattern detection, since the light is so bright it is impossible to image what it hits and what it does not with our cameras of limited dynamic range. (The human eye, of course, has far better dynamic range.) During the period when the light is off, we wait for the camera shutter speed to stabilize, then average the brightest spot over 10 consecutive frames to obtain a target position. Then, the shutter is opened, and visual feedback is used with a simple PD controller to guide the light to the target. When the device is deployed, we will make the update non-periodic and purely contingent on the detection of motion or of decreased solar cell output. See below for the thread that implements this logic, as well as blits the image onto the screen. void* display_thread(void* ptr ){ make_window(); while(g_main_loop){ if(pthread_cond_wait(&g_dispthread_cond, &g_dispthread_mutex) == 0){ pthread_mutex_unlock(&g_dispthread_mutex); double t1 = get_time(); g_first_frame=false; //convert into the XV format (this seems very inefficient to me...) for(unsigned int i=0; i< g_framewidth*g_frameheight; i++){ g_fb[i] = g_trackedfb[i]+ 0x8000; } double c_r, c_c; new_track(0, &tcam[0], g_trackedfb, g_framewidth, g_frameheight, CONTRAST_MIN, SEARCHR, GAUSSDROPOFF, NUMBER_OF_MARKERS, &c_r, &c_c); xv_image=XvCreateImage(display, info[adaptor].base_id, format_disp, (char*)g_fb, g_framewidth, g_frameheight*numCameras); XvPutImage(display, info[adaptor].base_id, window, gc, xv_image, 0, 0, g_framewidth, g_frameheight*numCameras, 0, 0, g_windowwidth, g_windowheight); free(xv_image); //do some dumb control (finally!) // initially, guide the light to the center of the screen. if(g_frame > CALIB_1 && g_frame <= CALIB_2){ g_target_c = 320.0; g_target_r = 240.0; servo_mirror(c_c, c_r); //get it stuck on the center! } int time = g_frame - CALIB_2; // below is the *main loop* for cycling the shutter open/close if(g_frame > CALIB_2){ if(time % 300 < 240){ servo_mirror(c_c, c_r); } if(time % 300 == 240){ enqueue('c'); enqueue(' '); } if(time % 300 >= 260 && time % 300 < 280 ){ g_target_c += c_c; g_target_r += c_r; } if(time % 300 == 280){ enqueue('x'); g_target_c /= 20.0; g_target_r /= 20.0; } } double t2 = get_time(); tracktime = t2 - t1 ; } //normalize_com(NUMBER_OF_MARKERS); XFlush(display); while(XPending(display)>0){ XNextEvent(display,&xev); switch(xev.type){ case ConfigureNotify: g_windowwidth=xev.xconfigure.width; g_windowheight=xev.xconfigure.height; break; case KeyPress: switch(XKeycodeToKeysym(display,xev.xkey.keycode,0)){ case XK_q: case XK_Q: g_main_loop = false; //cleanup(0); break; } break; } } //XPending } if ((void *)window != NULL){ XUnmapWindow(display,window); } fprintf(stderr,"dma1394: Unmapped Window.\n"); if (display != NULL){ XFlush(display); } return (void*) 0; } The PD controller uses very pessimistic values for the coefficients, as we discovered that the timing resolution on out older linux computer is low - about 5ms. This means that if too many velocity step commands are sent to the parallel port thread at one time, it will get backlogged, which will induce a phase-shift between control and actuation of velocity. Hence, the light must move rather slowly, on the order of one velocity step on each axis per frame. Again, below. void servo_mirror(double c_c, double c_r ){ double dc = c_c - g_target_c; //for now assume that we want to stabilize in double dr = c_r - g_target_r; // the center. double vgain = 8.0 ; double pgain = 1.0/80.0; int lim = 1; double c = dc + g_velPan*vgain ; int ccmd = 0; int rcmd = 0; if(c > 0){ for(int i=0; i<c*pgain && i < lim; i++){ enqueue('w'); ccmd --; } } if(c < 0){ for(int i=0; i<c*-1.0*pgain && i < lim; i++){ enqueue('s'); ccmd ++; } } vgain *= 1.5; //tilt mirror moves quicker! double r = dr + g_velTilt*vgain; if(r>0){ for(int i=0; i<r*pgain && i < lim; i++){ enqueue('d'); rcmd--; } } if(r<0){ for(int i=0; i<r*-1.0*pgain && i < lim; i++){ enqueue('a'); rcmd++; } } //this for debugging loop stability problems in matlab. //printf("%f %f %d %f %f %d\n", dc, g_velPan*vgain, ccmd, dr, g_velTilt*vgain, rcmd); //if(dr + g_velTilt*vgain > 0) enqueue('d'); OLD //if(dr + g_velTilt*vgain < 0) enqueue('a'); } Our video tracking algorithm first uses a tree-like algorithm to quickly and robustly search for the brightest region in the scene; we presume, somewhat simplistically, that this will be the target. When the device is put into use with an actual monkey cage, we'll surround the camera with high-intensity infrared LEDs to effectively illuminate a retroreflector placed on the monkey's head. Below is the code which performs this computation. //make a blur matrix //void blur(frame_info* frame, unsigned char * fb, int framewidth, int downsamp, int downsamp_w, int downsamp_h){ void blur(int camno, track_cam* tcam, unsigned char* fb, int framewidth, int downsamp_r, int downsamp_c, int downsamp_w, int downsamp_h){ //initialize contrasts for(int m=0; m<downsamp_r * downsamp_c; m++){ tcam[camno].frame.sum[m]=0; tcam[camno].frame.contr_min[m]=255; tcam[camno].frame.contr_max[m]=0; } for(int k=0; k<downsamp_r; k++){ for(int row=k*downsamp_h; row<k*downsamp_h+downsamp_h; row++){ for(int j=0; j<downsamp_c; j++){ for(int col=j*downsamp_w; col<j*downsamp_w+downsamp_w; col++){ tcam[camno].frame.sum[j+(k*downsamp_c)]+=int(fb[row*framewidth+col]); if(int(fb[row*framewidth+col])>tcam[camno].frame.contr_max[j+(k*downsamp_c)]){ tcam[camno].frame.contr_max[j+(k*downsamp_c)]=int(fb[row*framewidth+col]); //introducing a contrast check. } if(int(fb[row*framewidth+col])<tcam[camno].frame.contr_min[j+(k*downsamp_c)]){ tcam[camno].frame.contr_min[j+(k*downsamp_c)]=int(fb[row*framewidth+col]); //introducing a contrast check } } } } } } //blob_search function //search through the sum matrix and find the brightest sums //void blob_search(frame_info* frame, marker* marker, int num_markers, int contrast_min){ void blob_search(int camno, track_cam* tcam, int num_markers, int contrast_min, int downsamp_r, int downsamp_c){ //frame->num_blobs=0; //innocent until proven guilty for(int i=0; i<num_markers; i++){ int blob_val=0; for(int m=0; m<downsamp_r*downsamp_c; m++){ if(tcam[camno].frame.sum[m]>blob_val && tcam[camno].frame.contr_max[m]-tcam[camno].frame.contr_min[m]>contrast_min){ //has to have a big contrast to be a blob (CONTRAST is user defined macro) blob_val=tcam[camno].frame.sum[m]; //the new max' tcam[camno].marker[i].downsamp_loc=m; //the sum integer (0-255) //frame->num_blobs++; } } tcam[camno].frame.sum[tcam[camno].marker[i].downsamp_loc]=0; //kill the one we just found so we can find the next biggest one. } } //brightest_pix_search function //search through the blobs for the brightest pixel //void brightest_pix_search(unsigned char * fb, frame_info* frame, marker* marker, int num_markers, int framewidth, int downsamp, int downsamp_w, int downsamp_h){ void brightest_pix_search(unsigned char * fb, int camno, track_cam* tcam, int num_markers, int framewidth, int downsamp_r, int downsamp_c, int downsamp_w, int downsamp_h){ //br_pix_info[0] is the row //br_pix_info[1] is the col //br_pix_info[2] is the value for(int i=0; i<num_markers; i++){ tcam[camno].marker[i].br_pix_val=0; //always has to start low for(int row=int(floor(tcam[camno].marker[i].downsamp_loc/downsamp_c))*downsamp_h; row<int(floor(tcam[camno].marker[i].downsamp_loc/downsamp_c))*downsamp_h+downsamp_h; row++){ for(int col=tcam[camno].marker[i].downsamp_loc%downsamp_c*downsamp_w; col<tcam[camno].marker[i].downsamp_loc%downsamp_c*downsamp_w+downsamp_w; col++){ if(int(fb[row*framewidth+col])>tcam[camno].marker[i].br_pix_val){ //if it is greater than the brightest pixel then store its info tcam[camno].marker[i].br_pix_row=row; //save the row tcam[camno].marker[i].br_pix_col=col; //save the column tcam[camno].marker[i].br_pix_val=int(fb[row*framewidth+col]); //save the value } } } } } The blocking (or blobbing) and search algorithm yields the estimated location of the brightest pixel in the image. This is passed to a specialized array-growth region growing algorithm which dynamically expands a region around the suggested brightest pixel to include all pixels that are within a threshold of brightness to the brightest. The region growing algorithm then computes the center of mass from the list of pixel coordinates, which are then passed to the PD and target location routines. void region_grow(unsigned char * src, unsigned short* dest, int w, int h, int b_r, int b_c, double* c_r, double* c_c){ //need to do an expansion from the brightest point. //this is sorta a random-access op - which is bad. unsigned short fill = 0xff00; int n = 0; short r, c; int i, p; unsigned char thresh = 20 ; unsigned char brightest = src[w*b_r + b_c]; g_rows[n] = b_r; g_cols[n] = b_c; n++; int sta = 0; int end = 0; int lim = sizeof(g_rows)/sizeof(int); while(n < lim && n > sta){ //loop through all the new points, adding to the set as we go. end = n; for(i=sta; i < end; i++){ r = g_rows[i]; c = g_cols[i]; r++; //down if(r >= 0 && r < h && c >= 0 && c < w && n < lim){ p = r*w +c; if(brightest - src[p] < thresh){ src[p] = 0; dest[p] = fill; g_rows[n] = r; g_cols[n] = c; n++; } } r -= 2; //up. if(r >= 0 && r < h && c >= 0 && c < w && n < lim){ p = r*w +c; if(brightest - src[p] < thresh){ src[p] = 0; dest[p] = fill; g_rows[n] = r; g_cols[n] = c; n++; } } r++; //center c++; //to the right. if(r >= 0 && r < h && c >= 0 && c < w && n < lim){ p = r*w +c; if(brightest - src[p] < thresh){ src[p] = 0; dest[p] = fill; g_rows[n] = r; g_cols[n] = c; n++; } } c-=2; //to the left. if(r >= 0 && r < h && c >= 0 && c < w && n < lim){ p = r*w +c; if(brightest - src[p] < thresh){ src[p] = 0; dest[p] = fill; g_rows[n] = r; g_cols[n] = c; n++; } } }//end loop over past points. sta = end; } //calculate the center of mass. double cm_r = 0; double cm_c = 0; for(i=0; i<n; i++){ cm_r += g_rows[i]; cm_c += g_cols[i]; } cm_r /= n; cm_c /= n; *c_r = cm_r; *c_c = cm_c; //printf("point: %f %f %d \n", cm_r, cm_c, g_frame++); int cm_r_i, cm_c_i; cm_r_i = (int)cm_r; cm_c_i = (int)cm_c; if(cm_c_i >= 0 && cm_c_i < w && cm_r_i >= 0 && cm_r_i < h) dest[cm_r_i*w + cm_c_i] = 0xffff; } And that is, roughly, the entirety of the video tracking program! (Most of the rest of the code deals with the firewire bus and other less interesting details.) We conclude with a picture of the whole setup in the office. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Section 2: Microcontroller & microsteppingAs mentioned before, we chose MSP430F5438 100-pin 16 bit microcontroller because it offers sufficient timers and speed for our problem and because we were both familiar with the architecture. Four 16-bit timers are used to control microstepping mirror tilt and pan, since the stepper motors have two phases. The microcontroller only needs to provide digital signals; current is provided through H-bridge drivers in the control board of the mm-150 - the DIPs with heat sinks below.Opposite sides of the H-bridge are driven via hex inverters; hence, we only have to supply two PWM signals per motor, one per phase. Setting the PWM duty cycle to 50% will set the motor phase current to zero; by vectoring the duty cycle proportional to the sine and cosine of theta, where theta is the orientation of the motor * number of poles of the stepper, you can control microstepping. That, of course, is simplified; in practice, there are many details to contend with, namely:
We approximated sine and cosine, needed to vector the stepper motor phase currents, in fixed-point arithmetic first in C on linux - where the results could be plotted in matlab - before converting to MSP430 code. Since the trigonometric functions are repeating, we only need a polynomial approximation of sine from 0 to pi/2. The taylor series for sine is sin(x) = x - x^3/3! + x^5/5! - x^7/7! ...; a quick check in matlab showed that the first three terms are enough to get an accurate approximation in the domain of interest. The MSP430 does not have division, however, so we approximated 1/3! = 1/6 as (1/8 + 1/32 + 1/128) and 1/5! = 1/120 as 1/128; division by powers of two is possible with right bit-shift operations. We chose base 11 (5 bits whole, 11 bits fractional) representation to avoid overflow: if 2^11 -> 1, we need to represent (pi/2)^5 -> 9.5 ; ceil(log_2(9.5)) = 4 (plus one bit for safety). The C program below shows this test. #include <stdio.h> char qsin(short i){ //i goes from 0 pi/2 base 11 or... // 0 to 3217 unsigned int cube, fifth, result; cube = (i*i) >> 11; cube = (cube*i) >> 11; //max = 7937 fifth = (cube*i) >> 11; fifth = (fifth*i) >> 11; // max = 19585 //our approximation to sine based on taylor series: //original: sin(x) = x - x^3/3! + x^5/5! //sin(x) = x - x^3*(1/8+1/32+1/128) + x^5*(1/128) result = (unsigned int)i - ((cube >> 3) + (cube >> 5) + (cube >> 7)) + (fifth >> 7); //result is base 11. need it to be base 7. result = result >> 4; if(result > 127) result = 127; return (char)result; } //this is tricky, as it involves shifts, x-inversions, and y-inversions. //but it all makes sense if you plot out the respective functions. char isin(short i){ // i is base 2^11 //but we accept 0 to 2*pi or 12867 if(i >= 0 && i < 3217) return qsin(i); else if(i >= 3217 && i < 6434) return qsin(6434 - i); else if(i >= 6434 && i < 9651) return -1*qsin(i - 6434); else if(i >= 9651 && i < 12867) return -1*qsin(12867 - i); else return 0; } char icos(short i){ // i is base 2^11 //but we accept 0 to 2*pi or 12867 if(i >= 0 && i < 3217) return qsin(3217 - i); else if(i >= 3217 && i < 6434) return -1*qsin(i - 3217); else if(i >= 6434 && i < 9651) return -1*qsin(9651 - i); else if(i >= 9651 && i < 12867) return qsin(i - 9651); else return 0; } int main(void){ short i; for(i=0; i<12867; i++){ printf("%d\t%f\t%d\t%d\n", i, ((float)i)/2048.0, (int)(isin(i)), (int)(icos(i))); } return 0; } We compiled and ran this program on the command line: gcc integer_trig.c ./a.out > test.txt Then we imported the data into matlab and plotted (Actual double floating-point sine and cosine are plotted on the same axis as thin black and magenta lines, respectively) Later, we had to change the naive standard implementation of multiply to assembly to properly implement the fixed-point arithmetic - the MSP430's standard library did not implement the 16x16 multiply followed by shift correctly (it only keeps the bottom 16 bits). Note: this assembly function is for use with Code-Composer Studio, available from the Texas Instruments website. It seems that the IAR compiler uses different assembly syntax. ;******************************************************************************* .cdecls C,LIST,"msp430x54x.h" ; Include device header file ;------------------------------------------------------------------------------- .text ; Progam Start ;------------------------------------------------------------------------------- ;;.sect "mply_11" ;;.asmfunc "mply_11" .global mply_11 ;; this MUST BE PRECEDED BY TABS !!!!! mply_11: PUSH SR ; DINT ; turn off interrupts here. NOP ; required after DINT MOV.W R12, &MPY ; load the first operand. MOV.W R13, &OP2 ; load the second operand & start multiplication. MOV.W &RESLO, R12 ; low to R12 (this is the return value) MOV.W &RESHI, R13 ; high to R13 RRA.W R12 ; 1 RRA.W R12 ; 2 RRA.W R12 ; 3 RRA.W R12 ; 4 RRA.W R12 ; 5 RRA.W R12 ; 6 RRA.W R12 ; 7 RRA.W R12 ; 8 RRA.W R12 ; 9 RRA.W R12 ; 10 RRA.W R12 ; 11 RLA.W R13 ; 1 RLA.W R13 ; 2 RLA.W R13 ; 3 RLA.W R13 ; 4 RLA.W R13 ; 5 ;; r14 can be clobbered across a function call, according to the msp430 ABI MOV.W #0x001f, R14 AND.W R14, R12 ; mask off all but the bottom 5 bits from RESLO ADD.W R13, R12 ; add (logical OR) the results. R12 is the 11-bit fixed point result. POP.W SR ; RETA ; return from subroutine. .end Note the MSP430 does not have an opcode for multiple arithmetic shifts, nor does it have code for logical shifts - hence the need for repeated shifts and bitmasks! #include <msp430x54x.h> #define INCR 1 #define PI2 (12868) //we use a 11 bit fixed-point representationf of motor angles. // 12867 = 2*pi*2^11. #define