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{1575} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1573} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-36070680 Extracellular vesicles mediate the communication of adipose tissue with brain and promote cognitive impairment associated with insulin resistance
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{1572} |
ref: -2019
tags: Piantadosi cogntion combinators function logic
date: 09-05-2022 01:57 gmt
revision:0
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{1564} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
“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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Some investigations into denoising models & their intellectual lineage: Deep Unsupervised Learning using Nonequilibrium Thermodynamics 2015
Generative Modeling by Estimating Gradients of the Data Distribution July 2019
Denoising Diffusion Probabilistic Models June 2020
Improved Denoising Diffusion Probabilistic Models Feb 2021
Diffusion Models Beat GANs on Image Synthesis May 2021
In all of above, it seems that the inverse-diffusion function approximator is a minor player in the paper -- but of course, it's vitally important to making the system work. In some sense, this 'diffusion model' is as much a means of training the neural network as it is a (rather inefficient, compared to GANs) way of sampling from the data distribution. In Nichol & Dhariwal Feb 2021, they use a U-net convolutional network (e.g. start with few channels, downsample and double the channels until there are 128-256 channels, then upsample x2 and half the channels) including multi-headed attention. Ho 2020 used single-headed attention only at the 16x16 level. Ho 2020 in turn was based on PixelCNN++
which is an improvement to (e.g. add selt-attention layers) Conditional Image Generation with PixelCNN Decoders
Most recently, GLIDE: Towards Photorealistic Image Generation and Editing with Text-Guided Diffusion Models
Added text-conditional generation + many more parameters + much more compute to yield very impressive image results + in-painting. This last effect is enabled by the fact that it's a full generative denoising probabilistic model -- you can condition on other parts of the image! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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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{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 :-) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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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{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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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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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{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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{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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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
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SCAN: learning hierarchical compositional concepts
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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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Accelerated FRET-PAINT Microscopy
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Why multifactor?
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PMID-27690349 Nonlinear Hebbian Learning as a Unifying Principle in Receptive Field Formation
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{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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PMID-26352471 Labelling and optical erasure of synaptic memory traces in the motor cortex
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PMID-22388818 Corticostriatal plasticity is necessary for learning intentional neuroprosthetic skills.
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PMID-15928412[0] Naive coadaptive Control May 2005. see notes ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1472} |
ref: -0
tags: computational neuroscience opinion tony zador konrad kording lillicrap
date: 07-30-2019 21:04 gmt
revision:0
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Two papers out recently in Arxive and Biorxiv:
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{1467} |
ref: -2017
tags: neuromorphic optical computing nanophotonics
date: 06-17-2019 14:46 gmt
revision:5
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Progress in neuromorphic photonics
See also :
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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
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Deep Learning with Coherent Nanophotonic Circuits
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Nanoelectronic Programmable Synapses Based on Phase Change Materials for Brain-Inspired Computing
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PMID-25112683 Subcellular Neural Probes from Single-Crystal Gold Nanowires
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PMID-101388[0] Fine control of operantly conditioned firing patterns of cortical neurons.
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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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PMID-27545715 High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA.
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Audio AI: isolating vocals from stereo music using Convolutional Neural Networks
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Training neural networks with local error signals
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{1433} |
ref: -2008
tags: representational similarity analysis fMRI
date: 02-15-2019 02:27 gmt
revision:1
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PMID-19104670 Representational Similarity Analysis – Connecting the Branches of Systems Neuroscience
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PMID-28777724 Active inference, curiosity and insight. Karl J. Friston, Marco Lin, Christopher D. Frith, Giovanni Pezzulo,
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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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New Evidence for the Strange Geometry of Thought
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PMID-27934860 Scanning superlens microscopy for non-invasive large field-of-view visible light nanoscale imaging
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PMID-24711417 Evidence for a causal inverse model in an avian cortico-basal ganglia circuit
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PMID-26436341 Three-dimensional macroporous nanoelectronic networks as minimally invasive brain probes.
