3,005 research outputs found
Model-free reconstruction of neuronal network connectivity from calcium imaging signals
A systematic assessment of global neural network connectivity through direct
electrophysiological assays has remained technically unfeasible even in
dissociated neuronal cultures. We introduce an improved algorithmic approach
based on Transfer Entropy to reconstruct approximations to network structural
connectivities from network activity monitored through calcium fluorescence
imaging. Based on information theory, our method requires no prior assumptions
on the statistics of neuronal firing and neuronal connections. The performance
of our algorithm is benchmarked on surrogate time-series of calcium
fluorescence generated by the simulated dynamics of a network with known
ground-truth topology. We find that the effective network topology revealed by
Transfer Entropy depends qualitatively on the time-dependent dynamic state of
the network (e.g., bursting or non-bursting). We thus demonstrate how
conditioning with respect to the global mean activity improves the performance
of our method. [...] Compared to other reconstruction strategies such as
cross-correlation or Granger Causality methods, our method based on improved
Transfer Entropy is remarkably more accurate. In particular, it provides a good
reconstruction of the network clustering coefficient, allowing to discriminate
between weakly or strongly clustered topologies, whereas on the other hand an
approach based on cross-correlations would invariantly detect artificially high
levels of clustering. Finally, we present the applicability of our method to
real recordings of in vitro cortical cultures. We demonstrate that these
networks are characterized by an elevated level of clustering compared to a
random graph (although not extreme) and by a markedly non-local connectivity.Comment: 54 pages, 8 figures (+9 supplementary figures), 1 table; submitted
for publicatio
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
Training deep neural density estimators to identify mechanistic models of neural dynamics
Mechanistic modeling in neuroscience aims to explain observed phenomena in terms of underlying causes. However, determining which model parameters agree with complex and stochastic neural data presents a significant challenge. We address this challenge with a machine learning tool which uses deep neural density estimators-- trained using model simulations-- to carry out Bayesian inference and retrieve the full space of parameters compatible with raw data or selected data features. Our method is scalable in parameters and data features, and can rapidly analyze new data after initial training. We demonstrate the power and flexibility of our approach on receptive fields, ion channels, and Hodgkin-Huxley models. We also characterize the space of circuit configurations giving rise to rhythmic activity in the crustacean stomatogastric ganglion, and use these results to derive hypotheses for underlying compensation mechanisms. Our approach will help close the gap between data-driven and theory-driven models of neural dynamics
The Effect of Nonstationarity on Models Inferred from Neural Data
Neurons subject to a common non-stationary input may exhibit a correlated
firing behavior. Correlations in the statistics of neural spike trains also
arise as the effect of interaction between neurons. Here we show that these two
situations can be distinguished, with machine learning techniques, provided the
data are rich enough. In order to do this, we study the problem of inferring a
kinetic Ising model, stationary or nonstationary, from the available data. We
apply the inference procedure to two data sets: one from salamander retinal
ganglion cells and the other from a realistic computational cortical network
model. We show that many aspects of the concerted activity of the salamander
retinal neurons can be traced simply to the external input. A model of
non-interacting neurons subject to a non-stationary external field outperforms
a model with stationary input with couplings between neurons, even accounting
for the differences in the number of model parameters. When couplings are added
to the non-stationary model, for the retinal data, little is gained: the
inferred couplings are generally not significant. Likewise, the distribution of
the sizes of sets of neurons that spike simultaneously and the frequency of
spike patterns as function of their rank (Zipf plots) are well-explained by an
independent-neuron model with time-dependent external input, and adding
connections to such a model does not offer significant improvement. For the
cortical model data, robust couplings, well correlated with the real
connections, can be inferred using the non-stationary model. Adding connections
to this model slightly improves the agreement with the data for the probability
of synchronous spikes but hardly affects the Zipf plot.Comment: version in press in J Stat Mec
Neural population coding: combining insights from microscopic and mass signals