TIMER_SCL 128 #define SHUTTER_CLOSED 0 //defines used in the state-machine control of the shutter. #define SHUTTER_OPEN 1 #define SHUTTER_SMALL 2 //Start of Stepper Motor Program //ME270 Project short theta1 = 0; //the MSP430 is a 16-bit processor. short theta2 = 0; //hence, most datatypes should be 'short' for efficiency. short theta1_v = 0; //we cannot control the poition of the stepper motors directly, short theta2_v = 0; // since we only have 3 bits of control from the parallel port. // also, direct position control of postion would cause the stepper to miss steps // smooth position change and limited acceleration is guaranteed by controlling the velocity. short shutter_state = 0; // none of the steppers have encoders, // so we keep track of the shutter position here. short shutter_cmd ; //this is set in ISR (interupt service routine) // and read, and acted upon, in the main loop. short qsin(short i){ //i goes from 0 pi/2 base 11 or... // 0 to 3217 short cube, fifth, result; cube = mply_11(i,i); cube = mply_11(cube, i); fifth = cube; fifth = mply_11(fifth, i); fifth = mply_11(fifth, i); //our approximation to sine based on taylor series: //original: sin(x) = x - x^3/3! + x^5/5! //sin(x) = x - x^3/(8+32+128) + x^5/128 result = i - ((cube >> 3) + (cube >> 5) + (cube >> 7)) + (fifth >> 7); //result is base 11. need it to be base 7. (0 to 127) result = result >> 4; if(result > TIMER_SCL) result = TIMER_SCL; return (short)result; } // this is an even more simplified version of sin - // made in an attempt to make the microstepping smoother. // it turned out to not matter very much. to get very smooth stepping , // may have to develop an inverse model of the nonlinear stepper motors // ** quantitatively ** short qsin2(short i){ //i goes from 0 pi/2 base 11 or... // 0 to 3217 short cube, result; cube = mply_11(i,i); cube = mply_11(cube, i); //our approximation to sine based on taylor series: //original: sin(x) = x - x^3/3! + x^5/5! //sin(x) = x - x^3/(8+32+128) + x^5/128 result = i - (cube >> 3) ; //result is base 11. need it to be base 7. result = result >> 4; if(result > TIMER_SCL) result = TIMER_SCL; //maximum.. return (short)result; } short isin(short i){ // i is base 2^11 //but we accept 0 to 2*pi or 12867 if(i >= 0 && i < 3217) return qsin(i); else if(i >= 3217 && i < 6434) return qsin(6434 - i); else if(i >= 6434 && i < 9651) return -1*qsin(i - 6434); else if(i >= 9651 && i < 12867) return -1*qsin(12867 - i); else return 0; } short icos(short i){ // i is base 2^11 //but we accept 0 to 2*pi or 12867 if(i >= 0 && i < 3217) return qsin(3217 - i); else if(i >= 3217 && i < 6434) return -1*qsin(i - 3217); else if(i >= 6434 && i < 9651) return -1*qsin(9651 - i); else if(i >= 9651 && i < 12867) return qsin(i - 9651); else return 0; } //this interrupt is triggered by the parallel port. //because we only have 3 lines and need 8 commands, //after triggering (0 to 1 transition on PORT2.0 ), //the control program on the PC will either hold the pin up // (indicating a velocity step command) or drop it (indicating shutter/stop cmd). #pragma vector=PORT2_VECTOR __interrupt void port2_ISR (void) { //need to read the two pins to figure out which axis to change. short k; for(k=0; k<8; k++){ P9OUT ^= 0x4; } switch(P2IN & 0x7){ case 1: theta1_v += INCR; break; case 3: theta1_v -= INCR; break; case 5: theta2_v += INCR; break; case 7: theta2_v -= INCR; break; case 0: shutter_cmd = SHUTTER_CLOSED; break; case 2: shutter_cmd = SHUTTER_SMALL; break; case 6: shutter_cmd = SHUTTER_OPEN; break; case 4: theta1_v = 0; theta2_v = 0; break; } P2IFG = 0; //clear the interupt. } #pragma vector=TIMER1_A0_VECTOR __interrupt void timera1_ISR (void) { return; //if this vector is not here and the interupt is enabled, then the proc will crash! } // have to integrate the velocity at a consistent rate, // hence we pushed integration as well as the sine/cosine computation // into this timer interrupt. #pragma vector=TIMER1_A1_VECTOR __interrupt void timera11_ISR (void) { short ps, pc; P1OUT ^= 0xFF; //toggle P1 to indicate the update rate. (the led is there) TA1CTL = 0x0004; //reset counter TA1CTL = 0x0112; //turn back in interrupts. theta1 += theta1_v; theta2 += theta2_v; if(theta1 > PI2) theta1 -= PI2; if(theta1 < 0) theta1 += PI2; if(theta2 > PI2) theta2 -= PI2; if(theta2 < 0) theta2 += PI2; ps = isin(theta1)+TIMER_SCL; pc = icos(theta1)+TIMER_SCL; TA0CCR1 = ps; //update the counter (PWM output) registers. TA0CCR4 = pc; ps = isin(theta2)+TIMER_SCL; pc = icos(theta2)+TIMER_SCL; TA0CCR2 = ps; TA0CCR3 = pc; P1OUT ^= 0xFF; //toggle P1 to indicate the update rate. (the led is there) return; } //delay is used in moving the shutter. // too short, and the stepper motor controlling the shutter will skip steps! void delay(short time){ short k; short j = 0; for(k=0; k<time; k++){ j++; j++; } } void delay_long(short time){ short k,j,f; for(k=0; k<time; k++){ f = 0; for(j=0; j<100; j++){ f++; } } } // ideally, we would ramp the shutter velocity up and down to maximize speed // and minimize time - constant velocity works fine and fast. #define SHUTDLY 1600 void shutter_ccw(void){ P9OUT = 0x1; delay(SHUTDLY); P9OUT = 0x3; delay(SHUTDLY); P9OUT = 0x2; delay(SHUTDLY); P9OUT = 0x0; delay(SHUTDLY); } void shutter_cw(void){ P9OUT = 0x2; delay(SHUTDLY); P9OUT = 0x3; delay(SHUTDLY); P9OUT = 0x1; delay(SHUTDLY); P9OUT = 0x0; delay(SHUTDLY); } void shutter_open(void){ short i; if(shutter_state == SHUTTER_CLOSED){ //I was quite pleased to discover that the three shutters states // are exactly 5 full steps apart! for(i=0; i<5; i++){ shutter_ccw(); } } if(shutter_state == SHUTTER_SMALL){ for(i=0; i<5; i++){ shutter_cw(); } } shutter_state = SHUTTER_OPEN; } void shutter_close(void){ short i; if(shutter_state == SHUTTER_OPEN){ for(i=0; i<5; i++){ shutter_cw(); } } if(shutter_state == SHUTTER_SMALL){ for(i=0; i<10; i++){ shutter_cw(); } } shutter_state = SHUTTER_CLOSED; } void shutter_small(void){ short i; if(shutter_state == SHUTTER_OPEN){ for(i=0; i<5; i++){ shutter_ccw(); } } if(shutter_state == SHUTTER_CLOSED){ for(i=0; i<10; i++){ shutter_ccw(); } } shutter_state = SHUTTER_SMALL; } void main (void){ //SR = 0x02; short t1, t2, ps, pc; short k; WDTCTL = WDTPW + WDTHOLD; //stop the watchdog timer. // UCSCTL = Universal clock system control (registers). // sets the core clock of the device. _bis_SR_register(SCG0); //SR = SR | 0x40 ; // setup the digitally controlled oscillator. UCSCTL0 = 0x0700; //DCO = 5, MOD = 0 UCSCTL1 = 0x0060; //DCORSEL = 3, middle freq. UCSCTL2 = 0x101F; //FLL (frequency locked loop); doesnt matter here. UCSCTL4 = 0x0333; //select DCOCLK for all clock sources UCSCTL0 = 0x0900; //DCO = 9, MOD = 0 // DCO = internal high-frequency oscillator). //UCSCTL5 = 0x0000; // setup timer A (for controlling PWM outputs) TA0CCR0 = TIMER_SCL*2+1; //Timer A end pulse TA0CCR1 = TIMER_SCL; //Timer A start pulse TA0CCR2 = TIMER_SCL; //Timer A start pulse TA0CCR3 = TIMER_SCL; //Timer A start pulse TA0CCR4 = TIMER_SCL; //Timer A start pulse TA0CTL = 0x0110; //TASSEL = ACLK; input divider=1; MCx = count up mode; TA0CCTL0 = 0x0040; //sets the mode of the output: here=2, toggle/reset. // (produces pulses at 8Khz). TA0CCTL1 = 0x00C0; //output mode: toggle/set. TA0CCTL2 = 0x00C0; // same TA0CCTL3 = 0x00C0; // same TA0CCTL4 = 0x00C0; // same //setup timer B (for controlling theta & velocity updates). TA1CCR0 = 10000; //Timer A end pulse TA1CCR1 = 5000; //Timer A start pulse TA1CCR2 = 5000; //Timer A start pulse TA1CTL = 0x0004; TA1CTL = 0x0112; //TASSEL = ACLK; input divider=1; MCx = count up mode; TA1CCTL0 = 0x0050; //sets the mode of the output: here=2, toggle/reset. // (produces pulses at 8Khz). TA1CCTL1 = 0x00C0; //output mode: toggle/set. TA1CCTL2 = 0x00C0; // same P1DIR = 0x03; //P1.0 and P1.1 to output. (the LED) P1SEL = 0x00; P1OUT = 0; P8DIR = 0xFF; //for some reason Port 1 does not work for the dev board -- P8SEL = 0x7F; //hence, we switched over to Port 8, which also is connected // to the timers. // the P8SEL register selects the timer output as opposed to general purpose IO. //setup port2 (computer command via parallel port) interrupt. P2DIR = 0; //all inputs. P2IFG = 0; P2IE = 0x01; //enable interupts on P2.0 P2IES = 0; // low to high edge detect. _bis_SR_register(GIE | SCG0 ); //enable interrupts, dont go to sleep. P9DIR = 0x07; //test the shutter. first move all the way to the limit. // since we do not know the initial position. for(k=0; k<30; k++){ shutter_cw(); } shutter_ccw(); //step one out so we don't hit the limits later. shutter_state = SHUTTER_CLOSED; //this is where the init will leave it while(1){ //now just sit here waiting for a shutter command from the // parallel port ISR. if(shutter_state != shutter_cmd){ switch(shutter_cmd){ case SHUTTER_OPEN: shutter_open(); break; case SHUTTER_CLOSED: shutter_close(); break; case SHUTTER_SMALL: shutter_small(); break; } } } } We has some problem getting Port1 to work, hence had to use Port8 to get the PWM signals out -- see below. Note the shutter does not need to be microstepped and instead can be controlled as per a conventional stepper motor. The pins used are marked in yellow; pin 57 is a simple pulse output. Note that each PWM signal is generated from the same timer counter, hence they are synchronous (this is of course not necessary). Below are some examples of two phases of one motor output; in real life, of course, the PWM ratio continually changes. Below is the development board being probed to produce the plots above. We then used the pinouts of the NXP microcontrollers, intuited last time by probing their on-line function (specifically the auto-calibration sequence upon startup), to wire up a harness for external control of the H-bridges. Below is a picture of that (we removed the original microcontrollers to prevent contention), and the associated wiring labels.
The next task was to make a 5V to 3.2V regulator (the MSP430 only runs at 3.2V, max), nothing major just a LM317. See below. Finally, everything was wired together. The 3.2 V supply was jumpered, as the MSP430 USB programmer provided its own power. (Amazingly, the ultra low power MSP430 could run on power from the parallel port, too!) A level translator is needed to properly interface the 3.2V MSP430 to the 5V parallel port - we canibalized a spare JTAG adapter for this purpose. It was this that limited us to only 3 bits of control. And that, minus the difficulty we had getting the compiler working properly, is the entirety of the microcontroller part of the project. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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We approximated sine and cosine, needed to vector the stepper motor phase currents, in fixed-point arithmetic first in C on linux - where the results could be plotted in matlab - before converting to MSP430 code. Since the trigonometric functions are repeating, we only need a polynomial approximation of sine from 0 to pi/2. The taylor series for sine is sin(x) = x - x^3/3! + x^5/5! - x^7/7! ...; a quick check in matlab showed that the first three terms are enough to get an accurate approximation in the domain of interest. The MSP430 does not have division, however, so we approximated 1/3! = 1/6 as (1/8 + 1/32 + 1/128) and 1/5! = 1/120 as 1/128; division by powers of two is possible with right bit-shift operations. We chose base 11 (5 bits whole, 11 bits fractional) representation to avoid overflow: if 2^11 -> 1, we need to represent (pi/2)^5 -> 9.5 ; ceil(log_2(9.5)) = 4 (plus one bit for safety). The C program below shows this test. #include <stdio.h> char qsin(short i){ //i goes from 0 pi/2 base 11 or... // 0 to 3217 unsigned int cube, fifth, result; cube = (i*i) >> 11; cube = (cube*i) >> 11; //max = 7937 fifth = (cube*i) >> 11; fifth = (fifth*i) >> 11; // max = 19585 //our approximation to sine based on taylor series: //original: sin(x) = x - x^3/3! + x^5/5! //sin(x) = x - x^3*(1/8+1/32+1/128) + x^5*(1/128) result = (unsigned int)i - ((cube >> 3) + (cube >> 5) + (cube >> 7)) + (fifth >> 7); //result is base 11. need it to be base 7. result = result >> 4; if(result > 127) result = 127; return (char)result; } //this is tricky, as it involves shifts, x-inversions, and y-inversions. //but it all makes sense if you plot out the respective functions. char isin(short i){ // i is base 2^11 //but we accept 0 to 2*pi or 12867 if(i >= 0 && i < 3217) return qsin(i); else if(i >= 3217 && i < 6434) return qsin(6434 - i); else if(i >= 6434 && i < 9651) return -1*qsin(i - 6434); else if(i >= 9651 && i < 12867) return -1*qsin(12867 - i); else return 0; } char icos(short i){ // i is base 2^11 //but we accept 0 to 2*pi or 12867 if(i >= 0 && i < 3217) return qsin(3217 - i); else if(i >= 3217 && i < 6434) return -1*qsin(i - 3217); else if(i >= 6434 && i < 9651) return -1*qsin(9651 - i); else if(i >= 9651 && i < 12867) return qsin(i - 9651); else return 0; } int main(void){ short i; for(i=0; i<12867; i++){ printf("%d\t%f\t%d\t%d\n", i, ((float)i)/2048.0, (int)(isin(i)), (int)(icos(i))); } return 0; } We compiled and ran this program on the command line: gcc integer_trig.c ./a.out > test.txt Then we imported the data into matlab and plotted (Actual double floating-point sine and cosine are plotted on the same axis as thin black and magenta lines, respectively) Later, we had to change the naive standard implementation of multiply to assembly to properly implement the fixed-point arithmetic - the MSP430's standard library did not implement the 16x16 multiply followed by shift correctly (it only keeps the bottom 16 bits). Note: this assembly function is for use with Code-Composer Studio, available from the Texas Instruments website. It seems that the IAR compiler uses different assembly syntax. ;******************************************************************************* .cdecls C,LIST,"msp430x54x.h" ; Include device header file ;------------------------------------------------------------------------------- .text ; Progam Start ;------------------------------------------------------------------------------- ;;.sect "mply_11" ;;.asmfunc "mply_11" .global mply_11 ;; this MUST BE PRECEDED BY TABS !!!!! mply_11: PUSH SR ; DINT ; turn off interrupts here. NOP ; required after DINT MOV.W R12, &MPY ; load the first operand. MOV.W R13, &OP2 ; load the second operand & start multiplication. MOV.W &RESLO, R12 ; low to R12 (this is the return value) MOV.W &RESHI, R13 ; high to R13 RRA.W R12 ; 1 RRA.W R12 ; 2 RRA.W R12 ; 3 RRA.W R12 ; 4 RRA.W R12 ; 5 RRA.W R12 ; 6 RRA.W R12 ; 7 RRA.W R12 ; 8 RRA.W R12 ; 9 RRA.W R12 ; 10 RRA.W R12 ; 11 RLA.W R13 ; 1 RLA.W R13 ; 2 RLA.W R13 ; 3 RLA.W R13 ; 4 RLA.W R13 ; 5 ;; r14 can be clobbered across a function call, according to the msp430 ABI MOV.W #0x001f, R14 AND.W R14, R12 ; mask off all but the bottom 5 bits from RESLO ADD.W R13, R12 ; add (logical OR) the results. R12 is the 11-bit fixed point result. POP.W SR ; RETA ; return from subroutine. .end Note the MSP430 does not have an opcode for multiple arithmetic shifts, nor does it have code for logical shifts - hence the need for repeated shifts and bitmasks! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Section 1 : Reverse-engineering the light, part selectionRather than engineering our own articulated spotlight, we elected to buy a moving-mirror DJ light; creating our own light source would simply have taken too much time, and demanded optical experience that we lack. After a brief survey, we bought an Elekralite mm150 (moving mirror, 150W bulb) DJ light, one of the cheapest on the market ($650); despite this, it is very well constructed, as you will see below. The light was originally controlled through the stage-specific DMX bus, but the possibility of directly controlling the light through this was discarded after we learned that the resolution on each axis is only 8 bits (+- 127); given the large range of the pan mirror, this is insufficient for tracking. Hence we decided to reverse engineer the light to determine the best way to directly control the mirror and shutter.