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{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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{1394} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Materials and technologies for soft implantable neuroprostheses
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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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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{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
[head]
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PMID-24487777 Iridium oxide nanotube electrodes for sensitive and prolonged intracellular measurement of action potentials. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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
[head]
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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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{1375} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-22905231 Neuronal recordings with solid-conductor intracellular nanoelectrodes (SCINEs).
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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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{1369} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-22231664 Vertical nanowire electrode arrays as a scalable platform for intracellular interfacing to neuronal circuits.
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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
[0] [head]
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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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{1358} |
ref: -0
tags: china trustwothiness social engineering communism
date: 10-31-2016 05:42 gmt
revision:1
[0] [head]
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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1328} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Utah/blackrock group has been working on improving the longevity of their parlyene encapsulation with the addition of ~50nm Al2O3.
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{1266} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Thin films and microelectrode arrays for neuroprosthetics
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{1313} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Neural Stimulation and Recording with Bidirectional, Soft Carbon Nanotube Fiber Microelectrodes
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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
[head]
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PMID-8982987 Metallized polymer fibers as leadwires and intrafascicular microelectrodes
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{1288} |
ref: -0
tags: automatic programming inductive functional igor
date: 07-29-2014 02:07 gmt
revision:0
[head]
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Inductive Rule Learning on the Knowledge Level.
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{1269} |
ref: -0
tags: hinton convolutional deep networks image recognition 2012
date: 01-11-2014 20:14 gmt
revision:0
[head]
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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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{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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{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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{1226} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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{1243} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-5734597 (pdf) A novel platinum nanowire-coated neural electrode and its electrochemical and biological characterization
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{1238} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-23428842 Chronic intracortical microelectrode arrays induce non-uniform, depth-related tissue responses.
This result is supported by previous papers:
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{1235} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PLoS One: PMID-23251670 Ultra-Bright and -Stable Red and Near-Infrared Squaraine Fluorophores for In Vivo Two-Photon Imaging
PMID-22056675 A gene-fusion strategy for stoichiometric and co-localized expression of light-gated membrane proteins
PMID-22056675 Substantial Generalization of Sensorimotor Learning from Bilateral to Unilateral Movement Conditions
PMID-23408972 Credit Assignment during Movement Reinforcement Learning
PMID-23382796 Visuomotor Learning Enhanced by Augmenting Instantaneous Trajectory Error Feedback during Reaching
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0054771 Flexible Switching of Feedback Control Mechanisms Allows for Learning of Different Task Dynamics
PMID-23365648 Recognizing Sights, Smells, and Sounds with Gnostic Fields
PMID-23300606 Decoding Hindlimb Movement for a Brain Machine Interface after a Complete Spinal Transection
Journal of Neural Engineering: PMID-23449002 Model-based rational feedback controller design for closed-loop deep brain stimulation of Parkinson's disease.
PMID-23428966 Improving brain-machine interface performance by decoding intended future movements.
PMID-23428937 An implantable wireless neural interface for recording cortical circuit dynamics in moving primates.
PMID-23428877 Local-learning-based neuron selection for grasping gesture prediction in motor brain machine interfaces.
PMID-22954906 Sparse decoding of multiple spike trains for brain-machine interfaces.
PMID-23010756 Comprehensive characterization and failure modes of tungsten microwire arrays in chronic neural implants.
PMID-23283391 Performance of conducting polymer electrodes for stimulating neuroprosthetics.
PMID-23160018 Properties and application of a multichannel integrated circuit for low-artifact, patterned electrical stimulation of neural tissue.
Nature Methods: PMID-23524393 Whole-brain functional imaging at cellular resolution using light-sheet microscopy
PMID-23142873 Two-photon optogenetics of dendritic spines and neural circuits
Nanowires, useful for Flip's idea.