Behavior relies on the distributed and coordinated activity of neural populations. Population activity can be measured using multi-neuron recordings and neuroimaging. Neural recordings reveal how the heterogeneity, sparseness, timing, and correlation of population activity shape information processing in local networks, whereas neuroimaging shows how long-range coupling and brain states impact on local activity and perception. To obtain an integrated perspective on neural information processing we need to combine knowledge from both levels of investigation. We review recent progress of how neural recordings, neuroimaging, and computational approaches begin to elucidate how interactions between local neural population activity and large-scale dynamics shape the structure and coding capacity of local information representations, make them state-dependent, and control distributed populations that collectively shape behavior
Dynamic Adaptive Computation: Tuning network states to task requirements
Neural circuits are able to perform computations under very diverse
conditions and requirements. The required computations impose clear constraints
on their fine-tuning: a rapid and maximally informative response to stimuli in
general requires decorrelated baseline neural activity. Such network dynamics
is known as asynchronous-irregular. In contrast, spatio-temporal integration of
information requires maintenance and transfer of stimulus information over
extended time periods. This can be realized at criticality, a phase transition
where correlations, sensitivity and integration time diverge. Being able to
flexibly switch, or even combine the above properties in a task-dependent
manner would present a clear functional advantage. We propose that cortex
operates in a "reverberating regime" because it is particularly favorable for
ready adaptation of computational properties to context and task. This
reverberating regime enables cortical networks to interpolate between the
asynchronous-irregular and the critical state by small changes in effective
synaptic strength or excitation-inhibition ratio. These changes directly adapt
computational properties, including sensitivity, amplification, integration
time and correlation length within the local network. We review recent
converging evidence that cortex in vivo operates in the reverberating regime,
and that various cortical areas have adapted their integration times to
processing requirements. In addition, we propose that neuromodulation enables a
fine-tuning of the network, so that local circuits can either decorrelate or
integrate, and quench or maintain their input depending on task. We argue that
this task-dependent tuning, which we call "dynamic adaptive computation",
presents a central organization principle of cortical networks and discuss
first experimental evidence.Comment: 6 pages + references, 2 figure
Pairwise Ising model analysis of human cortical neuron recordings
During wakefulness and deep sleep brain states, cortical neural networks show
a different behavior, with the second characterized by transients of high
network activity. To investigate their impact on neuronal behavior, we apply a
pairwise Ising model analysis by inferring the maximum entropy model that
reproduces single and pairwise moments of the neuron's spiking activity. In
this work we first review the inference algorithm introduced in Ferrari,Phys.
Rev. E (2016). We then succeed in applying the algorithm to infer the model
from a large ensemble of neurons recorded by multi-electrode array in human
temporal cortex. We compare the Ising model performance in capturing the
statistical properties of the network activity during wakefulness and deep
sleep. For the latter, the pairwise model misses relevant transients of high
network activity, suggesting that additional constraints are necessary to
accurately model the data.Comment: 8 pages, 3 figures, Geometric Science of Information 2017 conferenc
A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data
Deducing the structure of neural circuits is one of the central problems of
modern neuroscience. Recently-introduced calcium fluorescent imaging methods
permit experimentalists to observe network activity in large populations of
neurons, but these techniques provide only indirect observations of neural
spike trains, with limited time resolution and signal quality. In this work we
present a Bayesian approach for inferring neural circuitry given this type of
imaging data. We model the network activity in terms of a collection of coupled
hidden Markov chains, with each chain corresponding to a single neuron in the
network and the coupling between the chains reflecting the network's
connectivity matrix. We derive a Monte Carlo Expectation--Maximization
algorithm for fitting the model parameters; to obtain the sufficient statistics
in a computationally-efficient manner, we introduce a specialized
blockwise-Gibbs algorithm for sampling from the joint activity of all observed
neurons given the observed fluorescence data. We perform large-scale
simulations of randomly connected neuronal networks with biophysically
realistic parameters and find that the proposed methods can accurately infer
the connectivity in these networks given reasonable experimental and
computational constraints. In addition, the estimation accuracy may be improved
significantly by incorporating prior knowledge about the sparseness of
connectivity in the network, via standard L penalization methods.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS303 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
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