680 research outputs found
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
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
Spike train statistics and Gibbs distributions
This paper is based on a lecture given in the LACONEU summer school,
Valparaiso, January 2012. We introduce Gibbs distribution in a general setting,
including non stationary dynamics, and present then three examples of such
Gibbs distributions, in the context of neural networks spike train statistics:
(i) Maximum entropy model with spatio-temporal constraints; (ii) Generalized
Linear Models; (iii) Conductance based Inte- grate and Fire model with chemical
synapses and gap junctions.Comment: 23 pages, submitte
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
Forward and Backward Modelling: From Single Cells to Neural Population and Back
Some aspects of forward and backward neural modelling are discussed, showing, that the neural mass models may provide a “golden midway” between the detailed conductance based neuron models and the oversimplified models, dealing with the input–output transformations only. Our analysis combines historical perspectives and recent developments concerning neural mass models as a third option for modelling large neural populations and inclusion of detailed anatomical data into them. The current source density analysis and the geometrical assumption behind the different methods, as an inverse modelling tool for determination of the sources of the local field potential is discussed, with special attention to the recent results about source localization on single neurons. These new applications may pave the way to the emergence of a new field of micro-electric imaging
Revealing networks from dynamics: an introduction
What can we learn from the collective dynamics of a complex network about its
interaction topology? Taking the perspective from nonlinear dynamics, we
briefly review recent progress on how to infer structural connectivity (direct
interactions) from accessing the dynamics of the units. Potential applications
range from interaction networks in physics, to chemical and metabolic
reactions, protein and gene regulatory networks as well as neural circuits in
biology and electric power grids or wireless sensor networks in engineering.
Moreover, we briefly mention some standard ways of inferring effective or
functional connectivity.Comment: Topical review, 48 pages, 7 figure
Inferring Synaptic Structure in presence of Neural Interaction Time Scales
Biological networks display a variety of activity patterns reflecting a web
of interactions that is complex both in space and time. Yet inference methods
have mainly focused on reconstructing, from the network's activity, the spatial
structure, by assuming equilibrium conditions or, more recently, a
probabilistic dynamics with a single arbitrary time-step. Here we show that,
under this latter assumption, the inference procedure fails to reconstruct the
synaptic matrix of a network of integrate-and-fire neurons when the chosen time
scale of interaction does not closely match the synaptic delay or when no
single time scale for the interaction can be identified; such failure,
moreover, exposes a distinctive bias of the inference method that can lead to
infer as inhibitory the excitatory synapses with interaction time scales longer
than the model's time-step. We therefore introduce a new two-step method, that
first infers through cross-correlation profiles the delay-structure of the
network and then reconstructs the synaptic matrix, and successfully test it on
networks with different topologies and in different activity regimes. Although
step one is able to accurately recover the delay-structure of the network, thus
getting rid of any \textit{a priori} guess about the time scales of the
interaction, the inference method introduces nonetheless an arbitrary time
scale, the time-bin used to binarize the spike trains. We therefore
analytically and numerically study how the choice of affects the inference
in our network model, finding that the relationship between the inferred
couplings and the real synaptic efficacies, albeit being quadratic in both
cases, depends critically on for the excitatory synapses only, whilst
being basically independent of it for the inhibitory ones
Linear response for spiking neuronal networks with unbounded memory
We establish a general linear response relation for spiking neuronal
networks, based on chains with unbounded memory. This relation allows us to
predict the influence of a weak amplitude time-dependent external stimuli on
spatio-temporal spike correlations, from the spontaneous statistics (without
stimulus) in a general context where the memory in spike dynamics can extend
arbitrarily far in the past. Using this approach, we show how linear response
is explicitly related to neuronal dynamics with an example, the gIF model,
introduced by M. Rudolph and A. Destexhe. This example illustrates the
collective effect of the stimuli, intrinsic neuronal dynamics, and network
connectivity on spike statistics. We illustrate our results with numerical
simulations.Comment: 60 pages, 8 figure
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