806 research outputs found
Parameters estimation for spatio-temporal maximum entropy distributions: application to neural spike trains
We propose a numerical method to learn Maximum Entropy (MaxEnt) distributions
with spatio-temporal constraints from experimental spike trains. This is an
extension of two papers [10] and [4] who proposed the estimation of parameters
where only spatial constraints were taken into account. The extension we
propose allows to properly handle memory effects in spike statistics, for large
sized neural networks.Comment: 34 pages, 33 figure
Entropy-based parametric estimation of spike train statistics
We consider the evolution of a network of neurons, focusing on the asymptotic
behavior of spikes dynamics instead of membrane potential dynamics. The spike
response is not sought as a deterministic response in this context, but as a
conditional probability : "Reading out the code" consists of inferring such a
probability. This probability is computed from empirical raster plots, by using
the framework of thermodynamic formalism in ergodic theory. This gives us a
parametric statistical model where the probability has the form of a Gibbs
distribution. In this respect, this approach generalizes the seminal and
profound work of Schneidman and collaborators. A minimal presentation of the
formalism is reviewed here, while a general algorithmic estimation method is
proposed yielding fast convergent implementations. It is also made explicit how
several spike observables (entropy, rate, synchronizations, correlations) are
given in closed-form from the parametric estimation. This paradigm does not
only allow us to estimate the spike statistics, given a design choice, but also
to compare different models, thus answering comparative questions about the
neural code such as : "are correlations (or time synchrony or a given set of
spike patterns, ..) significant with respect to rate coding only ?" A numerical
validation of the method is proposed and the perspectives regarding spike-train
code analysis are also discussed.Comment: 37 pages, 8 figures, submitte
A generative spike train model with time-structured higher order correlations
Emerging technologies are revealing the spiking activity in ever larger
neural ensembles. Frequently, this spiking is far from independent, with
correlations in the spike times of different cells. Understanding how such
correlations impact the dynamics and function of neural ensembles remains an
important open problem. Here we describe a new, generative model for correlated
spike trains that can exhibit many of the features observed in data. Extending
prior work in mathematical finance, this generalized thinning and shift (GTaS)
model creates marginally Poisson spike trains with diverse temporal correlation
structures. We give several examples which highlight the model's flexibility
and utility. For instance, we use it to examine how a neural network responds
to highly structured patterns of inputs. We then show that the GTaS model is
analytically tractable, and derive cumulant densities of all orders in terms of
model parameters. The GTaS framework can therefore be an important tool in the
experimental and theoretical exploration of neural dynamics
The effect of heterogeneity on decorrelation mechanisms in spiking neural networks: a neuromorphic-hardware study
High-level brain function such as memory, classification or reasoning can be
realized by means of recurrent networks of simplified model neurons. Analog
neuromorphic hardware constitutes a fast and energy efficient substrate for the
implementation of such neural computing architectures in technical applications
and neuroscientific research. The functional performance of neural networks is
often critically dependent on the level of correlations in the neural activity.
In finite networks, correlations are typically inevitable due to shared
presynaptic input. Recent theoretical studies have shown that inhibitory
feedback, abundant in biological neural networks, can actively suppress these
shared-input correlations and thereby enable neurons to fire nearly
independently. For networks of spiking neurons, the decorrelating effect of
inhibitory feedback has so far been explicitly demonstrated only for
homogeneous networks of neurons with linear sub-threshold dynamics. Theory,
however, suggests that the effect is a general phenomenon, present in any
system with sufficient inhibitory feedback, irrespective of the details of the
network structure or the neuronal and synaptic properties. Here, we investigate
the effect of network heterogeneity on correlations in sparse, random networks
of inhibitory neurons with non-linear, conductance-based synapses. Emulations
of these networks on the analog neuromorphic hardware system Spikey allow us to
test the efficiency of decorrelation by inhibitory feedback in the presence of
hardware-specific heterogeneities. The configurability of the hardware
substrate enables us to modulate the extent of heterogeneity in a systematic
manner. We selectively study the effects of shared input and recurrent
connections on correlations in membrane potentials and spike trains. Our
results confirm ...Comment: 20 pages, 10 figures, supplement
Correlations and functional connections in a population of grid cells
We study the statistics of spike trains of simultaneously recorded grid cells
in freely behaving rats. We evaluate pairwise correlations between these cells
and, using a generalized linear model (kinetic Ising model), study their
functional connectivity. Even when we account for the covariations in firing
rates due to overlapping fields, both the pairwise correlations and functional
connections decay as a function of the shortest distance between the vertices
of the spatial firing pattern of pairs of grid cells, i.e. their phase
difference. The functional connectivity takes positive values between cells
with nearby phases and approaches zero or negative values for larger phase
differences. We also find similar results when, in addition to correlations due
to overlapping fields, we account for correlations due to theta oscillations
and head directional inputs. The inferred connections between neurons can be
both negative and positive regardless of whether the cells share common spatial
firing characteristics, that is, whether they belong to the same modules, or
not. The mean strength of these inferred connections is close to zero, but the
strongest inferred connections are found between cells of the same module.
