5,054 research outputs found
Neural system identification for large populations separating "what" and "where"
Neuroscientists classify neurons into different types that perform similar
computations at different locations in the visual field. Traditional methods
for neural system identification do not capitalize on this separation of 'what'
and 'where'. Learning deep convolutional feature spaces that are shared among
many neurons provides an exciting path forward, but the architectural design
needs to account for data limitations: While new experimental techniques enable
recordings from thousands of neurons, experimental time is limited so that one
can sample only a small fraction of each neuron's response space. Here, we show
that a major bottleneck for fitting convolutional neural networks (CNNs) to
neural data is the estimation of the individual receptive field locations, a
problem that has been scratched only at the surface thus far. We propose a CNN
architecture with a sparse readout layer factorizing the spatial (where) and
feature (what) dimensions. Our network scales well to thousands of neurons and
short recordings and can be trained end-to-end. We evaluate this architecture
on ground-truth data to explore the challenges and limitations of CNN-based
system identification. Moreover, we show that our network model outperforms
current state-of-the art system identification models of mouse primary visual
cortex.Comment: NIPS 201
Tissue resolved, gene structure refined equine transcriptome.
BackgroundTranscriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome.ResultsThis equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome.ConclusionsWe have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome
High accuracy decoding of dynamical motion from a large retinal population
Motion tracking is a challenge the visual system has to solve by reading out
the retinal population. Here we recorded a large population of ganglion cells
in a dense patch of salamander and guinea pig retinas while displaying a bar
moving diffusively. We show that the bar position can be reconstructed from
retinal activity with a precision in the hyperacuity regime using a linear
decoder acting on 100+ cells. The classical view would have suggested that the
firing rates of the cells form a moving hill of activity tracking the bar's
position. Instead, we found that ganglion cells fired sparsely over an area
much larger than predicted by their receptive fields, so that the neural image
did not track the bar. This highly redundant organization allows for diverse
collections of ganglion cells to represent high-accuracy motion information in
a form easily read out by downstream neural circuits.Comment: 23 pages, 7 figure
Blindfold learning of an accurate neural metric
The brain has no direct access to physical stimuli, but only to the spiking
activity evoked in sensory organs. It is unclear how the brain can structure
its representation of the world based on differences between those noisy,
correlated responses alone. Here we show how to build a distance map of
responses from the structure of the population activity of retinal ganglion
cells, allowing for the accurate discrimination of distinct visual stimuli from
the retinal response. We introduce the Temporal Restricted Boltzmann Machine to
learn the spatiotemporal structure of the population activity, and use this
model to define a distance between spike trains. We show that this metric
outperforms existing neural distances at discriminating pairs of stimuli that
are barely distinguishable. The proposed method provides a generic and
biologically plausible way to learn to associate similar stimuli based on their
spiking responses, without any other knowledge of these stimuli
Diversity improves performance in excitable networks
As few real systems comprise indistinguishable units, diversity is a hallmark
of nature. Diversity among interacting units shapes properties of collective
behavior such as synchronization and information transmission. However, the
benefits of diversity on information processing at the edge of a phase
transition, ordinarily assumed to emerge from identical elements, remain
largely unexplored. Analyzing a general model of excitable systems with
heterogeneous excitability, we find that diversity can greatly enhance optimal
performance (by two orders of magnitude) when distinguishing incoming inputs.
Heterogeneous systems possess a subset of specialized elements whose capability
greatly exceeds that of the nonspecialized elements. Nonetheless, the behavior
of the whole network can outperform all subgroups. We also find that diversity
can yield multiple percolation, with performance optimized at tricriticality.
Our results are robust in specific and more realistic neuronal systems
comprising a combination of excitatory and inhibitory units, and indicate that
diversity-induced amplification can be harnessed by neuronal systems for
evaluating stimulus intensities.Comment: 17 pages, 7 figure
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Tbr1 instructs laminar patterning of retinal ganglion cell dendrites.