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{647} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.linux-mag.com/id/7187 -- has a very interesting and very well applied analogy between programs and laws. I am inclined to believe that they really are not all that different; legalese is structured and convoluted the way it is because it is, in effect, a programming language for laws, hence must be precise and unambiguous. Furthermore, the article is well written and evidences structured and balanced thought (via appropriate references to the real world). And he uses Debian ;-) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Artificial Cerebellum for robot control:
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{640} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Misc. interesting pick & place robotics projects on the web:
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A friend has many Excel files that he converts to labels for affixing to packages to be shipped. To print the proper number of labels (rather than one label with Qty=20), he needs to duplicate rows in the source excel file based on the Qty column. If you export the excel file to XML, this script should do the trick (you'll have to import the resultant XML): #!/usr/bin/perl $narg = $#ARGV + 1; if( $narg ne 2 ){ print "please specify the file to read followed by the file to write on the command line\n"; }else{ $source = $ARGV[0]; $dest = $ARGV[1]; local( $/) ; $/ = ""; open(FH, "< $source"); open(FHO, "> $dest"); $j = <FH>; #slurp the entire file into one string. # look for the header - if( $j =~ s/(.*?)<Sheet1>/<Sheet1>/s){ print FHO $1 ; } while ($j =~ /(<Sheet1>.*?<\/Sheet1>)/gs ){ $newl = $1; if( $newl =~ /<Qty>(\d+)<\/Qty>/ ){ $qty = $1; $newl =~ s/<Qty>\d+<\/Qty>/<Qty>1<\/Qty>/ ; for( $g=0; $g<$qty; $g++){ print FHO $newl ; } } } print FHO "</dataroot>" ; # assume that the footer is always this close FH; close FHO; }not very complicated, but worth posting, I guess. More examples on the internet = better ;-) Note that I hard-coded to split on <Sheet1> -- check your XML files!! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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My comments on this blog post, preseved here for posterity: I agree with William’s first point, spectrum is ‘owned’ by everybody; the government’s only purpose is to regulate it so that it remains an effective communication medium. Like the bandwidth that it uses, the communication system is optimally owned by users, hence it is a bad idea to auction off segments of spectrum for exclusive use by corporations. Examine at what happened to the 2.4 GHz band, an area where water absorption is high and most households have a 1kw noise generator (microwave oven): EVERYONE USES IT because it is FREE and OPEN, no licenses required. Just look at all the innovation created for this band: 802.11, bluetooth, ZigBee, cordless phones, wireless remotes, and others. If 802.11 was in the 700-1GHz band someone or a company could easily make long-distance wireless repeaters & mesh-network nodes, sell them to consumers, and everyone could SIP for FREE without paying Verizon / ATT etc. This could set it up as a pyramid scheme, where to get on the network you simply have to buy a mesh node repeater, and with it became part of the ‘corporation’ which provided your wireless services. A certain part of the purcase & access price would, of course, need to go to pay for backbone connections, service, matenance and extending connection to remote areas, but this too can be solved and managed efficiently with something like 1 phone = 1 share. With coprotations, you either have redundancy (two networks w/ twice as many cell towers) or a monopoly; neither are economically efficient. A re-allocation of prime wireless spectrum back to the correct owners - the citizens - would spur American Innovation greatly and simultaneously cut communication costs. The technology is changing, and the policy should too! Anyway, i’m sick of paying $0.10 for 100 bytes of data (txt messages) when audio data costs ~1/500th that. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-18004384[0] A synaptic memory trace for cortical receptive field plasticity.
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PMID-9448252[0] The acquisition of skilled motor performance: Fast and slow experience-driven changes in primary motor cortex
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“Seeing†through the tongue: cross-modal plasticity in the congenitally blind
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{634} |
ref: RAzsa-2008.01
tags: nAChR nicotinic acetylchoine receptor interneurons backpropagating LTP hippocampus
date: 10-08-2008 17:37 gmt
revision:0
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PMID-18215234[0] Dendritic nicotinic receptors modulate backpropagating action potentials and long-term plasticity of interneurons.
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PMID-18322089[0] Dopamine Receptor Activation Is Required for Corticostriatal Spike-Timing-Dependent Plasticity
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{631} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16563737[0] The computational neurobiology of learning and reward
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PMID-11257908[0] Multiple Reward Signals in the Brain
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PMID-10731222[0] Reward processing in primate orbitofrontal cortex and basal ganglia
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{627} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-9530495[0] Cortical plasticity: from synapses to maps
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PMID-8423485[0] Plasticity in the frequency representation of primary auditory cortex following discrimination training in adult owl monkeys
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{620} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17035544[0] Dopaminergic control of sleep-wake states ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-11506661[0] Parallel cortico-basal ganglia mechanisms for acquisition and execution of visuomotor sequences - a computational approach.
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PMID-18614035[0] Neuronal ensemble bursting in the basal forebrain encodes salience irrespective of valence.
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PMID-12383782[0] Reward, motivation, and reinforcement learning.
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{183} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17237780[0] Switching from automatic to controlled action by monkey medial frontal cortex.
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PMID-8985875 Neural information transferred from the putamen to the globus pallidus during learned movement in the monkey.
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{67} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16271465[] The basal ganglia: Learning new tricks and loving it
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{611} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-18667540[0] Learning a novel myoelectric-controlled interface task.
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{609} |
ref: -0
tags: differential dynamic programming machine learning
date: 09-24-2008 23:39 gmt
revision:2
[1] [0] [head]
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{289} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11395017[0] Neuronal correlates of motor performance and motor learning in the primary motor cortex of monkeys adapting to an external force field
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PMID-17690132 Disrupted prediction-error signal in psychosis: evidence for an associative account of delusions.
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{604} |
ref: Pastalkova-2008.09
tags: hippocampus Buzsaki sequences
date: 09-22-2008 21:25 gmt
revision:1
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PMID-18772431[0] Internally generated cell assembly sequences in the rat hippocampus.
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http://www.clinicaltrials.gov/ct2/show/NCT00558766?cond=Parkinson+Disease&rank=4 Salient points:
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It is not obvious how to run an external command in ocaml & get it's output from stdin. Here is my hack, which simply polls the output of the program until there is nothing left to read. Not very highly tested, but I wanted to share, as I don't think there is an example of the same on pleac let run_command cmd = let inch = Unix.open_process_in cmd in let infd = Unix.descr_of_in_channel inch in let buf = String.create 20000 in let il = ref 1 in let offset = ref 0 in while !il > 0 do ( let inlen = Unix.read infd buf !offset (20000- !offset) in il := inlen ; offset := !offset + inlen; ) done; ignore(Unix.close_process_in inch); if !offset = 0 then "" else String.sub buf 0 !offset ;; Note: Fixed a nasty string-termination/memory-reuse bug Sept 10 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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http://www.cs.colostate.edu/eeg/links.html
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PMID-15858046[] Redundancy and Synergy of Neuronal Ensembles in Motor Cortex
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{329} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17234689[0] Volitional control of neural activity: implications for brain-computer interfaces (part of a symposium)
humm.. this paper came out a month ago, and despite the fact that he is much older and more experienced than i, we have arrived at the same conclusions by looking at the same set of data/papers. so: that's good, i guess. ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-11081826 EMG activation patterns during force production in precision grip. III. Synchronisation of single motor units.
Dr. hepp-Raymond himself seems to be a prolific researcher, judging from his pubmed search results. e.g.:
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Robots & others designed & made at the Tokyo Institute of Technology (from the Hirose / Fukushima Robotics lab)
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Robotics Research at Carnegie Mellon University (CMU):
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http://www.dana.org/news/cerebrum/detail.aspx?id=3066 -- great article, with a well thought out, delicate treatment of the ethical/moral/ legal issues created by the interaction between the biological roots of violence (or knowlege thereof) and legal / social systems. He posits that there must be a continuum between ratinoal free will and irrational, impulsive violent behavior, with people biased to both by genetics, development, traumatic head injury, and substance abuse (among others). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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images/588_1.pdf -- Good lecture on LDA. Below, simple LDA implementation in matlab based on the same: % data matrix in this case is 36 x 16, % with 4 examples of each of 9 classes along the rows, % and the axes of the measurement (here the AR coef) % along the columns. Sw = zeros(16, 16); % within-class scatter covariance matrix. means = zeros(9,16); for k = 0:8 m = data(1+k*4:4+k*4, :); % change for different counts / class Sw = Sw + cov( m ); % sum the means(k+1, :) = mean( m ); %means of the individual classes end % compute the class-independent transform, % e.g. one transform applied to all points % to project them into one plane. Sw = Sw ./ 9; % 9 classes criterion = inv(Sw) * cov(means); [eigvec2, eigval2] = eig(criterion); See {587} for results on EMG data. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Below, emg classification by computing the autoregressive coefficients and feeding them into linear discriminant analysis (LDA). LDA code from here; data in myopen svn. Nine classes of movement in the data, 4 repetitions of each. The input data is 16-dimensional: 4 AR coefficients per 4 channels. This is consistent with Blair Lock's thesis. For reference, here is an imagesc() of the raw coefficients (the 4 different color bands correspond to the 4 different channels): | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Myopen amplifiers & analog/digital filters & NLMS are working properly! Below, a recording from my deltiod as I held my arm up: (only one EMG channel active, ground was my knee)) Yellow traces are raw inputs from ADC, blue are the output from the IIR / adaptive filters; hence, you only see 8 of the 16 channels. Read from bottom to top (need a -1 in some opengl matrix somewhere...) Below, the system with no input except for free wires attached to one channel (and picking up ambient noise). For this channel, NLMS could not remove the square wave - too many harmonics - but for all other channels the algorthim properly removes 60hz interference :) Now, let me clean this EEG paste off my shoulder & leg ;) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{438} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
I needed to evaluate different fixed-point filters & implement them in a way which would more-or-less easily transfer to hand-coded blackfin assembly. Hence, I wrote a small program in C to test two likely alternatives: a 5th order elliptic filter, with 82db stopband rejection, or a 4th order elliptic, with 72 db stopband rejection. see {421} also, and this useful reference. (also at {584}) UPDATE: this filter is not stable/ suitable for the 1.15 signed fraction format of the blackfin processor. As in the reference, you must use a non-canonic form which puts the numerator before the denominator. I had a great deal of difficulty trying to determine why the output of the Direct Form II filter was giving crap results with poles/zeros designed for lowpass operation. The reason appears to be that the Direct FormII filter requires dynamic range > +-1 for the w's (first feedback section). The numerator / b coefficients for these highpass filters is usually [1 -2 1] - a highpass - which returns 0 when passed saturated data. See the signal flowchart below. The program for implementing these filters as cascaded biquad/ triquads follows. The method of generating the filter coefficients is in the comments. Note that the filter coefficients for the triquad exceed and absolute magnitude of 2, hence the triquad implementation has a fixed-point format of s.2.13 (one bit sign, 2 bits whole part, 13 bits fractional part). The biquad has s.1.14 format - one bit for the whole part. Also note that I incorporated a scale factor of x2 into the first stage, and x4 into the second stage, as the output of the ADC is only 12 bits and we can afford to expand it to the full range. The filter responses, as designed (in floating point). 5th order is on the left, 4th on the right. The filter output to white noise, in the time domain. 5th order has, in this impementation, a 'softer shoulder', which i do not think is appropriate for this application. The same output in fourier space, confirming the softer shoulder effect. this was actually kinda unespected .. I thought an extra pole/zero would help! I guess the triquad & lower res coefficient quantization is less efficient.. ? #include <stdio.h> // gcc -Wall filter_test.c -o filter_test //need to test fixed-point filtering in C (where it is easy) //before converting to hand-coded assembly. short w1_1[2]= {0,0}; short w1_2[3]= {0,0,0}; short w2_1[2]= {0, 0}; short w2_2[2]= {0, 0}; /* filter 1: 5th order. biquad then a triquad. [B1, A1] = ellip(5,0.2,84, 6/31.25); %84db = 14 bits. rb = roots(B1); ra = roots(A1); pa1 = poly(ra(1:2)); pa2 = poly(ra(3:5)); pb1 = poly(rb(1:2)); pb2 = poly(rb(3:5)); b1_1 = round(pb1*sqrt(B1(1))*2^15) a1_1 = round(pa1* 2^14)* -1 b1_2 = round(pb2*sqrt(B1(1))*2^15) a1_2 = round(pa2*2^13)*-1 % triquad. */ //biquad1: short b1_1[3] = {1199, 87, 1199}; short a1_1[2] = {24544 -14085}; //triquad1: short b1_2[4] = {1199, 2313, 2313, 1199}; short a1_2[3] = {18090, -14160, 3893}; /*filter 2: can be implemented by 2 biquads. [B3, A3] = ellip(4,0.5,72, 6/31.25); rb = roots(B3); ra = roots(A3); pa1 = poly(ra(1:2)); pa2 = poly(ra(3:4)); pb1 = poly(rb(1:2)); pb2 = poly(rb(3:4)); b2_1 = round(pb1*sqrt(B3(1))*2^15) a2_1 = round(pa1* 2^14)* -1 b2_2 = round(pb2*sqrt(B3(1))*2^16) %total gain = 8. a2_2 = round(pa2*2^14)*-1 */ //biquad2: short b2_1[3] = {2082, 914, 2082}; short a2_1[2] = {24338, -13537}; //biquad2 (2): short b2_2[3] = {4163, 6639, 4163}; short a2_2[2] = {24260, -9677}; int madd_sat(int acc, short a, short b){ //emulate the blackfin //signed-integer mode of operating. page 567 in the programming reference. int c; long long l, lo, hi; lo = (long long)(-2147483647); hi = (long long)(2147483647); c = (int)a * (int)b; l = (long long)acc + (long long)c; if(l < lo) l = lo; if(l > hi) l = hi; acc = (int)l; return acc; } //need to deal with samples one at a time, as they come in, from different channels //need to quantize the coeficients //need to utilize a biquad topology / filter structure. // (this is simple - just segregate the poles. order 5 filter req. biquad & triquad. short filter_biquad(short in, short* a1, short* b1, short* w1){ int acc; short out, w; //in varies from 0 to 0x0fff - ADC is straight binary. (0 to 4095). unsigned. acc = madd_sat(0, in, 16384); acc = madd_sat(acc, w1[0], a1[0]); acc = madd_sat(acc, w1[1], a1[1]); w = (short)(acc >> 14); //hopefully this does sign-extended shift. acc = madd_sat(0, w, b1[0]); acc = madd_sat(acc, w1[0], b1[1]); acc = madd_sat(acc, w1[1], b1[0]); //symmetry. out = (short)(acc >> 14); w1[1] = w1[0]; w1[0] = w; return out; } short filter_triquad(short in, short* a2, short* b2, short* w2){ int acc; short out, w; //this one is a bit different, as the coefficients are > 2 in the denom. // hence have to normalize by a different fraction. //multiply the numerator by 4 for a net gain of 8. acc = madd_sat(0 , in, 8192); acc = madd_sat(acc, w2[0], a2[0]); acc = madd_sat(acc, w2[1], a2[1]); acc = madd_sat(acc, w2[2], a2[2]); w = acc >> 13; acc = madd_sat(0 , w, b2[0]); acc = madd_sat(acc, w2[0], b2[1]); acc = madd_sat(acc, w2[1], b2[1]); acc = madd_sat(acc, w2[2], b2[0]); //symmetry. out = (short)(acc >> 13); w2[2] = w2[1]; w2[1] = w2[0]; w2[0] = w; return out; } int main( int argv, char* argc[]){ //read the samples from stdin. int in, out; while(scanf("%d", &in)){ //compare 5th and 4th order filters directly. in -= 2048; out = filter_biquad(in, a1_1, b1_1, w1_1); out = filter_triquad(out, a1_2, b1_2, w1_2); printf("%d ", out); out = filter_biquad(in, a2_1, b2_1, w2_1); out = filter_biquad(out, a2_2, b2_2, w2_2); printf("%d ", out); } return 0; } // gcc -Wall filter_test.c -o filter_test // cat filter_test_in.dat | ./filter_test > filter_test_out.dat Below, some matlab code to test the filtering. % make some noisy data. x = randn(2000, 1); x = x .* 1000; x = x + 2048; i = find(x >= 4096) x(i) = 4095; i = find(x < 0); x(i) = 0; x = round(x); fid = fopen('filter_test_in.dat', 'w'); for k = 1:length(x) fprintf(fid, '%d ', x(k)); end fprintf(fid, 'quit'); fclose(fid); Here is a blackfin assembly implementation of the filter, Note the filter weights (i0) and delays (i1, i2) need to be on two different cache/sram banks, or the processor will stall. Also note that , as per the second diagram above, the delays for biquad 1 output are synonymous to the delays for biquad 2 input, hence they are only represented once in memory. /* directform 1 biquad now, form II saturates 1.15 format. operate on the two samples in parallel (both in 1 32bit reg). r0 x(n) -- the input from the serial bus. r1 x(n-1) (yn-1) -- ping-pong the delayed registers. r2 x(n-2) (yn-2) -- do this so save read cycles. r3 y(n-1) (xn-1) r4 y(n-2) (xn-2) r5 b0 b1 -- (low high) r6 a0 a1 i0 reads the coeficients into the registers; it loops every 32 bytes (16 coef, 4 biquads) i1 reads the delays. it loops every 640 bytes = 10 delays * 4 bytes/delay * 16 stereo channels. only increments. i2 writes the delays, loops every 640 bytes. also only increments. if i1 and i2 are dereferenced in the same cycle, the processor will stall -- each of the 1k SRAM memory banks has only one port. format of delays in memory: [x1(n-1) , x1(n-2) , x2(n-1) aka y1(n-1) , x2(n-2) aka y1(n-2) , x3(n-1) aka y2(n-1) , x3(n-2) aka y2(n-2) , x4(n-1) aka y3(n-1) , x4(n-2) aka y3(n-2) , y4(n-1) , y4(n-2) ] --that's 10 delays, 4 bytes each. */ r5 = [i0++] || r1 = [i1++]; a0 = r0.l * r5.l , a1 = r0.h * r5.l || r6 = [i0++] || [i2++] = r0; a0 += r1.l * r5.h, a1 += r1.h * r5.h || r2 = [i1++] ; a0 += r2.l * r5.l, a1 += r2.h * r5.l || r3 = [i1++] ; a0 += r3.l * r6.l, a1 += r3.h * r6.l || r4 = [i1++] ; r0.l = (a0 += r4.l * r6.h), r0.h = (a1 += r4.h * r6.h) (s2rnd) || [i2++] = r1; r5 = [i0++] || [i2++] = r0; a0 = r0.l * r5.l, a1 += r0.h * r5.l || r6 = [i0++] || [i2++] = r3; a0 += r3.l * r5.h, a1 += r3.h * r5.h || r1 = [i1++]; a0 += r4.l * r5.l, a1 += r4.h * r5.l || r2 = [i1++]; a0 += r1.l * r6.l, a1 += r1.h * r6.l; r0.l = (a0 += r2.l * r6.h), r0.h = (a1 += r2.h * r6.h) (s2rnd); r5 = [i0++] || [i2++] = r0; a0 = r0.l * r5.l, a1 = r0.h * r5.l || r6 = [i0++] || [i2++] = r1; a0 += r1.l * r5.h, a1 += r1.h * r5.h || r3 = [i1++]; a0 += r2.l * r5.l, a1 += r2.h * r5.l || r4 = [i1++]; a0 += r3.l * r6.l, a1 += r3.h * r6.l; r0.l = (a0 += r4.l * r6.h), r0.h = (a1 += r4.h * r6.h) (s2rnd); r5 = [i0++] || [i2++] = r0; a0 = r0.l * r5.l, a1 += r0.h * r5.l || r6 = [i0++] || [i2++] = r3; a0 += r3.l * r5.h, a1 += r3.h * r5.h || r1 = [i1++]; a0 += r4.l * r5.l, a1 += r4.h * r5.l || r2 = [i1++]; a0 += r1.l * r6.l, a1 += r1.h * r6.l; r0.l = (a0 += r2.l * r6.h), r0.h = (a1 += r2.h * r6.h) (s2rnd); [i2++] = r0; //save the delays. [i2++] = r1; //normally this would be pipelined. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{584} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