Of personal interest: Richardson-Lucy (RL) deconvolution for sub-diffraction limit imaging. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056624 Collaborative Filtering for Brain-Computer Interaction Using Transfer Learning
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0055518 Brain Training Game Boosts Executive Functions, Working Memory and Processing
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0061390 Cognitive Training Improves Sleep Quality and Cognitive Function among Older Adults with Insomnia
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0054402 Perceived Multi-Tasking Ability, Impulsivity, and Sensation Seeking
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0052500 Learning and Long-Term Retention of Large-Scale Artificial Languages
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0052042 Non-Hebbian Learning Implementation in Light-Controlled Resistive Memory Devices
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0058284 Attractor Metabolic Networks
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0059196 Prenatal Exposure to a Polychlorinated Biphenyl (PCB) Congener Influences Fixation Duration on Biological Motion at 4-Months-Old: A Preliminary Study
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0060437 Hunger in the Absence of Caloric Restriction Improves Cognition and Attenuates Alzheimer's Disease Pathology in a Mouse Model
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{999} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
IEEE-4065599 (pdf) Comments on Microelectrodes
____References____ ' ''' () | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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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{1214} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-7972766 Brain and cerebrospinal fluid motion: real-time quantification with M-mode MR imaging.
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{897} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21654037[0] In vivo deployment of mechanically adaptive nanocomposites for intracortical microelectrodes
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{913} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-21499255[0] Reversible large-scale modification of cortical networks during neuroprosthetic control.
Other notes:
____References____
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{270} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-16838014[] Neuronal ensemble control of prosthetic devices by a human with tetraplegia
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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{1157} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-22448159 Spike sorting of heterogeneous neuron types by multimodality-weighted PCA and explicit robust variational Bayes.
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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.
____References____
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{991} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19299613[0] Spinal cord stimulation restores locomotion in animal models of Parkinson's disease.
____References____
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{1098} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-18037630[0] Bilateral stimulation in the caudal zona incerta nucleus for tremor control
____References____
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{1120} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Relevant papers:
VIM:
Stem cells / Gene therapy:
Non-dbs:
____References____
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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
[head]
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PMID-7326562 Locomotor control in macaque monkeys
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{1136} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11285003 Dopaminergic control of synaptic plasticity in the dorsal striatum.
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{1141} |
ref: -0
tags: putamen functional organization basal ganglia
date: 02-24-2012 21:01 gmt
revision:0
[head]
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PMID-6705861 Single cell studies of the primate putamen. I. Functional organization.
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{168} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-7284825[0] Connections of the subthalamic nucleus in the monkey.
____References____
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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
____References____
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{970} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-19050033[0] Levodopa enhances synaptic plasticity in the substantia nigra pars reticulata of Parkinson's disease patients
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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-7711769[0] Functional anatomy of the basal ganglia. I. The cortico-basal ganglia-thalamo-cortical loop.
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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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{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
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PMID-14607789[0] The subthalamic nucleus in the context of movement disorders
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PMID-7711765[0] Functional anatomy of the basal ganglia. II. The place of subthalamic nucleus and external pallidum in basal ganglia circuitry.
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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-21867795[0] Deep brain stimulation: BCI at large, where are we going to?
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PMID-10888744[0] Axonal branching pattern of neurons of the subthalamic nucleus in primates
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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-1707079 Subthalamic nucleus of the monkey: connections and immunocytochemical features of afferents.
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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-980081[0] Treatment and prognosis of hemiballismus.
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PMID-16280671[0] Deep-brain stimulation in Parkinson's disease: long-term efficacy and safety - What happened this year?
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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-6869036[0] The Piper rhythm--a phenomenon related to muscle resonance characteristics?
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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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{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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IEEE-5969351 (pdf) New class of chronic recording multichannel neural probes with post-implant self-deployed satellite recording sites | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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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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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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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-3957372[0] Solid-state electrodes for multichannel multiplexed intracortical neuronal recording.
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PMID-95711[0] Spike separation in multiunit records: A multivariate analysis of spike descriptive parameters
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PMID-19621062 Emergence of a stable cortical map for neuroprosthetic control.
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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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-14624244[0] Learning to control a brain-machine interface for reaching and grasping by primates.
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PMID-18923392[0] Direct control of paralysed muscles by cortical neurons.
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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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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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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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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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PMID-17978021[0] Biomimetic Brain Machine Interfaces for the Control of Movement.
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PMID-1510294[0] A Glass/silicon Composite Intracortical Electrode Array.