Visual information is delivered to the brain by >40 types of retinal ganglion cells (RGCs). Diversity in this representation arises within the inner plexiform layer (IPL), where dendrites of each RGC type are restricted to specific sublaminae, limiting the interneuronal types that can innervate them. How such dendritic restriction arises is unclear. We show that the transcription factor Tbr1 is expressed by four mouse RGC types with dendrites in the outer IPL and is required for their laminar specification. Loss of Tbr1 results in elaboration of dendrites within the inner IPL, while misexpression in other cells retargets their neurites to the outer IPL. Two transmembrane molecules, Sorcs3 and Cdh8, act as effectors of the Tbr1-controlled lamination program. However, they are expressed in just one Tbr1+ RGC type, supporting a model in which a single transcription factor implements similar laminar choices in distinct cell types by recruiting partially non-overlapping effectors
Coexistence of critical sensitivity and subcritical specificity can yield optimal population coding
The vicinity of phase transitions selectively amplifies weak stimuli,
yielding optimal sensitivity to distinguish external input. Along with this
enhanced sensitivity, enhanced levels of fluctuations at criticality reduce the
specificity of the response. Given that the specificity of the response is
largely compromised when the sensitivity is maximal, the overall benefit of
criticality for signal processing remains questionable. Here it is shown that
this impasse can be solved by heterogeneous systems incorporating functional
diversity, in which critical and subcritical components coexist. The subnetwork
of critical elements has optimal sensitivity, and the subnetwork of subcritical
elements has enhanced specificity. Combining segregated features extracted from
the different subgroups, the resulting collective response can maximise the
tradeoff between sensitivity and specificity measured by the
dynamic-range-to-noise-ratio. Although numerous benefits can be observed when
the entire system is critical, our results highlight that optimal performance
is obtained when only a small subset of the system is at criticality.Comment: 7 pages, 4 figure
Information transmission in normal vision and optogenetically resensitised dystrophic retinas
Phd ThesisThe retina is a sophisticated image processing machine, transforming the visual scene as
detected by the photoreceptors into a pattern of action potentials that is sent to the brain
by the retinal ganglion cells (RGCs), where it is further processed to help us understand
and navigate the world. Understanding this encoding process is important on a number
of levels. First, it informs the study of upstream visual processing by elucidating the
signals higher visual areas receive as input and how they relate to the outside world.
Second, it is important for the development of treatments for retinal blindness, such
as retinal prosthetics. In this thesis, I present work using multielectrode array (MEA)
recordings of RGC populations from ex-vivo retinal wholemounts to study various aspects
of retinal information processing. My results fall into two main themes. In the rst part, in
collaboration with Dr Geo rey Portelli and Dr Pierre Kornprobst of INRIA, I use
ashed
gratings of varying spatial frequency and phase to compare di erent coding strategies that
the retina might use. These results show that information is encoded synergistically by
pairs of neurons and that, of the codes tested, a Rank Order Code based on the relative
order of ring of the rst spikes of a population of neurons following a stimulus provides
information about the stimulus faster and more e ciently than other codes. In the later
parts, I use optogenetic stimulation of RGCs in congenitally blind retinas to study how
visual information is corrupted by the spontaneous hyperactivity that arises as a result
of photoreceptor degeneration. I show that by dampening this activity with the gap
junction blocker meclofenamic acid, I can improve the signal-to-noise ratio, spatial acuity
and contrast sensitivity of prosthetically evoked responses. Taken together, this work
provides important insights for the future development of retinal prostheses
Clustering of neural activity: A design principle for population codes
We propose that correlations among neurons are generically strong enough to organize neural activity patterns into a discrete set of clusters, which can each be viewed as a population codeword. Our reasoning starts with the analysis of retinal ganglion cell data using maximum entropy models, showing that the population is robustly in a frustrated, marginally sub-critical, or glassy, state. This leads to an argument that neural populations in many other brain areas might share this structure. Next, we use latent variable models to show that this glassy state possesses well-defined clusters of neural activity. Clusters have three appealing properties: (i) clusters exhibit error correction, i.e., they are reproducibly elicited by the same stimulus despite variability at the level of constituent neurons; (ii) clusters encode qualitatively different visual features than their constituent neurons; and (iii) clusters can be learned by downstream neural circuits in an unsupervised fashion. We hypothesize that these properties give rise to a “learnable” neural code which the cortical hierarchy uses to extract increasingly complex features without supervision or reinforcement
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