images/584_1.pdf -- this is a highly useful paper, but is no longer available on the author's website. For the good of all, i post it here. These may also have utility:
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{582} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Bjork has a special place in my heart - and not only because of stuff like this: http://www.youtube.com/watch?v=jX9y6AA5oOo ;) When I was in college - not so far back as Post, but before Selmasongs - we used to play a lot of pool. Not so much that we didn't get any work done, but enough that we started getting good. Near the end of that year we filmed a bunch of games & made a music video set to Underworld's remix of "Human Behavior". I don't know what happened to the actual end product, but I do clearly recall my mom complaining about the repetitive beats while I was cutting the shots so the ball collisions would align with snare/bass hits. Sometime later that year I was blown away by the real deal, the "All is full of love" music video, projected on the side of the art museum at ~ 2am when the mind is labile... Bjork & her music pervaded that period for me. I've found that music can 'tag' periods of life for me, such that when I remember the music first then the events. This winter it was Interpol, last fall was Metric, spring 2007 was Arca (you *have* to hear them!). When me and my brother went to Portugal for a few weeks we found two Pixies mix tapes in the tiny car that my friend generously let us use. Hence, Frank Black soaked our ears while the incredible Portuguese sun soaked our skin. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{580} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Notes from installing Ocaml via GODI on a Debian Lenny system (oh, dependencies!):
Final list: apt-get install libpcre3-dev libatlas-sse2-dev liblapack-dev libglut3-dev libxmu-dev libgtk2.0-dev libgtkgl2.0-dev | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{579} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
oldies but goodies:
Both are in Debian of course :) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{502} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Outline: The goal is to use a nRF24L01 to make an asymmetrical, bidirectional link. The outgoing bandwidth should be maximized, ~1.5mbps, and the incoming bandwidth can be much smaller, ~17kbps, though on both channels we want guaranteed latency, < 4ms for the outgoing data, and < 10ms for the incoming data. Furthermore, the processor that is being used to run this, a blackfin BF532, does not seem to play well when both SPI DMA is enabled and most CPU time is being spent in SPORT ISR reading samples & processing them. Fortunately, the SPI port and SPORT can be run synchronously (provided the SPI port is clocked fast enough), allowing the processor to run one 'thread' e.g. no interrupts. It seem that with high-priority interrupts, the DMA engine is not able to service the SPI perfectly, and without DMA, data comes out of the SPI in drips and drabs, and cannot keep the radio's fifo full. Hence, must program a synchronous radio controller, where states are stored in variables and not in the program counter (PC register, saved upon interrupt, etc). As in other postings on the nRF24L01, the plan is to keep the transmit fifo full for most of the 4ms allowed by the free-running pll, then transition back into either standby-I mode, or send a status packet. The status packet is always acknowledged by the primary receiver with a command packet, and this allows both synchronization and incoming bandwidth. Therefore, there are 4 classes of transfers:
screenshot of the derived code working (yea, my USB logic analyzer only runs on windows..yeck): old versions: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{577} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
I found this on my computer tucked away into a dusty corner. Such fascinating information should not be left hidden - | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{511} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
simple backups to an external usb disk: rsync --verbose --progress --stats --recursive --times --perms --links --del --ignore-errors /home/tlh24/ /media/usb0/ note:
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{575} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
these guys use the blackfin, too: http://www.surveyor.com/ check out the board - very clean and neat! The robot itself - with tank treads and a radio - costs $465 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{576} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
why do threads suck in ocaml? because join calculus is better! (well maybe) http://jocaml.inria.fr/ example of jocaml working well (indeed, faster than everything else): http://eigenclass.org/hiki/wide-finder-conclusions | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{227} |
ref: notes-0
tags: expectation maximization EM clustering autosorting
date: 06-16-2008 19:40 gmt
revision:5
[4] [3] [2] [1] [0] [head]
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so, I coded up the EM algorithm - it was not hard, though i did have to put the likelihood calculation in C++ because i couldn't figure out how to vectorize it properly. It fits the clusters pretty well, but it does not tell you how many clusters there are! clustering with 5 underlying gaussians: plot of the log-likelihood of fitted gaussian mixtures vs. number of gaussians: the code is in subversion, of course. James has code for gibbs-sampling to the correct number of components! Here is an example of the output - it quickly removes the unnecessary gaussian components: images/227_4.pdf -- original CEM (classification expectation maximization) paper, 1992, by Celeux and Govaert. Note that CEM with no variance estimation and gaussian clusters is the same as k-means, see {224}. See also http://klustakwik.sourceforge.net/ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{572} |
ref: bookmark-0
tags: memory supermemo leraning psychology Hermann Ebbinghaus
date: 05-08-2008 15:25 gmt
revision:0
[head]
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http://www.wired.com/medtech/health/magazine/16-05/ff_wozniak -- wonderful article, well written. Leaves you with a sense of Piotr Wozniak (SuperMemo's inventor) crazy, slightly surreal, impassioned, purposeful, but self-regressive (and hence fundamentally stationary) life.
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{571} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{567} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Ocaml books / references:
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{565} |
ref: Walker-2005.12
tags: algae transfection transformation protein synthesis bioreactor
date: 03-21-2008 17:22 gmt
revision:1
[0] [head]
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Microalgae as bioreactors PMID-16136314
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{375} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
This is from the CSR reference design for the BlueCore5 chip. They also note that you have to pay attention to the aspect ratio of the vias - with laser drilling, this means that they needed a 63um prepreg between layers 1 and 2 (ground), with start copper thickness of 18um. PTH = plated-through-hole. (refers to a type of via) For 0.8mm BGA, you can loosen the design rules to the following: "
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{551} |
ref: notes-0
tags: DNA transfection yasuda experiment8
date: 03-17-2008 20:11 gmt
revision:2
[1] [0] [head]
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"
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{546} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.sgvsarc.com/demo.htm
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{552} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
From the New Yorker, Feb 25:
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cairo-ocaml is broken in Debian (lenny) in that it is incompatible with liblabl-gtk2 in the repository; to compile ocaml programs (e.g. Geoproof) that depend on it, you need to :
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{536} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{545} |
ref: notes-0
tags: telecommunications FCC wireless regulation government
date: 02-26-2008 04:18 gmt
revision:2
[1] [0] [head]
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http://news.zdnet.com/2010-1035_22-6231729.html
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{544} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
How much carbon dioxide (CO2) is released to heat the water for a 5-minute shower?
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{542} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
windows is retarded: http://www.jsifaq.com/SF/Tips/Tip.aspx?id=10986 I got this error installing service pack 2 on a triple-boot MacBook.
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{539} |
ref: -0
tags: laser power concentration GFP mCherry calibration
date: 02-01-2008 19:22 gmt
revision:0
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above, a set of curves for determining fluorescent protein concentration (GFP & mCherry) from received photon count in a two-photon microscope. Unfortunately, these depend on efficiency & power of the entire setup, so the curve is non-transferable to other microscopes. one pass of mCherry @ 5x dilution did not seem the same as the others -- perhaps the reading light was left on? % given a series of files, % calculate a quadratic to convert intensity to concentration. % assumed formula: % green intensity = background + const*[GFP]*laserpower^2 % red intensity = background + const*[RFP]*laserpower^2 + % const2[GFP]*laserpower^2 close all cd('/var/ftp/tim_hanson/T002-0130_08/solutions'); basename = 'T002-gfp-100xdil-'; int_gfp100 = IntensReadfile('T002-gfp-100xdil-', 11, 2); int_gfp10 = IntensReadfile('T002-gfp-10xdil-', 8, 2); int_mcherry10 = IntensReadfile('T002-mcherry-10xdil-', 7, 2); int_mcherry5 = IntensReadfile('T002-mcherry-5xdil-', 7, 2); int_mcherry5_2 = IntensReadfile('T002-mcherry-5xdil2-', 7, 2); int_mcherry5_4 = IntensReadfile('T002-mcherry-5xdil4-', 6, 2); bg_green = (int_gfp100(1) + int_gfp10(1))/2; bg_red = (int_mcherry10(1) + int_mcherry5(1)... + int_mcherry5_2(1) + int_mcherry5_4(1))/4; powers = (0:0.1:1).^2; int_gfp_all = [int_gfp100-bg_green, (int_gfp10-bg_green)/10]; pow_gfp_all = [powers(1:11), powers(1:8)]; green_intensity_perpower = pow_gfp_all'\int_gfp_all' green_lab = ['green intensity = ' num2str(green_intensity_perpower) ' * power^2 + ' ... num2str(bg_green) ' (photons/10us) @ 8.7 ug/ml conc. gfp']; figure plot(sqrt(powers(1:11)), int_gfp100, 'o'); hold on plot(sqrt(powers(1:8)), (int_gfp10-bg_green)/10+bg_green, 'or'); plot(sqrt(pow_gfp_all), pow_gfp_all * green_intensity_perpower + bg_green, 'gx'); legend('100x dilution','10x dilution','parabolic fit'); title('intensity of gfp vs. laser power normalized to 100x dilution') xlabel(green_lab); int_mch_all = [(int_mcherry10-bg_red)/10, (int_mcherry5-bg_red)/20, ... (int_mcherry5_2-bg_red)/20, (int_mcherry5_4-bg_red)/20]; pow_mch_all = [powers(1:7), powers(1:7), powers(1:6), powers(1:7)]; red_intensity_perpower = pow_mch_all'\int_mch_all' red_lab = ['red intensity = ' num2str(red_intensity_perpower) ' * power^2 + ' ... num2str(bg_red) ' (photons/10us) @ 8.7 ug/ml conc. mcherry']; figure plot(sqrt(powers(1:7)), (int_mcherry10-bg_red)/10+bg_red, 'o'); hold on plot(sqrt(powers(1:7)), (int_mcherry5-bg_red)/20+bg_red, 'or'); plot(sqrt(powers(1:7)), (int_mcherry5_2-bg_red)/20+bg_red, 'ok'); plot(sqrt(powers(1:6)), (int_mcherry5_4-bg_red)/20+bg_red, 'om'); plot(sqrt(pow_mch_all), pow_mch_all * red_intensity_perpower + bg_red, 'gx'); legend('10x dilution','5x dilution','5x dilution(2)','5x dilution(4)','parabolic fit'); title('intensity of mcherry vs. laser power normalized to 100x dilution') xlabel(red_lab) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{538} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{537} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{530} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{532} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.biotele.com/Delgado.htm
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{533} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.nccommerce.com/NR/rdonlyres/CC5488D0-9B3E-4C32-BEF4-4B88630CE3F1/0/BusinessNotes.pdf ; linked from NC department of commerce business center
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{531} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.uspto.gov/go/pac/doc/general/
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{528} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{388} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{526} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
I'm posting my comments about http://flock.com/ here just in case they are removed from the actual site This is all very interesting. I just downloaded it, and flock seems to work well. I'm probably not going to use it unless there is some demonstrable technical superiority (e.g. leaks less memory than firefox), as the social sites just distract me from getting work done. Anyway, I have a question: how are you going to make money? How are you paying the developers? If you are not and it is all OSS, where is the source? It seems like the VC's are just throwing money away for the (hypothetical) good of the social-network crowd. Or, rather, you are indirectly funding the popularity of sites that flock makes it easy to get at. Are these sites (e.g. facebook) paying you? Wait -- flock allows you to look at content and not the ads. They are not paying you. Perhaps you are moving along the lines of Opera, and intending to get people addicted to flock to a degree that they demand it on their mobile devices. Mobile devices are closed (for now .. check google), hence you can make money licensing software to phone manufacturers. I imagine that you'll have to rewrite the Mozilla core to do this (unless phones become significantly more powerful - not likely, they are battery devices. ) Mozilla is (L)GPL - you'll have to release the source. To the best of my knowledge, with non-physical goods money can only be made from gradients in knowledge (pun.. intended), therefore you will have to keep the source closed. If this is the case, you'll be able to make money (on this, i don't know what else you have planned) for a while, and when you can no longer, I hope you open the source like netscape. Technically, though, excellent job! your website is also very pretty! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{377} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
the contenders:
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{94} |
ref: bookmark-0
tags: particle_filter unscented monte_carlo MCMC
date: 12-11-2007 16:46 gmt
revision:2
[1] [0] [head]
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{522} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
from http://www.fcc.gov/oet/info/rules/part15/part15-9-20-07.pdf :
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{478} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{514} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
spectrum options for broadband wireless
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{513} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
BBC deploys perl-on-rails in their highly restricted production environment.
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{507} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://edboyden.org/05.09.boyden.html (2005) -- or just http://edboyden.org/
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{506} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
So, you want to write inline assembly for the blackfin processor, perhaps to speed things up in a (very) time-constrained environment? Check this first:
Nobody seems to have a complete modifier list for the blackfin, which is needed to actually write something that won't be optimized out :) here is my list --
examples:
Constraints for particular machines - does not include blackfin.
; register operands ; d (r0..r7) ; a (p0..p5,fp,sp) ; e (a0, a1) ; b (i0..i3) ; f (m0..m3) ; B ; c (i0..i3,m0..m3) CIRCREGS ; C (CC) CCREGS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{504} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.camsig.co.uk/ -- blackfin is hot like chernobyl. 1" sq 600mhz webserver etc.
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{500} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
This was written for the plik-l mailing list, Nov 16 2007 I actually had a bit of an argument yesterday with my dentist, no less, about global warming:
Mostly I'd have to agree with the dentist - the oil is going to be burned eventually, because it is just such a cheap source of energy. We are going to have to deal with the consequences. However, for coal - of which we have a far greater supply, and is considerably more dangerous / expensive to obtain - there is good reason to search for alternatives, and putting a tax on oil/natural gas now fund development of alternatives is probably very future-responsible, and will shift the energy climate so we relinquish coal (and maybe some oil) earlier, resulting in less CO2 in the atmosphere. There are infinitely many things more worthy/long-range responsible than the war, but our leaders have not touched on that. Correct me if I'm wrong, but there is little evidence that they even measured the worth of all alternatives, and decided rationally, based on integrating (over time and path probability) best-of-present knowledge of benefits and consequences. Or maybe they decided rationally, but with the worth of alternatives measured *personally*. It is this that truly angers me. Bayes for president 2008! Comments:
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{503} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
quote: Consumers also pay high taxes for telecommunication services, averaging about 13 percent on some telecom services, similar to the tax rate on tobacco and alcohol, Mehlman said. One tax on telecom service has remained in place since the 1898 Spanish-American War, when few U.S. residents had telephones, he noted. "We think it's a mistake to treat telecom like a luxury and tax it like a sin," he said. from: The internet could run out of capacity in two years comments:
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{404} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
page 6 on the spec sheet. 55 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{497} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://dotpublic.istumbler.net/
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{394} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
so, you want to control the LEDs on a BF537-STAMP board? You'll need a linux box with a serial port, then will need to do a few things:
set serverip 192.168.1.149 set ipaddr 192.168.1.200 tftpboot 0x1000000 blink bootelf 0x1000000
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{493} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17614134[0] Equalization filters for multiple-channel electromyogram arrays.
