A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data
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Publication:641075
Abstract: 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.
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Cited in
(21)- Reconstruction of sparse connectivity in neural networks from spike train covariances
- Reconstruction of sparse recurrent connectivity and inputs from the nonlinear dynamics of neuronal networks
- Learning neural connectivity from firing activity: efficient algorithms with provable guarantees on topology
- Reconstruction of recurrent synaptic connectivity of thousands of neurons from simulated spiking activity
- Adaptive importance sampling for control and inference
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- Efficient methods for sampling spike trains in networks of coupled neurons
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- A mathematical framework for inferring connectivity in probabilistic neuronal networks
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- Inferring evoked brain connectivity through adaptive perturbation
- Modeling the impact of common noise inputs on the network activity of retinal ganglion cells
- Accurate Connection Strength Estimation Based on Variational Bayes for Detecting Synaptic Plasticity
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