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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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-13969854[0] Control and Training of Individual Motor Units
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{1016} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
bibtex: Lilly-1958 Correlations between Neurophysiological Activity in the Cortex and Short-Term Behavior in the Monkey
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bibtex:Lilly-1950 A Method of Recording the Moving Electrical Potential Gradients in the Brain. The 25-Channel Bavatron and Electro-Iconograms.
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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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-17793797[0] Tungsten Microelectrode for Recording from Single Units.
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PMID-11240278[0] Functions of mammalian spinal interneurons during movement
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PMID-17554826[0] A fully integrated mixed-signal neural processor for implantable multichannel cortical recording.
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bibtex:Olson-2005 Evidence of a mechanism of neural adaptation in the closed loop control of directions
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PMID-2345003[0] Strength characterization of silicon microprobes in neurophysiological tissues.
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{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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PMID-20705858[0] Three-Dimensional, Flexible Nanoscale Field-Effect Transistors as Localized Bioprobes
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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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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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http://www.neuroanatomy.wisc.edu/virtualbrain/BrainStem/06Olive.html
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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; | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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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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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PMID-15132510[0] A fully Integrated Neural Recording Amplifier with DC Input Stabilization
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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-8351520[0] Dynamics of the hippocampal ensemble code for space.
PMID-8036517[1] Reactivation of hippocampal ensemble memories during sleep.
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{741} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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-15651568[0] A compact large voltage-compliance high output-impedance programmable current source for implantable microstimulators.
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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-16291944[0] Stable ensemble performance with single-neuron variability during reaching movements in primates.
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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-20404313[0] Spinal cord stimulation failed to relieve akinesia or restore locomotion in Parkinson disease.
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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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{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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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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{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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PMID-4399123[0] The connexions of the striatum and globus pallidus: synthesis and speculation. !! great figures, great synthesis !!
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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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PMID-10681435 Cortical correlates of learning in monkey adapting to a new dynamical environment. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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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"The Truth Wears Off" by Jonah Lehrer, the New Yorker.
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{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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Historical notes from using the Kinarm... this only seems to render properly in firefox / mozilla. To apply cartesian force fields to the arm, the original kinarm PLCC (whatever that stands for) converted joint velocities to cartesian veolocities using the jacobian matrix. All well and good. The equation for endpoint location of the kinarm is:
L_1 = 0.115 meters, l_2 = 0.195 meters in our case. The jacobian of this function is: etc. and (I think!) where tau is the shoulder and elbow torques and F is the cartesian force. The flow of the PLCC is then:
substitute to see if the matrices look similar ...
where
I'm surprised that we got something even like curl and viscous forces - the matrices are not similar. This explains why the forces seemed odd and poorly scaled, and why the constants for the viscious and curl fields were so small (the units should have been N/(cm/s) - 1 newton is a reasonable force, and the monkey moves at around 10cm/sec, so the constant should have been 1/10 or so. Instead, we usually put in a value of 0.0005 ! For typical values of the shoulder and elbow angles, the determinant of the matrix is 200 (the kinarm PLCC works in centimeters, not meters), so the transpose has entries ~ 200 x too big. Foolishly we compensated by making the constant (or entries in A) 200 times to small. i.e. 1/10 * 1/200 = 0.0005 :( The end result is that a density-plot of the space spanned by the cartesian force and velocity is not very clean, as you can see in the picture below. The horizontal line is, of course, when the forces were turned off. A linear relationship between force and velocity should be manifested by a line in these plots - however, there are only suggestions of lines. The null field should have a negative - slope line in upper left and lower right; the curl field should have a positive sloped line in the upper right and negative in the lower left (or vice-vercia). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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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{827} |
ref: OSuilleabhain-1998.11
tags: analysis tremor parkinsons disease
date: 07-19-2010 19:22 gmt
revision:2
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PMID-9827772[0] Time-frequency analysis of tremor
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Studies in astronomical time series analysis. II - Statistical aspects of spectral analysis of unevenly spaced data Scargle, J. D.
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images/824_1.pdf -- Eurisko by DB Lenat, the program that made the fleet which won the 1981 and 1982 Traveller's challenge, as I discovered in this New Yorker article by Malcolm Gladwell.