____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{448} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Adobe acrobat reader 7.0 leaks a prodigious amount of memory on my linux system (Debian Etch, stable). However, some pdfs will only open in acroread, so i want to keep the application around for occasional use. Because of the memory leaks, it is not good to have it loaded by default by iceweasel / firefox (evince or xpdf is better). To do this:
that's it! :) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{491} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://forums.debian.net/viewtopic.php?t=21166 yea, what's going on here? copy of message: Hello, so, I've tried to compile the most simple of programs with g++. I'm on debian 'testing', a recent install. I have separate /home and / partitions, where the / partition was wiped & reinstalled after i deleted most of /usr/bin (doh!!!!). Anyway, I was running stable, but now am running testing. Most of my settings on /home transfered over .. admirably well! But, I cannot compile :( :( after trying to compile my favorite software (kicad, yum), and failing, i turned back to a test: #include <stdio.h> int main(void){ printf("hello, world\n"); }tried to compile with : g++ hello_world.cpp -g -v -Wall -o hello resulting in this noise: Using built-in specs. Target: i486-linux-gnu Configured with: ../src/configure -v --enable-languages=c,c++,fortran,objc,obj-c++,treelang --prefix=/usr --enable-shared --with-system- zlib --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --enable-nls --with-gxx-include-dir=/usr/include/c++/4.1.3 --program-suffix=-4.1 --enable-__cxa_atexit --enable-clocale=gnu --enable-libstdcxx-debug --enable-mpfr --enable-checking=release i486-l inux-gnu Thread model: posix gcc version 4.1.3 20070831 (prerelease) (Debian 4.1.2-16) /usr/lib/gcc/i486-linux-gnu/4.1.3/cc1plus -quiet -v -D_GNU_SOURCE hello_world.cpp -quiet -dumpbase hello_world.cpp -mtune=generic -auxb ase hello_world -g -Wall -version -o /tmp/ccIXOF5F.s ignoring nonexistent directory "/usr/local/include/i486-linux-gnu" ignoring nonexistent directory "/usr/lib/gcc/i486-linux-gnu/4.1.3/../../../../i486-linux-gnu/include" ignoring nonexistent directory "/usr/include/i486-linux-gnu" #include "..." search starts here: #include <...> search starts here: /usr/include/c++/4.1.3 /usr/include/c++/4.1.3/i486-linux-gnu /usr/include/c++/4.1.3/backward /usr/local/include /usr/lib/gcc/i486-linux-gnu/4.1.3/include /usr/include End of search list. GNU C++ version 4.1.3 20070831 (prerelease) (Debian 4.1.2-16) (i486-linux-gnu) compiled by GNU C version 4.1.3 20070831 (prerelease) (Debian 4.1.2-16). GGC heuristics: --param ggc-min-expand=100 --param ggc-min-heapsize=131072 Compiler executable checksum: 50856c9e65492124a77f9baaf4dc8b80 as -V -Qy -o /tmp/ccOGkgre.o /tmp/ccIXOF5F.s GNU assembler version 2.18 (i486-linux-gnu) using BFD version (GNU Binutils for Debian) 2.18 /usr/lib/gcc/i486-linux-gnu/4.1.3/collect2 --eh-frame-hdr -m elf_i386 --hash-style=both -dynamic-linker /lib/ld-linux.so.2 -o hello /us r/lib/gcc/i486-linux-gnu/4.1.3/../../../../lib/crt1.o /usr/lib/gcc/i486-linux-gnu/4.1.3/../../../../lib/crti.o /usr/lib/gcc/i486-linux-g nu/4.1.3/crtbegin.o -L/usr/lib/gcc/i486-linux-gnu/4.1.3 -L/usr/lib/gcc/i486-linux-gnu/4.1.3 -L/usr/lib/gcc/i486-linux-gnu/4.1.3/../../.. /../lib -L/lib/../lib -L/usr/lib/../lib /tmp/ccOGkgre.o -lstdc++ -lm -lgcc_s -lgcc -lc -lgcc_s -lgcc /usr/lib/gcc/i486-linux-gnu/4.1.3/c rtend.o /usr/lib/gcc/i486-linux-gnu/4.1.3/../../../../lib/crtn.o ok looks good - try: ./hello bash: ./hello: Permission denied then: gdb hello Starting program: /home/tlh24/hello /bin/bash: /home/tlh24/hello: Permission denied /bin/bash: /home/tlh24/hello: Success success? not quite. ok, try another thing : ldd hello ldd: exited with unknown exit code (126) what is going on here? ideas? cat hello yeilds ELF4 file with some GCC strings + crt stuff. looks okay, yes executable bits set ???? | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{487} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
here is the final, concluding, email i sent to nordic semiconductor concerning my 'troubles' with their chip. I post it here in hopes that it may help somebody else out there via the magic of the internet. See {485} for the development of the mode-switch solution (2) and {484} for the dropped packet investigation. Hi xxx, Ok, i figured out both of my problems:
As a result, I'm getting 99.99 % reliability on bidirectional bandwidth of 1.39mbps PTX->PRX and 18.3kbps PRX->PTX. So, I'm a happy person :) :) Hence, I don't have to try another radio solution. Just wanted to pass the information along in case it would help your other customers. cheers, Tim Hanson | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{485} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Problem: switching modes on the nordic radios. see also {486}
solution-
present performance: txed packets = 118513 rxed packets = 118218 (note: computer has seen 118512 packets ) (and 118414 status packets, ratio: 0.999165 ) (note: 'stage ratio 0.997511 )(this includes code validation) now, if i boost the SPI clock on the bridge up to 5 mhz (headstage clock still running at 8.25mhz) to eliminate race-case (?) & add in 16 data packets before the status packets, perfection: txed packets = 44151 rxed packets = 44151 (note: computer has seen 750583 packets ) (and 44152 status packets, ratio: 1.000023 ) (note: 'stage ratio 1.000000 )after adding separate counters for TXed status and TXed data packets: txed packets = 808640 rxed packets = 50538 txed status packets = 50540 (note: computer has seen 808639 packets, ratio : 0.999999 ) (and 50540 status packets, ratio: 1.000000 ) (note: 'stage ratio 0.999960 )yay!! almost no dropped packets!! This equates to :
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{486} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
here is an email I wrote to nordic semiconductor technical support concerning switching reception/transmission modes. see also {487} & {485} Hello, I've been having problems with switching modes on the nRF24L01. I want to implement a asymmetric bidirectional link, where there is a periodic (every ~36ms) time when the primary transmitter sends a status packet, then listens for a 32-byte command packet from the primary receiver. The command packet is for conveying configuration information, etc. I am driving both radios with blackfin DSPs using the built-in SPI port @ 4mhz, and am very careful with the CSN signal. The shock-burst feature is not enabled. Unidirectional transfer works great - I get nearly 0% dropped packets when the primary transmitter & receiver never change modes, up to a rate of about 1.5mbps. Of course, I am careful not to let the radio stay in TX mode for more than 4 ms - every 3ms i give it a 'break' by de-asserting CE. But bidirectional does not work reliably. Here is my procedure, on the primary transmitter side, for sending a status packet then changing from TX to RX & back to TX, with the initial condition that CE is asserted:
The process on the primary receiver is basically the same, but inverted. Upon receiving a packet of the correct type, it switches to transmit mode, sends off a packet, waits for the TX_DS interrupt, and switches back to RX mode. Like I said, when the transmitter and receiver never switch modes, the packets always get through without any corruption. When they switch roles for one packet, only ~ 78% get through, making the status packet -> command packet reply about 62% reliable. This is when the radio is only sending status packets - hence mostly it is in what the datasheet calls 'standby-II mode'. When the radio is also transmitting data packets, the status packet -> command packet relay is about 79% reliable, suggesting that the first packet after a switch from RX to TX mode is somehow being lost. Indeed, when I look at the IRQ signals on an oscilloscope, it is apparent that a certain percentage of the time the TX_DS interrupt is not followed by a RX_DR interrupt. so - what am I doing wrong??!! I'm desperate to make this work, and have tried almost every permutation! thanks, Tim Hanson | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{484} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
experimential results with the Nordic nRF24l01 (recall, as per {477}, that all SPI signals have an in-line 100 ohm resistor on both the headstage and bridge)
finally, it is solved!how:
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{477} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
I've been having problems transmitting packets in a pipelined fashion using the nordic nRF24L01 tranciever IC. Namely, I cannot send multiple packets at once by keeping the on-chip 3-packet fifo full (note packets are 32 bytes data, max; with header/CRC, they are close to 40 bytes). If this fifo is full, the radio should remain in transmit mode - see {470}, and also {484} Above, what happens when I let the fifo go dry / empty, and force the PLL to resync for each transmitted packet, as per the following sequence:
Note just about all packets are received properly and that the RX irq closely follows the TX irq. Above, what happens when i try to pipeline transmission, e.g.
One initial theory was that noise on the SPI bus was corrupting the packets. However:
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{483} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{480} |
ref: bookmark-0
tags: RonPaul American presidential candidate libertarian
date: 10-30-2007 22:38 gmt
revision:0
[head]
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http://www.grist.org/feature/2007/10/16/paul/?source=weekly
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{479} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://pespmc1.vub.ac.be/books/IntroCyb.pdf -- dated, but still interesting, useful, a book in and of itself!
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{470} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{378} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.palowireless.com/infotooth/tutorial/baseband.asp
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{475} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.neuroconnex.com/ -- looks like they have some excellent products, but not sure how to purchase them.
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{473} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://au.geocities.com/ozbrick850/engine-turbo-keithspage.html -- excellent discussions of the volvo 850 / S70 T5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{472} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
buglabs, makers of plug n' play configurable handheld platform based on open-source technologies
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{464} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
The problem: I have an interrupt status routine (ISR) which can interrupt the main, radio-servicing routine at any time. To keep the ISR from corrupting the register values of the main routine while it works, these registers must be pushed, and later popped, to the stack. Now, doing this takes time, so I'd prefer to pop / push as few registers as possible. Namely, I don't want to push/pop the hardware loop registers - LC0 (loop counter 0), LB0 (loop bottom 0, where the hardware loop starts) & LT0 (loop top 0, where the hardware loop ends). Gcc seems to only touch bank 1, never bank 0, so I don't have to save the 3 regs above. However, to make sure, I've written a perl file to examine the assembled code: my $file = "decompile.asm"; open(FH, $file); @j = <FH>; my $i=0; my @badregs = ("LC0", "LB0", "LT0"); foreach $reg (@badregs){ foreach $k (@j){ if($k =~ /$reg/){ $i++; print "touch register $reg : $k"; } } } #tell make if we found problems or not. if($i>0){ exit 1; }else{ exit 0; } 'make' looks at the return value perl outputs, as instructed via the makefile (relevant portion below): headstage.ldr:headstage.dxe rm -f *.ldr $(LDR) -T BF532 -c headstage.ldr $< bfin-elf-objdump -d headstage.dxe > decompile.asm perl register_check.pl if it finds assembly which accesses the 'bad' registers, make fails. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{471} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Little Stupid Details - what they are, and how to avoid them
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{467} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Self-learning fuzzy neural network with optimal on-line leaning for water injection control of a turbocharged automobile.
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{466} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
What I have learned about licensing & Duke (or really, licensing at universities in general), in no particular order:
conclusions:
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{465} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
good explanation of 32-bit CRC (from the blackfin BF537 hardware ref): | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{444} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
nordic semi links: here is the connection list for the nRF24L01 module made by sparkfunelectronics
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{463} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.ntlf.com/html/lib/quotes.htm
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{460} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{457} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
be forewarned : this is poorly organized! From the New Yorker, October 1 2007: "We've been here before, but this time the stars are really coming into alignment. Our health-care system has continued to deteriorate. We spend twice as much as the French and the Germans and two and a half times as much as the Brits, yet we dies sooner and our babies die in greater numbers. Thirty-eight million americans were uninsured in 200; now it's 47M. Employer-bnased health insurance is increasingly expensive, stingy, and iffy. Companies, especially manufacturing companies, are beginning to realize that being deputized to pay the health-care costs of their employees and retirees puts them at a competitive disadvantage in the global economy. " Therefore, then there will be two segments of the population supportive of centralized / federalized health care: the workers (myself one, i have to pay for health insurance myself; its (BCBSNC) costs ~$160/month and I can't be certian of it's quality or coverage just yet), and the employers. The employers have seen an increase of 63% for single coverage and 58% for family coverage since 2001.[1] Who else is there? oh, yea, the healthcare industry ( $224 billion in biotech 2000, $184B spent on pharmaceuticals 2003, $606B by private health insurance, which made $209B in profits) also, how are we going to fund this? Medicare has $30 Trillion in unfunded liability, which is three times that of the US mortgage debt. Ultimately, i think the problem is that the government and private insurance do not want to pay for the uninsured, but when such a situation occurs, they are morrally obliged to do so, and hence much somehow subsidize / hide the costs of this. It is argued that if everyone was provided with basic healthcare through the government, then the difficulty and inefficiency of hiding the cost would be avoided.
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{458} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Its also very difficult to compare western euro productivty to US productivity due to healthcare costs. The US system employs a payroll deduction to lessen the input of the employer and reduce ECI while the european system does not. Further, this underweights those costs in CPI. Statisticians in europe catch that difference while the BLS does not. One could point out, for example, that Europeans enjoy more leisure time, better health, less poverty, less inequality and thus more economic security, greater intergenerational economic mobility, better access to high-quality social services like health care and education, and manage to do it all in a far more environmentally sustainable way (Europe generates about half the CO2 emissions for the same level of GDP) compared to the US. I bet these facts don't show up in McKinsey's business productivity study. Then there are the aspects of the American model that may be impossible and unwise for Europeans to copy, but boost US productivity statistics nonetheless: Much of the surprising acceleration of U. S. productivity growth since 1995 originates in the trade sector, particularly retail trade . . . perhaps the most important factor of production in making this format possible is a large plot of virgin land which is much more widely available in the sprawling American metropolitan areas . . . The American explosion of productivity growth in retailing calls attention to basic life-style choices that constitute yet another form of ʺAmerican Exceptionalism.ʺ While the American form of metropolitan organization may promote productivity growth, Europeans are rightly skeptical of unmeasured costs of low urban density in America as promoted by explicit government policies. Europeans decry side-effects of the American system that may promote productivity without creating consumer welfare, including excess energy use, pollution, and time spent in traffic congestion. Tom Geraghty.
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{451} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
September 27 2007 - after my old 1999 9-3 was fatally rear-ended on 15-501 south in chapel hill (on September the 11th, none the less), I used the insurance money to buy a used Saab 900 SE 5-speed 1997, 87k miles, $4500. Somehow, i got a better car and saved money at the same time :) It's really in nice shape considering it's age, as the pictures will attest. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{450} |
ref: notes-0
tags: leadership dilbert redirection politics trolls
date: 09-28-2007 18:11 gmt
revision:0
[head]
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a very nice synopsis of how leadership works: | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{447} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
things required to enable interrupts on a blackfin processor, not necessarily in order though all are required (also see the list, in the programming ref, on page 4-31):
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{446} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{439} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