Taken together, our results suggest that grid cells in the same module do
indeed form a local network of interconnected neurons with a functional
connectivity that supports a role for attractor dynamics in the generation of
the grid pattern.Comment: Accepted for publication in PLoS Computational Biolog
CalciumGAN: A Generative Adversarial Network Model for Synthesising Realistic Calcium Imaging Data of Neuronal Populations
Calcium imaging has become a powerful and popular technique to monitor the
activity of large populations of neurons in vivo. However, for ethical
considerations and despite recent technical developments, recordings are still
constrained to a limited number of trials and animals. This limits the amount
of data available from individual experiments and hinders the development of
analysis techniques and models for more realistic size of neuronal populations.
The ability to artificially synthesize realistic neuronal calcium signals could
greatly alleviate this problem by scaling up the number of trials. Here we
propose a Generative Adversarial Network (GAN) model to generate realistic
calcium signals as seen in neuronal somata with calcium imaging. To this end,
we adapt the WaveGAN architecture and train it with the Wasserstein distance.
We test the model on artificial data with known ground-truth and show that the
distribution of the generated signals closely resembles the underlying data
distribution. Then, we train the model on real calcium signals recorded from
the primary visual cortex of behaving mice and confirm that the deconvolved
spike trains match the statistics of the recorded data. Together, these results
demonstrate that our model can successfully generate realistic calcium imaging
data, thereby providing the means to augment existing datasets of neuronal
activity for enhanced data exploration and modeling
Transformation of stimulus correlations by the retina
Redundancies and correlations in the responses of sensory neurons seem to
waste neural resources but can carry cues about structured stimuli and may help
the brain to correct for response errors. To assess how the retina negotiates
this tradeoff, we measured simultaneous responses from populations of ganglion
cells presented with natural and artificial stimuli that varied greatly in
correlation structure. We found that pairwise correlations in the retinal
output remained similar across stimuli with widely different spatio-temporal
correlations including white noise and natural movies. Meanwhile, purely
spatial correlations tended to increase correlations in the retinal response.
Responding to more correlated stimuli, ganglion cells had faster temporal
kernels and tended to have stronger surrounds. These properties of individual
cells, along with gain changes that opposed changes in effective contrast at
the ganglion cell input, largely explained the similarity of pairwise
correlations across stimuli where receptive field measurements were possible.Comment: author list corrected in metadat
Analyzing Short-Term Noise Dependencies of Spike-Counts in Macaque Prefrontal Cortex Using Copulas and the Flashlight Transformation
Simultaneous spike-counts of neural populations are typically modeled by a Gaussian distribution. On short time scales, however, this distribution is too restrictive to describe and analyze multivariate distributions of discrete spike-counts. We present an alternative that is based on copulas and can account for arbitrary marginal distributions, including Poisson and negative binomial distributions as well as second and higher-order interactions. We describe maximum likelihood-based procedures for fitting copula-based models to spike-count data, and we derive a so-called flashlight transformation which makes it possible to move the tail dependence of an arbitrary copula into an arbitrary orthant of the multivariate probability distribution. Mixtures of copulas that combine different dependence structures and thereby model different driving processes simultaneously are also introduced. First, we apply copula-based models to populations of integrate-and-fire neurons receiving partially correlated input and show that the best fitting copulas provide information about the functional connectivity of coupled neurons which can be extracted using the flashlight transformation. We then apply the new method to data which were recorded from macaque prefrontal cortex using a multi-tetrode array. We find that copula-based distributions with negative binomial marginals provide an appropriate stochastic model for the multivariate spike-count distributions rather than the multivariate Poisson latent variables distribution and the often used multivariate normal distribution. The dependence structure of these distributions provides evidence for common inhibitory input to all recorded stimulus encoding neurons. Finally, we show that copula-based models can be successfully used to evaluate neural codes, e. g., to characterize stimulus-dependent spike-count distributions with information measures. This demonstrates that copula-based models are not only a versatile class of models for multivariate distributions of spike-counts, but that those models can be exploited to understand functional dependencies
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