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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." | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{818} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Say you have a program, called from a perl script, that may run for a long time. Get at the program's output as it appears? Simple - open a pipe to the programs STDOUT. See http://docstore.mik.ua/orelly/perl/prog3/ch16_03.htm Below is an example - I wanted to see the output of programs run, for convenience, from a perl script (didn't want to have to remember - or get wrong - all the command line arguments for each). #!/usr/bin/perl $numArgs = $#ARGV + 1; if($numArgs == 1){ if($ARGV[0] eq "table"){ open STATUS, "sudo ./video 0xc1e9 15 4600 4601 0 |"; while(<STATUS>){ print ; } close STATUS ; }elsif($ARGV[0] eq "arm"){ open STATUS, "sudo ./video 0x1ff6 60 4597 4594 4592 |"; while(<STATUS>){ print ; } close STATUS ; }else{ print "$ARGV[0] not understood - say arm or table!\n"; } } | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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!) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{793} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Andrew Ng's notes on learning theory
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{790} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.carolinamtnclub.com/%5CHiking%5Cgoogle%5C511.htm awesome place! but watch out for the cows! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{786} |
ref: -0
tags: linux keyboard international characters symbols
date: 10-01-2009 14:09 gmt
revision:1
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{690} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-10404201 Real-time control of a robot arm using simultaneously recorded neurons in the motor cortex.
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{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! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{764} |
ref: work-0
tags: ocaml mysql programming functional
date: 07-03-2009 19:16 gmt
revision:2
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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{733} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Moral Saints by Susan Wolf
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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
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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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{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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{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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{680} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17406665[0] Daytime naps, motor memory consolidation and regionally specific sleep spindles.
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{689} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-18958234 Endocannabinoid Signaling is Critical for Habit Formation.
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{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 :-) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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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{609} |
ref: -0
tags: differential dynamic programming machine learning
date: 09-24-2008 23:39 gmt
revision:2
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{590} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{588} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{551} |
ref: notes-0
tags: DNA transfection yasuda experiment8
date: 03-17-2008 20:11 gmt
revision:2
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{536} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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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{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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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{354} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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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{304} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-4991377[0] Predicting measures of motor performance from multiple cortical spike trains. Recordings have been obtained simultaneously from several, individually selected neurons in the motor cortex of unanesthetized monkey as the animal performed simple arm movements. With the use of comparatively simple quantitative procedures, the activity of small sets of cells was found to be adequate for rather accurate real-time prediction of the time course of various response measurements. In addition, the results suggest that hypotheses concerning the response variables "controlled" by cortical motor systems may well depend upon whether or not the temporal relations between simultaneously active neurons are taken into account. cited in miguel's book, "Methods for Neural ensemble recordings". However, I can't get the text online. ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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PMID-4219745[0] Relation of basal ganglia, cerebellum, and motor cortex units to ramp and ballistic limb movements.
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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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{259} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-17271543[] http://hardm.ath.cx:88/pdf/sanchez2004.pdf ____References____ | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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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{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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go there!! be frightened!! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{247} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-8235208[] Effects of the stimulation of the subthalamic nucleus in Parkinson disease
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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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{233} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-10380964 Monkey globus pallidus external segment neurons projecting to the neostriatum.
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{229} |
ref: notes-0
tags: SNR MSE error multidimensional mutual information
date: 03-08-2007 22:33 gmt
revision:2
[1] [0] [head]
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http://ieeexplore.ieee.org/iel5/516/3389/00116771.pdf or http://hardm.ath.cx:88/pdf/MultidimensionalSNR.pdf
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{211} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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! | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{151} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PMID-11741014 Computational approaches to motor control. Tamar Flash and Terry Sejnowski.
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{31} |
ref: bookmark-0
tags: job_search professional employment wisdom
date: 0-0-2006 0:0
revision:0
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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
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http://www.cs.ubc.ca/~murphyk/Bayes/bnintro.html very, very good! many references, well explained too. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{45} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
http://www.newscientist.com/article/dn8859-methanolpowered-artificial-muscles-start-to-flex.html | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{63} | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
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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. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
{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
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