abandoned because I realized that I could work on 2 channels at once (as there are 2 MACs onboard) & could use the s2rnd multiply-accumulate flay & could load registers 32bits at a time! ah well, might as well archive my efforts :) r6.h = 2048; r0.l = r0.l - r6.h (s) || r1.l = w[i0++] || r2.l = w[i1++]; //subtract offset, load a1[0] into r1.l, w1[0] into r2.l a0 = r0.l * r1.l (is) || r1.h = w[i0++]; //mac in*a1[0], load a[1] to r1.h a0 += r2.l * r1.h (is) || r1.l = w[i0++]|| r2.h = w[i1--]; //mac w[0]*a1[1], load a1[2] into r1.l, w1[1] to r2.h r4 = (a0 += r2.h * r1.l) (is) || r3.l = w[i0++]; //mac w1[1]*a1[2] store to r4, b1[0] to r3.l r4 = r4 >>> 14 || r3.h = w[i0++]; //arithmetic right shift, 32 bit inst, b1[1] to r3.h, r4 is new w1. a0 = r4.l * r3.l (is) || w[i1++] = r4.l; //mac w1*b1[0], save w1 into w1[0] a0 += r2.l * r3.h (is) || w[i1++] = r2.l; //mac w1[0]*b[1], save w1[0] into w1[1] r4 = (a0 += r2.h * r3.l) (is) || r1.l = w[i0++] || r2.l = w[i1++];//mac w1[1]*b1[0] store r4, a2[0] to r1.l, w2[0] to r2.l r4 = r4 >>> 14 || r1.h = w[i0++] || r2.h = w[i1--]; //arith. right shift, a2[1] to r1.h, w2[1] to r2.h a0 = r4.l * r1.l (is); //mac in*a2[0], a2[2] into r1.l a0 += r2.l * r1.h (is) || rl.l = w[i0++]; //mac w2[0]*a2[1], b2[0] into r3.l r4 = (a0 += r2.h * r1.l) (is) || r3.l = w[i0++]; //mac w2[1]*a2[2] store r4, b2[1] into r3.h r4 = r4 >>> 14 || r3.h = w[i0++]; //arithmetic shift to get w2, b2[2] to r3.h a0 = r4.l * r3.l (is) || w[i1++] = r4.l; //mac w2 * b2[0], store w2 to w2[0] a0 += r2.l * r3.h (is) || w[i1++] = r2.l; //mac w2[0]*b2[1], store w2[0] to w2[1]. i1 now pointing to secondary channel. r4 = (a0 += r2.h * r3.l) (is) || i0 -= 10; //mac w2[1]*b2[0]. reset coeff ptr. done with pri chan, save in r5. r5 = r4 >>> 14; //time for the secondary channel! r0.h = r0.h - r6.h (s) || r1.l = w[i0++] || r2.l = w[i1++]; //subtract offset, load a1[0] to r1.1, w1[0] to r2.l a0 = r0.h * r1.l (is) || r1.h = w[i0++] ; //mac in*a1[0], a1[1] to r1.h, save out samp pri. a0 += r2.l * r1.h (is) || r1.l = w[r0++] || r2.h = w[i1--]; //mac w1[0]*a1[1], a1[2] to r1.l, w1[1] to r2.h r4 = (a0 += r2.h * r1.l) (is) || r3.l = w[i0++]; //mac, b1[0] to r3.l r4 = r4 >>> 14 || r3.h = w[i0++]; //arithmetic shift, b1[1] to r3.h a0 = r4.l * r3.l (is) || w[i1++] = r4.l; //mac w1*b1[0], save w1 to w1[0] a0 += r2.l * r3.h (is) || w[i++] = r2.l; //mac w1[0], save w1[0] to w1[1] r4 = (a0 += r2.h * r3.l) (is) || r1.l = w[i0++] || r2.l = w[i1++]; //mac w1[1]*b1[0] store r4, a2[0] to r1.l, w2[0] to r2.l r4 = r4 >>> 14 || r2.h = w[i1--]; // r4 output of 1st biquad, w2[1] to r2.h a0 = r4.l * r1.l (is) || r1.h = w[i0++] ; //mac in* a2[0], a2[1] to r1.h a0 += r2.l * r1.h (is) || r1.h = w[i0++] ; //mac w2[0]*a2[1], a2[2] to r1.l r4 = (a0 += r2.h * r1.l) (is) || r3.l = w[i0++]; //mac w2[1]*a2[2], b2[0] to r3.l r4 = r4 >>> 14 || r3.h = w[i0++]; //r4 is w2, b2[2] to r3.h a0 = r4.l * r3.l (is) || w[i++] = r4.l ; //mac w2 * b2[0], store w2 to w2[0] a0 += r2.l * r3.h (is) || w[i++] = r2.l; //mac w2[0] * b2[1], store w2[0] to w2[1]. i1 now pointing to next channel. r4 = (a0 += r2.h * r3.l) (is) || i0 -= 10; //mac w2[1] * b2[0], reset coeff. ptr, save in r4. r4 = r4 >>> 14; here is a second (but still not final) attempt, once i realized that it is possible to issue 2 MACS per cycle // I'm really happy with this - every cycle is doing two MMACs. :) /* // i0 i1 (in 16 bit words) r1 = [i0++] || r4 = [i1++]; // 2 2 r1= a0 a1 r4= w0's a0 = r0.l * r1.l, a1 = r0.h * r1.l || r2 = [i0++] || r5 = [i1]; // 4 2 r2= a2 a2 r5= w1's a0 += r4.l * r1.h, a1 = r4.h * r1.h || r3 = [i0++] || [i1--] = r4; // 6 0 r3= b0 b1 w1's=r4 r0.l = (a0 += r5.l * r2.l), r0.h = (a1 += r5.h * r2.l)(s2rnd); a0 = r0.l * r3.l, a1 = r0.h * r3.l || [i1++] = r0; // 6 2 w0's = r0 a0 += r4.l * r3.h, a1 += r4.h * r3.h || r1 = [i0++] || i1 += 4; // 8 4 r1 = a0 a1 //load next a[0] a[1] to r1; move to next 2nd biquad w's; don't reset the coef pointer - move on to the next biquad. r0.l = (a0 += r5.l * r3.l), r0.h = (a1 += r5.h * r3.l)(s2rnd) || r4 = [i1++]; // 8 6 r4 = w0's, next biquad //note: the s2rnd flag post-multiplies accumulator contents by 2. see pg 581 or 15-69 //second biquad. a0 = r0.l * r1.l, a1 = r0.h * r1.l || r2 = [i0++] || r5 = [i1]; // 10 6 r2= a2 a2 r5 = w1's a0 += r4.l * r1.h, a1 += r4.h * r1.h || r3 = [i0++] || [i1--] = r4; // 12 4 r3= b0 b1 w1's = r4 r0.l = (a0 += r5.l * r2.l), r0.h = (a1 += r5.h * r2.l)(s2rnd); // a0 = r0.l * r3.l, a1 = r0.h * r3.l || [i1++] = r0; // 12 6 w0's = r0 a0 += r4.l * r3.h, a1 += r4.h * r3.h || r1 = [i0++] || i1 += 4; // 14 8 r1 = a0 a1 r0.l = (a0 += r5.l * r3.l), r0.h = (a1 += r5.h * r3.l)(s2rnd) || r4 = [i1++]; // 14 10 r4 = w0's //third biquad. a0 = r0.l * r1.l, a1 = r0.h * r1.l || r2 = [i0++] || r5 = [i1]; // 16 10 r2= a2 a2 r5 = w1's a0 += r4.l * r1.h, a1 += r4.h * r1.h || r3 = [i0++] || [i1--] = r4; // 18 8 r3= b0 b1 w1's = r4 r0.l = (a0 += r5.l * r2.l), r0.h = (a1 += r5.h * r2.l)(s2rnd); // a0 = r0.l * r3.l, a1 = r0.h * r3.l || [i1++] = r0; // 18 10 w0's = r0 a0 += r4.l * r3.h, a1 += r4.h * r3.h || r1 = [i0++] || i1 += 4; // 20 12 r1 = a0 a1 r0.l = (a0 += r5.l * r3.l), r0.h = (a1 += r5.h * r3.l)(s2rnd) || r4 = [i1++]; // 20 14 r4 = w0's //fourth biquad. a0 = r0.l * r1.l, a1 = r0.h * r1.l || r2 = [i0++] || r5 = [i1]; // 22 14 a0 += r4.l * r1.h, a1 += r4.h * r1.h || r3 = [i0++] || [i1--] = r4; // 24 12 r0.l = (a0 += r5.l * r2.l), r0.h = (a1 += r5.h * r2.l)(s2rnd); a0 = r0.l * r3.l, a1 = r0.h * r3.l || [i1++] = r0; // 24 14 a0 += r4.l * r3.h, a1 += r4.h * r3.h || i1 += 4; // 24 16 r0.l = (a0 += r5.l * r3.l), r0.h = (a1 += r5.h * r3.l)(s2rnd); // 48: loop back; 32 bytes: move to next channel. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{443} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Here's the deal: myself, Jan & the rest of the double-one aught seven crew will be hosting a club swimming barbecue ~6 this friday. Since we'll only be warming up by the end of the club swimming bbq, and probably people will not want to leave anyway, this event is to extend the festivities indefinitely. We feel that this is essential, as recent news - for example the delicious (and completely unanticipated) subprime mortgage fun, the even more delicious lead paint that China has been supplying for augmenting our children's collective intelligence, and the incredibly momentous expenditure of more than $450 trillion on the Iraq war - are due cause for a little bit of indulgence and celebration! So come party like Bernanke, and drop cash out of helicopters! (Since we are all going to be generous and drop cash like we're the fed, 1107 would greatly appreciate it if you could direct a bit of that generosity on food / beer etc for the party. (so as to keep us all fed.) thanks :) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{442} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://mirror.mricon.com/french/french.html -- "how i learned french in a year"
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{441} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
So, in order to measure how quantizing filter coeficients affects filter response, I quantized the coefficients of a 8th order bandpass filter designed with: [B1, A1] = ellip(4,0.8,70, [600/31.25e3 6/31.25]);here is a function that quantizes & un-quantizes the filter coeff, then compares the frequency responses: function [Bq, Aq, Bcoef, Acoef] = filter_quantize(B, A) % quantize filter coeficients & un-quantize so as to get some idea to % the *actual* fixed-point filter performance. % assume that everything in broken into biquads. base = 10; Aroots = roots(A); Broots = roots(B); order = length(Aroots)/2; % the number of biquads. scale = B(1).^(1/order); % distribute the gain across the biquads. for o = 0:order-1 Acoef_biquad(o+1, :) = poly(Aroots(o*2+1 : o*2+2)); Bcoef_biquad(o+1, :) = poly(Broots(o*2+1 : o*2+2))*scale; end Bcoef = round(Bcoef_biquad .* 2^base); Acoef = round(Acoef_biquad .* 2^base); % now, reverse the process. Bq2 = Bcoef ./ 2^base; Aq2 = Acoef ./ 2^base; for o = 0:order-1 Arootsq(o*2+1: o*2+2) = roots(Aq2(o+1, :)); Brootsq(o*2+1: o*2+2) = roots(Bq2(o+1, :)); end Aq = poly(Arootsq); Bq = poly(Brootsq).*B(1); [H, W] = freqz(B, A); [Hq, Wq] = freqz(Bq, Aq); figure plot(W, db(abs(H)), 'b') hold on plot(W, db(abs(Hq)), 'r') axis([0 pi -100 0])The result: high frequency is not much affected but low frequency is strongly affected. But this is at a quatization to 10 bits - quantization to 15 bits lead to reasonably good performance. I'm not sure if this conclusively indicates / counterindicates downsampling prior to highpassing for my application, but i would say that it does, as if you downsample by 2 the highpass cutoff frequency will be 2x larger hence the filter will be less senitive to quantization errors which affect low frequencies. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{440} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{437} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
so, you want to look at internal registers on your embedded blackfin processor? register access is probably enough to help A LOT with debugging!
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{432} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{428} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
to get the activewire board working under linux (debian):
I have no idea why this is required. perhaps my board is broken abit? hex (1): :03000000020100FA :10010000907F947400F0907F9D7410F0907F9774AE :1001100010F012012D12012D12012D907F97740005 :10012000F012012D12012D12012D02010C786490A4 :0C013000FB50A3E582458370F9D8F4224F :00000001FF hex(2): :1007B600D204C203C200C202C201120653D2E843E7 :1007C600D820907FAB74FFF0907FA9F0907FAAF0BD :1007D6005391EF907FAFE04401F0907FAEE0440D7F :1007E600F0D2AF20014C750C00750B00750A007530 :1007F60009007F487E927D007C00AB0CAA0BA90AFB :10080600A809C31207A5502020011D7A0079007897 :1008160000E50C2401F50CEA350BF50BE9350AF574 :100826000AE83509F50980CA2001B8D205120D7B00 :0F08360080B1300105120100C20112045180F39C :010845002290 :10010000907FE9E070030201DF14700302025B24B8 :10011000FE70030202CF24FB70030201D9147003A6 :100120000201D31470030201C71470030201CD242D :10013000056003020323120E33400302032F907F56 :10014000EBE024FE6016146040240270707403908B :100150007FD4F07437907FD5F002032F907FEAE0D0 :10016000FF120A2D8B0D8A0E890FEA496011AE022B :10017000EE907FD4F0AF01EF907FD5F002032F9087 :100180007FB4E04401F002032F907FEAE0FF120AFF :100190007C8B0D8A0E890FEA496018AE02EE907FC3 :1001A000D4F0AF01EF907FD5F0120705907FB5F046 :1001B00002032F907FB4E04401F002032F907FB43C :1001C000E04401F002032F120DFD02032F120E1F57 :1001D00002032F120E1702032F120DEF02032F122C :1001E0000E35400302032F907FE8E0247F60241443 :1001F00060312402705BA200E433FF25E0FFA2021D :10020000E4334F907F00F0E4A3F0907FB57402F0E8 :1002100002032FE4907F00F0A3F0907FB57402F00A :1002200002032F907FECE0F45480FFC4540FFFE0F2 :1002300054072F25E024B4F582E4347FF583E0549D :10024000FD907F00F0E4A3F0907FB57402F002030C :100250002F907FB4E04401F002032F120E374003C9 :1002600002032F907FE8E024FE601D240260030259 :10027000032F907FEAE0B40105C20002032F907FB4 :10028000B4E04401F002032F907FEAE07038907FE1 :10029000ECE0F45480FFC4540FFFE054072F25E036 :1002A00024B4F582E4347FF583E4F0907FECE054ED :1002B00080FF131313541FFFE054072F907FD7F0D4 :1002C000E04420F08069907FB4E04401F080601247 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:0D064600D086D084D085D082D083D0E03221 :020A7C008F10D9 :100A7E00E4F5117512FF751304751409AB12AA1360 :100A8E00A91490000112071EB4031DAF110511EF3A :100A9E00B51001221207057E0029FFEE3AA907754F :0E0AAE0012FFF513891480D47B007A007900C2 :010ABC002217 :100A2D00E4FE7512FF751303751449AB12AA13A9D1 :100A3D001490000112071E6402702DAD060EEDB567 :100A4D0007012290000212076D85F010F51162105A :100A5D00E5106211E511621029FDE5103AA9057541 :0E0A6D0012FFF513891480C37B007A00790014 :010A7B002258 :100DA000120B58E52624FA600E146006240770F32F :0C0DB000D322E4F526D322E4F526D3225A :100DBC00120B85E52624FA600E146006240770F3E6 :0C0DCC00D322E4F526D322E4F526D3223E :100AEC007400F58690FDA57C05A3E582458370F91D :010AFC0022D7 :03000000020E0BE2 :0C0E0B00787FE4F6D8FD7581260207B65A :10070500BB010689828A83E0225002E722BBFE02F2 :09071500E32289828A83E4932225 :10071E00BB010CE58229F582E5833AF583E0225090 :10072E0006E92582F8E622BBFE06E92582F8E222DA :0D073E00E58229F582E5833AF583E49322F4 :10074B00F8BB010DE58229F582E5833AF583E8F0E4 :10075B00225006E92582C8F622BBFE05E92582C890 :02076B00F22278 :10076D00BB0110E58229F582E5833AF583E0F5F0CA :10077D00A3E0225009E92582F886F008E622BBFEA7 :10078D000AE92582F8E2F5F008E222E5832AF583ED :08079D00E993F5F0A3E99322B2 :1007A500EB9FF5F0EA9E42F0E99D42F0E89C45F0AA :0107B5002221 :00000001FF | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{427} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
I wanted to take lines like this: 272 :1007A500EB9FF5F0EA9E42F0E99D42F0E89C45F0AAand convert them into proper hex files. hence, perl: perl -e 'open(FH, "awfirm.hex"); @j = <FH>; foreach $H (@j){ $H =~ s/^s+d+s//; $H =~ s/\//; print $H; }' | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{422} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
For the past few days I've been trying to figure out a way to do vacuum-assisted pick & place for home SMT PCB assembly. Fortunately, I had a vacuum pump - this one bought, without motor, from now defunct Duke University Surplus for $25. I got the motor from my parents, and had to go to Northern Equipment for the pulley and belt (fyi: also bought a hot air gun, Wel-Bilt brand, which promptly broke upon testing at home.) I filled it with 10w30 synthetic motor oil, since some of original vacuum oil had leaked out during the (years?) of neglect at the surplus store. The whole assembly was far heavier than i could move, so i welded together a little cart for it out of old sideskate axles & bed frames. The wheels are from a cheap wal-mart skateboard that i used like 3 years ago to make the pogoboard. I also had to figure out how to neck down the 1.5" vacuum port on top of the huge pump to 1/4 id tubing, which took about 15 mins of searching in home depot... Above - Valves clamped to the table so i can operate them with my right hand while my left hand manipulates the fine SMT devices. Top valve is to control the vacuum pressure, bottom is a dump valve to release vacuum in the tip. I used three hypodermic needles, of varying diameter, as the tips for picking up small items. For the large chips, e.g. 176 pin LQFP-s, I ganked the ink tube out of a ballpoint pen. & glued it to the syringe connector (which is nice and easily replaceable). All tips were ground down at about a 40 deg angle to hold the parts (and to make the tips dull enough so i wouldn't continually stab myself while working...) simple and effective! see also {423} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{412} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
B&T HVAC Durham: 919-942-0380 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{409} |
ref: bookmark-0
tags: optimization function search matlab linear nonlinear programming
date: 08-09-2007 02:21 gmt
revision:0
[head]
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http://www.mat.univie.ac.at/~neum/ very nice collection of links!! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{407} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.baconbutty.com/blog-entry.php?id=13 how to make a text area where tab key inserts 'tab' into the text (like here - for tables!) "
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{405} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{403} |
ref: bookmark-0
tags: blackfin ELF freestanding applications boot
date: 08-01-2007 14:40 gmt
revision:0
[head]
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http://www.johanforrer.net/BLACKFIN/index.html very good, very instructive. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{398} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{392} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{387} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{386} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://video.google.com/videoplay?docid=-3254488777215293198 need to learn more about this infamous federal reserve! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{384} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
notes on reading magstripe cards:
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{381} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://hardm.ath.cx:88/pdf/lowpowermicrocontrollers.pdf also see IBM's eLite DSP project. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{379} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{374} |
ref: notes-0
tags: entrepreneur MIT notes LLC tax law securities advice
date: 05-22-2007 15:25 gmt
revision:0
[head]
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http://enterpriseforum.mit.edu/mindshare/startingup/index.html
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{373} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://xtronics.com/reference/viscosity.htm the source site - http://xtronics.com/ - has a lot of interesting information. The author seems as enamored with Debian as I am. (hence, there is plenty of Debian information there :) for example, they have a quick reference on kicad: http://xtronics.com/reference/kicad.html | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{372} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
oh yea!!! nice work mate!! http://www.rohrbacher.net/kicad/quicklib.php btw, kicad is the shit - and it is now in Debian!! I love debian! I love kicad! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{371} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{370} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
An awesome pencil drawing of al gore, in May 20th issue of NYtimes magazine. Curibata, Brazil - a city unusual for its urban planning, ecological mind, bussing system, affluence (compared to the rest of Brazil, and ratio of parks to buildings. I would like to go there. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{362} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
An experiment with bluetooth, jabra, and hypothetical wireless lowfi neural recording:
# HCId options options { # Automatically initialize new devices autoinit yes; # Security Manager mode # none - Security manager disabled # auto - Use local PIN for incoming connections # user - Always ask user for a PIN # security auto; # Pairing mode # none - Pairing disabled # multi - Allow pairing with already paired devices # once - Pair once and deny successive attempts pairing multi; # Default PIN code for incoming connections passkey "0000"; } # Default settings for HCI devices device { # Local device name # %d - device id # %h - host name name "%h-%d"; # Local device class # class 0x3e0100; #--host class 0x500204; # Default packet type #pkt_type DH1,DM1,HV1; # Inquiry and Page scan iscan enable; pscan enable; # Default link mode # none - no specific policy # accept - always accept incoming connections # master - become master on incoming connections, # deny role switch on outgoing connections lm accept; # Default link policy # none - no specific policy # rswitch - allow role switch # hold - allow hold mode # sniff - allow sniff mode # park - allow park mode lp rswitch,hold,sniff,park; } And here is /etc/bluetooth/rfcomm.conf: (I added the device MAC and turned on automatic binding.. not sure if that was a good thing to do) rfcomm0 { # Automatically bind the device at startup bind yes; # Bluetooth address of the device device 00:16:8F:BF:7B:E0; # RFCOMM channel for the connection channel 1; # Description of the connection comment "Example Bluetooth device"; }
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{361} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
things that I want to send to miguel:
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{360} |
ref: thesis-0
tags: clementine 042607 operant conditioning
date: 04-27-2007 16:45 gmt
revision:3
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tried 2d again... some success. looked at 29 (still good for x control, but not in BMI mode), channe 71 (still by default silent, correlated to behavior) channel 18 (did not work well) channel 84 (did not work) and channel 54 (like 71, highly correlated to behavior - not sure if the mk learned to control it). have videos etc. channel 54, new for today and might, might be > 71.. though looking back at the videos, 71 seems pretty good. (it is also a bad idea to keep switching the game..) channels 54 and 71 are different from 29 in that 29 never goes completely silent; 71 goes silent when thew mk is paying attention, 54 when he is not moving. 29 can be modulated + and -, 71 and 54 just + (or so). of course, the monkey is usually in motion so both have high variance and silent periods are short-ish channel 29, as always channel 71, as before (very stable!) channel 54 movies (in the order that they were taken): | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{359} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{358} |
ref: thesis-0
tags: clementine 042507 operant conditioning
date: 04-25-2007 20:19 gmt
revision:2
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OK, today clementine played absolutely abysmally - he did practically nothing, though he did do pole control for a little bit. I think we must stop doing pole control - it is too easy, he must become accustomed to doing brain control from the beginning. Anyway, monkeys never like learning new things (compare to people!); I just have to give him more time. The units are stable (in my agitated state, i forgot to make screenshots). Channel 54 might be very excellent for brain control - however, i did not test it today. If it is still there tomorrow, i will try. http://m8ta.com/tim/clem042507_trainY.MPG (ignore the first few seconds - he was not trying so hard/was not paying attention) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{356} |
ref: thesis-0
tags: clementine 042407 operant conditioning
date: 04-25-2007 00:21 gmt
revision:1
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Today, as yesterday, I tried operantly conditioning primary units on channels 29 (x) and 71 (y) for BMI control. The first few minutes were run in pole control for Miguel's visitors, but i did not save the data. Again as before the monkey was not quite motivated to perform the task. Tomorrow he ought to be thirsty - & I'll try to start him on 2d control after tweaking the gain and offset parameters on the individual axes. During 2d control tomorrow the target size should be expanded also to about 3 to keep the monkey's interest. There seems to be a bug in the BMI- when two units are sorted, both contribute to the firing rate estimate. I noticed this during X control today, which somewhat decreased the performance. Y performance was slightly better than yesterday, but still not great - he hasn't quite figured it out yet. XY was shitty, i guess. Among other things, I really need to test the recording system - perhaps make a new file format that is extensible yet compressed? maybe labeled data streams? something like plexon files? Or perhaps just record it to the analog files (that would be easy!) nahh. todo:
channel 29, at the end of the session: channel 71. both these channels seem very stable - I hope the mk gets it before the evaporate! there are no bmisql outputs as I did not run this analysis. movies:
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{355} |
ref: thesis-0
tags: clementine 042307 operant conditioning
date: 04-24-2007 01:37 gmt
revision:2
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Today, once again, I tried BMI both via pole control and with operant conditioning. The latter worked the best; because the fit/predictions were so shitty i didn't even try brain control with the wiener filter or kalman filter. Here is the output of BMIsql on ~6500 data slices, 18 neurons, 5 taps: here is the prediction summary... note that target x position is doing rather well (probably because we are training units to respond to this) output of BMIsql: order of columns: unit,channel, lag, snr, variable 2.0000 29.0000 0 1.0872 6.0000 1.0000 53.0000 3.0000 1.0870 3.0000 1.0000 53.0000 2.0000 1.0820 3.0000 1.0000 82.0000 1.0000 1.0801 7.0000 1.0000 82.0000 5.0000 1.0678 1.0000 1.0000 82.0000 4.0000 1.0625 1.0000 1.0000 82.0000 2.0000 1.0563 7.0000 1.0000 53.0000 1.0000 1.0558 6.0000 1.0000 8.0000 0 1.0550 8.0000 1.0000 70.0000 3.0000 1.0549 2.0000 1.0000 70.0000 2.0000 1.0536 2.0000 2.0000 82.0000 4.0000 1.0524 1.0000 2.0000 82.0000 5.0000 1.0516 1.0000 1.0000 53.0000 4.0000 1.0506 3.0000 1.0000 70.0000 4.0000 1.0503 2.0000 2.0000 29.0000 1.0000 1.0497 5.0000 2.0000 82.0000 3.0000 1.0494 1.0000 1.0000 82.0000 3.0000 1.0464 7.0000 1.0000 8.0000 1.0000 1.0454 8.0000 1.0000 24.0000 1.0000 1.0450 8.0000 1.0000 24.0000 0 1.0442 8.0000 1.0000 8.0000 2.0000 1.0415 8.0000 1.0000 70.0000 5.0000 1.0396 2.0000 2.0000 82.0000 1.0000 1.0395 7.0000 1.0000 24.0000 2.0000 1.0392 8.0000 1.0000 70.0000 1.0000 1.0389 2.0000 1.0000 81.0000 1.0000 1.0356 8.0000 1.0000 8.0000 3.0000 1.0355 8.0000 2.0000 29.0000 2.0000 1.0334 8.0000 1.0000 81.0000 2.0000 1.0326 8.0000 1.0000 24.0000 4.0000 1.0318 8.0000 1.0000 8.0000 4.0000 1.0298 8.0000 1.0000 24.0000 3.0000 1.0297 8.0000 1.0000 28.0000 3.0000 1.0293 11.0000 2.0000 82.0000 2.0000 1.0292 4.0000 1.0000 28.0000 1.0000 1.0286 11.0000 1.0000 28.0000 4.0000 1.0262 11.0000 1.0000 28.0000 2.0000 1.0243 11.0000 1.0000 28.0000 0 1.0238 11.0000 2.0000 29.0000 3.0000 1.0221 8.0000 1.0000 53.0000 0 1.0215 9.0000 1.0000 81.0000 3.0000 1.0207 8.0000 Operant conditioning worked exceptionally well for the X axis (channel 29, yellow unit 1 - adding both unit's activity together did not work, the monkey would not play). see http://m8ta.com/tim/clem042307_trainX.MPG For a while he tried controlling the cursor position with the joystick, then after a while he realized this was unnecessary and just modulated unit 29. Initially I tried operant conditioning of channel 82 for the Y axis, but it quickly appeared that he did not care and that it would not work. Hence I switched to channel 71, which was tried on Saturday the 20th. As before, this unit was tonically active while he was asleep, and almost silent while he was paying attention. an attention neuron? possibly. It also showed high firing rate changes when he struggled, suggesting volitional control. He was somewhat able to control it today... see http://m8ta.com/tim/clem042307_trainY.MPG | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{354} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{353} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-6809905[0] Relation of size and activity of motor cortex pyramidal tract neurons during skilled movements in the monkey
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{352} |
ref: bookmark-0
tags: postmodernism pseudoscience Alan Sokal
date: 04-23-2007 03:47 gmt
revision:0
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http://www.physics.nyu.edu/faculty/sokal/pseudoscience_rev.pdf
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{350} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nathan, Misha, and their lives went to Japan for a week to work with the roboticists @ ATR. During the off time, they spent time exploring and photographing Japan. Misha lent me his camera to video record Clementine, and in the process of trying to free up space in the camera's memory, I found these excellent pictures taken by (presumably) Misha. There were other very nice pictures, but they contain Misha, Nathan etc so I excluded them. the photo below is by far the best. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{347} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
This training fulfills six (6) hours of RCR training required by Duke University Graduate School. However, participants MUST commit to and attend all FOUR sessions held as follows:
Leader: Zeljko Vujaskovic, MD, PhD, DCRU Associate Director http://tinyurl.com/2sjrpf | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{71} |
ref: Francis-2005.11
tags: Joe_Francis motor_learning reaching humans delay intertrial interval
date: 04-09-2007 22:48 gmt
revision:1
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PMID-16132970[0] The Influence of the Inter-Reach-Interval on Motor Learning. Previous studies have demonstrated changes in motor memories with the passage of time on the order of hours. We sought to further this work by determining the influence that time on the order of seconds has on motor learning by changing the duration between successive reaches (inter-reach-interval IRI). Human subjects made reaching movements to visual targets while holding onto a robotic manipulandum that presented a viscous curl field. We tested four experimental groups that differed with respect to the IRI (0.5, 5, 10 or 20 sec). The 0.5 sec IRI group performed significantly worse with respect to a learning index than the other groups over the first set of 192 reaches. Each group demonstrated significant learning during the first set. There was no significant difference with respect to the learning index between the 5, 10 or 20 sec IRI groups. During the second and third set of 192 reaches the 0.5 sec IRI group's performance became indistinguishable from the other groups indicating that fatigue did not cause the initial poor performance and that with continued training the initial deficit in performance could be overcome. ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{129} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-10607637[0] Internal models for motor control and trajectory planning
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{106} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15208695[0] PDF HTML summary Optimal feedback control and the neural basis of volitional motor control by Stephen S. Scott ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{104} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
this seems to be the same as {339}, with a different pubmed id & different author list. bug in the system! PMID-16193273[0] On the relations between single cell activity in the motor cortex and the direction and magnitude of three-dimensional dynamic isometric force* the majority of cells responded to direction
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{80} |
ref: Chan-2006.12
tags: computational model primate arm musculoskeletal motor_control Moran
date: 04-09-2007 22:35 gmt
revision:1
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PMID-17124337[0] Computational Model of a Primate Arm: from hand position to joint angles, joint torques, and muscle forces ideas:
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{32} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.ixo.de/info/usb_jtag/ open source USB Jtag adapter, works with dragon (I think!) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{277} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15888522[0] Motor cortex neural correlates of output kinematics and kinetics during isometric-force and arm-reaching tasks.
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{278} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17143147[0] Decoding movement intent from human premotor cortex neurons for neural prosthetic applications
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{276} |
ref: Hatsopoulos-2005.1
tags: motor control M1 Hatsopoulos
date: 04-09-2007 22:26 gmt
revision:1
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PMID-16160087[] Encoding in the Motor Cortex: Was Evarts Right After All? Focus on "Motor Cortex Neural Correlates of Output Kinematics and Kinetics During Isometric-Force and Arm-Reaching Tasks"
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{338} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-7703686[0] Movement parameters and neural activity in motor cortex and area 5
Duke does not have online access to the article :( ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{286} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-8463818[0] Contribution of the monkey corticomotoneuronal system to the control of force in precision grip
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{345} |
ref: HeppReymond-1999.09
tags: force motor control grip electrophysiology
date: 04-09-2007 20:20 gmt
revision:0
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PMID-10473750[0] Context-dependent force coding in motor and premotor cortical areas.
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{344} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-2027042[0] Making arm movements within different parts of space: the premotor and motor cortical representation of a coordinate system for reaching to visual targets.
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{294} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-2376768[0] Making arm movements within different parts of space: dynamic aspects in the primate motor cortex
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{337} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-2723767[0] A comparison of movement direction-related versus load direction-related activity in primate motor cortex, using a two-dimensional reaching task.
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{335} |
ref: Georgopoulos-1992.06
tags: motor control force Georgopoulos
date: 04-09-2007 19:56 gmt
revision:1
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PMID-1609282[0] The motor cortex and the coding of force.
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{343} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-3928831[0] Cerebellar nuclear cell activity during antagonist cocontraction and reciprocal inhibition of forearm muscles. by kalaska concering the interpositus dentate & isometric task.
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{284} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-96223[0] Correlation of neural discharge with pattern and force of muscular activity, joint position, and direction of intended next movement in motor cortex and cerebellum.
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{340} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-12522173[0] Systematic changes in motor cortex cell activity with arm posture during directional isometric force generation.
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{339} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-8817266[0] On the relations between single cell activity in the motor cortex and the direction and magnitude of three-dimensional static isometric force.
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{333} |
ref: BrashersKrug-1996.07
tags: consolidation motor learning Shadmher Bizzi
date: 04-09-2007 14:35 gmt
revision:2
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PMID-8717039[0] Consolidation in human motor memory
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{332} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17234696[0] Brain-computer interfaces: communication and restoration of movement in paralysis
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{328} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-4219745[0] Relation of basal ganglia, cerebellum, and motor cortex units to ramp and ballistic limb movements.
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{326} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-9331494[0] Force and the motor cortex.
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{325} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-8768391[0] Temporal precision of spike trains in extrastriate cortex of the behaving macaque monkey
PMID-16339894[1] Neurons of the cerebral cortex exhibit precise interspike timing in correspondence to behavior.
PMID-7770778[2] Reliability of spike timing in neocortical neurons.
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{324} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16790591[0] Linear encoding of muscle activity in primary motor cortex and cerebellum
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{302} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17271333[0] Neuron selection and visual training for population vector based cortical control.
PMID-16705272[1] Selection and parameterization of cortical neurons for neuroprosthetic control
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{258} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17271178[0] automatic spike sorting for neural decoding
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{259} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17271543[] http://hardm.ath.cx:88/pdf/sanchez2004.pdf ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{296} |
ref: Kettner-1988.08
tags: 3D motor control population_vector Schwartz Georgopoulos
date: 04-05-2007 17:09 gmt
revision:1
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A triptych of papers (good job increasing your publication count, guys!):
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{152} |
ref: Amirikian-2000.01
tags: Georgopulos directional tuning motor cortex SUA electrophysiology
date: 04-05-2007 16:34 gmt
revision:2
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PMID-10678534[0] Directional tuning profiles of motor cortical cells
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{295} |
ref: Georgopoulos-1982.11
tags: georgopoulos kalaska caminiti M1 motor control tuning population_vector
date: 04-05-2007 16:27 gmt
revision:0
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PMID-7143039[0] On the relations between the direction of two-dimensional arm movements and cell discharge in primate motor cortex
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{292} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15217341[0] Cortical Neuro Prosthetics
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{290} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-14610628[0] A critical evaluation of the force control hypothesis in motor control.
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{279} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11600665[] Neural Activity in Primary Motor Cortex Related to Mechanical Loads Applied to the Shoulder and Elbow During a Postural Task
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PMID-12879039[0] Military-funded research is not unethical heh! ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{218} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ok, so i just (19 Feb 2007) did some simple experiments with the small (100W) mercury vapor lamp that i have + a hard-drive magnet + a solenoid.
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{260} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Friday March 30 Jen shared an interesting algorithm for spike sorting: dist=pdist(psi); %This finds the Euclidean distances for all of the points (waveforms) in psi; %dist is of the form of a row vector of length m(m-1)/2. Could convert into a %distance matrix via squareform function, but is computationally inefficient. %m is the number of waveforms in psit. link=linkage(dist); %This performs a nearest neighbor linkage on the distance matrix and returns %a matrix of size (m-1)x3. Cols 1 and 2 contain the indices of the objects %were linked in pairs to form a new cluster. This new cluster is assigned the %index value m+i. There are m-1 higher clusters that correspond to the interior %nodes of the hierarchical cluster tree. Col 3 contains the corresponding linkage %distances between the objects paired in the clusters at each row i. [H,T]=dendrogram(link,0); %This creates a dendrogram; 0 instructs the function to plot all nodes in %the tree. H is vector of line handles, and T a vector of the cluster %number assignment for each waveform in psit. It looks real nice in theory, and computes very quickly on 2000 x 32 waveform data (provided you don't want to plot) -- however, I'm not sure if it works properly on synthetic data. Here are the commands that i tried: v = [randn(1000, 32); (randn(1000, 32) + rvecrep(ones(1,32),1000))]; [coef, vec] = pca(v); vv = v * vec(:, 1:2); dist = pdist(vv); link = linkage(dist); [H,T]=dendrogram(link,0); figure DensityPlotOpenGL(vv(:,1), vv(:,2)) -- the fitted dendogram, without PCA
-- the fitted dendogram, with PCA
-- the asociated PCA plot of the data, clearly showing two clusters. need to figure out how jen made the colorized plots | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{257} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-9502820[] Neuronal signals in the monkey ventral striatum related to progress through a predictable series of trials
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{226} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{250} |
ref: engineering-0
tags: schematic capture layout PCB design engineering
date: 03-17-2007 23:44 gmt
revision:0
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{247} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-8235208[] Effects of the stimulation of the subthalamic nucleus in Parkinson disease
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{244} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17216714 Motor and cognitive functions of the neostriatum during bilateral blocking of its dopamine receptors
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{243} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17035544 Dopaminergic control of sleep-wake states.
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{238} |
ref: SidibAc)-1997.06
tags: GPi anatomy retrograde tracing VL ventrolateral CM centromedian thalamus GPe striatum
date: 03-11-2007 06:08 gmt
revision:0
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PMID-9183697 Efferent connections of the internal globus pallidus in the squirrel monkey: I. Topography and synaptic organization of the pallidothalamic projection.
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{235} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-10995857[0] Corticostriatal activity in primary motor cortex of the macaque.
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{25} |
ref: Dum-2003.01
tags: cerebellum dentate_nucleus projections cerebrum prefrontal posterior_pareital M1 PM thalamus somatotopic
date: 03-11-2007 04:42 gmt
revision:2
[1] [0] [head]
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PMID-12522208 An unfolded map of the cerebellar dentate nucleus and its projections to the cerebral cortex
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{233} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-10380964 Monkey globus pallidus external segment neurons projecting to the neostriatum.
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{230} |
ref: engineering notes-0
tags: homopolar generator motor superconducting magnet
date: 03-09-2007 14:39 gmt
revision:0
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http://hardm.ath.cx:88/pdf/homopolar.pdf
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{228} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.borbelyaudio.com/adobe/ae599bor.pdf
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{225} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
First Experiments to test plasma confinement by magnetic dipole
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{223} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
calculations for a strong DC loop magnet using 1/8" copper capillary tubing:
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{216} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
to search for files that match a perl regular expression: (here all plexon files recorded in 2007) locate PLEX | perl -e 'while ($k = <STDIN>){ if( $k =~ /PLEXdddd07/){ print $k; }}' | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{211} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{27} |
ref: notes-0
tags: VOR OKR climbing_fibers cerebellum purkinje cells
date: 02-05-2007 23:45 gmt
revision:1
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{190} |
ref: Lavin-2005.05
tags: dopamine PFC VTA prefrontal_cortex ventral_tegmentum 2005
date: 02-05-2007 20:37 gmt
revision:1
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PMID-15901782[0]Mesocortical Dopamine Neurons Operate in Distinct Temporal Domains Using Multimodal Signaling
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{133} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15727537 The mesocortical dopamine projection to anterior cingulate cortex plays no role in guiding effort-related decisions. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{198} |
ref: Teich-1997.03
tags: fractal LGN RGC electrophysiology SUA fano_factor
date: 02-05-2007 19:00 gmt
revision:0
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PMID-9058948[0] Fractal character of the neural spike train in the visual system of the cat
http://hardcarve.com/wikipic/Teich1997_fanofactor.gif ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{176} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15010499[0] Recursive Bayesian Decoding of Motor Cortical Signals by Particle Filtering
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{197} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15151178[0] Sequential Rearrangements of the Ensemble Activity of Putamen Neurons in the Monkey Brain as a Correlate of Continuous Behavior
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{143} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17190032[0] http://hardm.ath.cx:88/pdf/Marzullo2006_CingulateCortexBMI.pdf
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{23} |
ref: Vyssotski-2006.02
tags: neurologger neural_recording recording_technology EEG SUA LFP electrical engineering
date: 02-05-2007 06:21 gmt
revision:6
[5] [4] [3] [2] [1] [0] [head]
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PMID-16236777[0] Miniature neurologgers for flying pigeons: multichannel EEG and action and field potentials in combination with GPS recording. Recording neuronal activity of animals moving through their natural habitat is difficult to achieve by means of conventional radiotelemetry. This illustration shows a new approach, exemplified by a homing pigeon carrying both a small GPS path recorder and a miniaturized action and field potential logger (“neurologgerâ€), the entire assembly weighing maximally 35 g, a load carried easily by a pigeon over a distance of up to 50 km. Before release at a distant location, the devices are activated and store both positional and neuronal activity data during the entire flight. On return to the loft, all data are downloaded and can be analyzed using software for path analysis and electrical brain activity. Thus single unit activity or EEG patterns can be matched to the flight path superimposed on topographical maps. Such neurologgers may also be useful for a variety of studies using unrestrained laboratory animals in different environments or test apparatuses. The prototype on the hand-held pigeon records and stores EEG simultaneously from eight channels up to 47 h, or single unit activity from two channels during 9 h, but the number of channels can be increased without much gain in weight by sandwiching several of these devices. Further miniaturization can be expected. For details, see Vyssotski AL, Serkov AN, Itskov PM, Dell Omo G, Latanov AV, Wolfer DP, and Lipp H-P. Miniature neurologgers for flying pigeons: multichannel EEG and action and field potentials in combination with GPS recording. [1] ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{7} |
ref: bookmark-0
tags: book information_theory machine_learning bayes probability neural_networks mackay
date: 0-0-2007 0:0
revision:0
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http://www.inference.phy.cam.ac.uk/mackay/itila/book.html -- free! (but i liked the book, so I bought it :) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{15} |
ref: bookmark-0
tags: monte_carlo MCMC particle_filter probability bayes filtering biblography
date: 0-0-2007 0:0
revision:0
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http://www-sigproc.eng.cam.ac.uk/smc/papers.html -- sequential monte carlo methods. (bibliography)
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{22} |
ref: Brown-2001.11
tags: Huntingtons motor_learning intentional implicit cognitive deficits
date: 0-0-2007 0:0
revision:0
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PMID-11673321 http://brain.oxfordjournals.org/cgi/content/full/124/11/2188 :
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{29} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Iterative Linear Quadratic regulator design for nonlinear biological movement systems
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{35} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Overview: a projector light should have good luminous efficiency, have a long life, and most importantly have plenty of energy in the red region of the spectrum. most metal halides have yellow/green lines and blue lines, few have good red lines. http://www.osram.no/brosjyrer/english/K01KAP5_en.pdf in 1000 watt, the Osram Powerstar HQI-TS 1000/d/s looks the best: CRI > 90, 5900K color temperature. Unfortunately, I cannot seem to find any american places to buy this bulb, nor can i determine its average life. It can be bought, at a price, from http://www.svetila.com/eProdaja/product_info.php/products_id/442 { n.b. the osram HMI bulbs are no good-the lifetime is too short} In 400 watt, the Eye Clean Arc MT400D/BUD looks quite good, with a CRI of 90, 6500K color temp. http://www.eyelighting.com/cleanarc.html. EYE also has a ceraarc line, but the 400w bulb is not yet in production (and it has a lower color temperature, 4000K). Can be bought from http://www.businesslights.com/ (N.B. they have spectral charts for many of the lights!)
and fYI, the electrodelass bulbs are made by Osram and are called "ICETRON". They are rather expensive, but last 1e5 hours (!). Typical output is 80 lumens/watt more things of interest:
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{37} |
ref: bookmark-0
tags: Unscented sigma_pint kalman filter speech processing machine_learning SDRE control UKF
date: 0-0-2007 0:0
revision:0
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{76} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
experiment: animals initially learn that a light always lights up after pressing a switch which causes the administration of opioids. in successive trials the animal is not rewarded for pressing the switch, however the light (sometimes?) lights up following lever depression - and the animals continue to press the lever in the abscence of reward -- the reward has been transferred to the conditioned stimulus? http://druglibrary.org/schaffer/heroin/ase/chap_4.htm | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{77} |
ref: Kilgard-1998.03
tags: dopamine basal_forebrain nucleus_basalis cortical_plasticity
date: 0-0-2007 0:0
revision:0
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PMID-9497289[0] Cortical map reorganization enabled by nucleus basalis activity
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{98} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://hardm.ath.cx/pdf/unscentedKalmanFilter.pdf -- the square root transform. contains a nice tabulation of the original algorithm, which i what I use. http://hardm.ath.cx/pdf/unscentedKalmanFilter2000.pdf -- the original, with examples of state, parameter, and dual estimation http://en.wikipedia.org/wiki/Kalman_filter -- wikipedia page, also has the unscented kalman filter http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf - Julier and Ulhmann's original paper. a bit breif. http://www.cs.ubc.ca/~murphyk/Papers/Julier_Uhlmann_mar04.pdf -- Julier and Ulhmann's invited paper, quite excellent. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{103} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
The Computational Neurobiology of Reaching and Pointing - online notes | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{105} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SELECT file, COUNT(file) FROM info2 WHERE unit>1 AND maxinfo/infoshuf > 10 AND analog < 5 GROUP BY file ORDER BY COUNT(file) DESC to count the number of files matching the criteria.. and get aggregate frequentist statistics. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{109} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.bcs.rochester.edu/people/alex/bcs547/readings/WolpertGhahr00.pdf
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{110} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Iso learning approximates a solution to the inverse controller problem in an usupervised behavioral paradigm http://hardm.ath.cx/pdf/isolearning2002.pdf
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{113} |
ref: Barik-1996.1
tags: parkinsons dopamine cerebellum D3 essential tremor ET
date: 0-0-2007 0:0
revision:0
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{117} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11160530 Context Dependency in the Globus Pallidus Internal Segment During Targeted Arm Movements
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{118} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-10970430 Electrophysiological and morphological characteristics of three subtypes of rat globus pallidus neurone in vitro
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{127} |
ref: bookmark-0
tags: thalamus basal ganglia neuroanatomy centromedian red nucleus images
date: 0-0-2007 0:0
revision:0
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http://www.neuroanatomy.wisc.edu/coro97/contents.htm --coronal sections through the thalamus, very nice! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{128} |
ref: bookmark-0
tags: neuroanatomy pulvinar thalamus superior colliculus image gray brainstem
date: 0-0-2007 0:0
revision:0
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http://en.wikipedia.org/wiki/Image:Gray719.png --great, very useful! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{131} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
spindle neurons are found in the insular cortex as well as the anterior cingulate cortex, but only, apparently, in great apes. Activity in the insular cortex has been found to be correlated to feeling empathy. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{141} |
ref: learning-0
tags: motor control primitives nonlinear feedback systems optimization
date: 0-0-2007 0:0
revision:0
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http://hardm.ath.cx:88/pdf/Schaal2003_LearningMotor.pdf not in pubmed. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{140} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-15649663 Composite adaptive control with locally weighted statistical learning.
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{145} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-12899266 Response error correction-a demonstration of improved human-machine performance using real-time EEG monitoring
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{146} |
ref: van-2004.11
tags: anterior cingulate cortex error performance monitoring 2004
date: 0-0-2007 0:0
revision:0
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PMID-15518940 Errors without conflict: implications for performance monitoring theories of anterior cingulate cortex.
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{147} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-12899253 Boosting bit rates and error detection for the classification of fast-paced motor commands based on single-trial EEG analysis
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{148} |
ref: Vidal-2000.01
tags: EEG ERN error negativity conflict resolution 2000
date: 0-0-2007 0:0
revision:0
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PMID-10686362 Is the 'error negativity' specific to errors?
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{151} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11741014 Computational approaches to motor control. Tamar Flash and Terry Sejnowski.
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{153} |
ref: Stefani-1995.09
tags: electrophysiology dopamine basal_ganglia motor learning
date: 0-0-2007 0:0
revision:0
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PMID-8539419 Electrophysiology of dopamine D-1 receptors in the basal ganglia: old facts and new perspectives.
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{155} |
ref: Wannier-2002.01
tags: globus_pallidus electrophysiology caudate putamen basal_ganglia
date: 0-0-2007 0:0
revision:0
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PMID-11924876 Neuronal activity in primate striatum and pallidum related to bimanual motor actions
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{157} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-14526085 Performance Monitoring by the Anterior Cingulate Cortex During Saccade Countermanding locations of neurons http://www.sciencemag.org/content/vol302/issue5642/images/large/se3831902004.jpeg | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{167} |
ref: GarciaRill-1991.01
tags: PPN pedunculopontine nucleus brainstem sleep locomotion consciousness 1991
date: 0-0-2007 0:0
revision:0
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PMID-1887068 The Pedunculopontine nucleus
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{184} |
ref: Harris-1998.08
tags: motor_control error variance optimal_control 1998 wolpert
date: 0-0-2007 0:0
revision:0
[head]
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PMID-9723616[0] Signal-dependent noise determines motor planning
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{189} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.cnsforum.com/imagebank/section/receptor_systems_Dopaminergic/default.aspx
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{191} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-14749432 Action Potential Timing Determines Dendritic Calcium during Striatal Up-States
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{192} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11073866 Ventral Tegmental Area Afferents to the Prefrontal Cortex Maintain Membrane Potential ‘Up’ States in Pyramidal Neurons via D1 Dopamine Receptors
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{193} |
ref: Di-1994.06
tags: dopamine NMDA striatum globus_pallidus ion_channels neurotransmitters
date: 0-0-2007 0:0
revision:0
[head]
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PMID-7521083 Modulatory functions of neurotransmitters in the striatum: ACh/dopamine/NMDA interactions.
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{4} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{8} |
ref: bookmark-0
tags: machine_learning algorithm meta_algorithm
date: 0-0-2006 0:0
revision:0
[head]
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Boost learning or AdaBoost - the idea is to update the discrete distribution used in training any algorithm to emphasize those points that are misclassified in the previous fit of a classifier. sensitive to outliers, but not overfitting. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{14} |
ref: bookmark-0
tags: urban art san_francisco california vector_art mod_art store
date: 0-0-2006 0:0
revision:0
[head]
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http://www.linuxjournal.com/article/8497 here you go timmyh, enjoy.. /joeyo | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{17} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://mattl.co.uk/apache2subversiondebianhowto.html pretty good. SSL and subversion seems to cause problems with apache2 on this 'unstable' Debian build - it complains of a BAD MAC header after a deterministic number of bytes are transmitted. Therefore I moved to port 80 from 443. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{18} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SELECT * FROM `base` WHERE MATCH(`From`, `To`) AGAINST('hanson') ORDER BY `Date` DESC Limit 0, 100
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/etc/apt/sources.list: #deb file:///cdrom/ sarge main deb http://mirrors.kernel.org/debian/ unstable main contrib non-free deb-src http://mirrors.kernel.org/debian/ unstable main contrib non-free deb http://security.debian.org/ stable/updates main contrib non-freelater run as root: # apt-get update # aptitude install aptitude # aptitude -f --with-recommends dist-upgrade # rebootthen you'll probably want to get a newer kernel, ala: http://www.howtoforge.com/forums/showthread.php?t=21 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{20} |
ref: bookmark-0
tags: neural_networks machine_learning matlab toolbox supervised_learning PCA perceptron SOM EM
date: 0-0-2006 0:0
revision:0
[head]
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http://www.ncrg.aston.ac.uk/netlab/index.php n.b. kinda old. (or does that just mean well established?) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{26} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.thomaslockehobbs.com/ -- interetsing photoblog of a globetrotter & laconic harvard intellectual http://www.uni-weimar.de/architektur/InfAR/lehre/Entwurf/Patterns/107/ca_107.html Modern buildings are often shaped with no concern for natural light - they depend almost antirely on artificial light. But buildings which displace natural light as the major source of illumination are not fit places to spend the day. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{28} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LD_PRELOAD=/lib/libgcc_s.so.1 matlab this allows you to command-line call mysql or other programs that use linux's standard libgcc. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{31} |
ref: bookmark-0
tags: job_search professional employment wisdom
date: 0-0-2006 0:0
revision:0
[head]
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{33} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Claymakers 705 Foster St. Durham, NC 27701 (919) 530 - 8355 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{34} |
ref: bookmark-0
tags: linear_algebra solution simultaneous_equations GPGPU GPU LUdecomposition clever
date: 0-0-2006 0:0
revision:0
[head]
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{40} |
ref: bookmark-0
tags: Bayes Baysian_networks probability probabalistic_networks Kalman ICA PCA HMM Dynamic_programming inference learning
date: 0-0-2006 0:0
revision:0
[head]
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http://www.cs.ubc.ca/~murphyk/Bayes/bnintro.html very, very good! many references, well explained too. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{42} |
ref: bookmark-0
tags: microdrilling surgery craniotomy impedance
date: 0-0-2006 0:0
revision:0
[head]
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http://www.pathscientific.com/products.html Pathformer is an electrosurgical hand-held meidcal device that cuts holes in nails and skin. It operates on mesoscissioning technology, cutting the nail/skin with a microcutting tool, using skin impedance as a feedback for stopping the cutting intervention. Pathformer is approved by FDA for creating holes in nails for treating subungual hematoma (black toe). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.iovs.org/cgi/reprint/46/4/1322.pdf A related machine learning classifier, the relevance vector machine (RVM), has recently been introduced, which, unlike SVM, incorporates probabalistic output (probability of membership) through Bayesian inference. Its decision function depends on fewer input variables that SVM, possibly allowing better classification for small data sets with high dimensionality.
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{45} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.newscientist.com/article/dn8859-methanolpowered-artificial-muscles-start-to-flex.html | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{47} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{48} |
ref: bookmark-0
tags: Linux device_drivers memory virtual_memory PCI address_translation
date: 0-0-2006 0:0
revision:0
[head]
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http://www.tldp.org/LDP/khg/HyperNews/get/devices/addrxlate.html | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{51} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.ddj.com/dept/architect/184414658 very logical, well organized. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{52} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.evl.uic.edu/eolmst1/GLSL/ easy to compile on my debian system - all the development libraries had debian packages! also of interest :
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{57} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.cs.rug.nl/~rudy/matlab/
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{59} |
ref: bookmark-0
tags: statistics logistic regression binomial logit BIC AIC SPSS
date: 0-0-2006 0:0
revision:0
[head]
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http://www2.chass.ncsu.edu/garson/PA765/logistic.htm
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{61} |
ref: bookmark-0
tags: smith predictor motor control wolpert cerebellum machine_learning prediction
date: 0-0-2006 0:0
revision:0
[head]
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http://prism.bham.ac.uk/pdf_files/SmithPred_93.PDF
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{63} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{64} |
ref: bookmark-0
tags: neural_recording recording_technology electrical engineering DSP
date: 0-0-2006 0:0
revision:0
[head]
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{66} |
ref: bookmark-0
tags: machine_learning classification entropy information
date: 0-0-2006 0:0
revision:0
[head]
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http://iridia.ulb.ac.be/~lazy/ -- Lazy Learning. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{70} |
ref: notes, bookmark-0
tags: spikes action_potentials neurons subthreshold depolarization c.elegans
date: 0-0-2006 0:0
revision:0
[head]
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"Millisecond-timescale, genetically targeted optical control of neural activity" http://www.nature.com/neuro/journal/v8/n9/full/nn1525.html what they did:
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{72} |
ref: abstract-0
tags: tlh24 error signals in the cortex and basal ganglia reinforcement_learning gradient_descent motor_learning
date: 0-0-2006 0:0
revision:0
[head]
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Title: Error signals in the cortex and basal ganglia. Abstract: Numerous studies have found correlations between measures of neural activity, from single unit recordings to aggregate measures such as EEG, to motor behavior. Two general themes have emerged from this research: neurons are generally broadly tuned and are often arrayed in spatial maps. It is hypothesized that these are two features of a larger hierarchal structure of spatial and temporal transforms that allow mappings to procure complex behaviors from abstract goals, or similarly, complex sensory information to produce simple percepts. Much theoretical work has proved the suitability of this organization to both generate behavior and extract relevant information from the world. It is generally agreed that most transforms enacted by the cortex and basal ganglia are learned rather than genetically encoded. Therefore, it is the characterization of the learning process that describes the computational nature of the brain; the descriptions of the basis functions themselves are more descriptive of the brain’s environment. Here we hypothesize that learning in the mammalian brain is a stochastic maximization of reward and transform predictability, and a minimization of transform complexity and latency. It is probable that the optimizations employed in learning include both components of gradient descent and competitive elimination, which are two large classes of algorithms explored extensively in the field of machine learning. The former method requires the existence of a vectoral error signal, while the latter is less restrictive, and requires at least a scalar evaluator. We will look for the existence of candidate error or evaluator signals in the cortex and basal ganglia during force-field learning where the motor error is task-relevant and explicitly provided to the subject. By simultaneously recording large populations of neurons from multiple brain areas we can probe the existence of error or evaluator signals by measuring the stochastic relationship and predictive ability of neural activity to the provided error signal. From this data we will also be able to track dependence of neural tuning trajectory on trial-by-trial success; if the cortex operates under minimization principles, then tuning change will have a temporal relationship to reward. The overarching goal of this research is to look for one aspect of motor learning – the error signal – with the hope of using this data to better understand the normal function of the cortex and basal ganglia, and how this normal function is related to the symptoms caused by disease and lesions of the brain. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{75} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{79} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
20% of the firing variance was accouted for by the gaze angle. the monkey was free to fixate where he wanted to in this experiment. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{81} |
ref: Stapleton-2006.04
tags: Stapleton Lavine poisson prediction gustatory discrimination statistical_model rats bayes BUGS
date: 0-0-2006 0:0
revision:0
[head]
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{85} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{90} |
ref: bookmark-0
tags: mirror reflective projection lens design NEC optics
date: 0-0-2006 0:0
revision:0
[head]
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http://www.nec.co.jp/techrep/en/journal/g06/n03/060319.html very neat - and I'm surprised that they put all of this on the web! you can almost make one of these yourself with the information within. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{93} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
In a MCMC, the invariant distribution is a eigenvector of the state transition matrix whose eigenvalue is 1! page 372 of http://www.inference.phy.cam.ac.uk/itprnn/book.pdf |