A Bayesian approach for inferring neuronal connectivity from calcium fluorescent imaging data
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Publication:641075
DOI10.1214/09-AOAS303zbMATH Open1223.62162arXiv1107.4228MaRDI QIDQ641075FDOQ641075
Authors: Yuriy Mishchenko, Joshua T. Vogelstein, Liam Paninski 
Publication date: 21 October 2011
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
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.
Full work available at URL: https://arxiv.org/abs/1107.4228
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Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Monte Carlo methods (65C05) Neural biology (92C20) Biomedical imaging and signal processing (92C55)
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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
- An \(L_1\)-regularized logistic model for detecting short-term neuronal interactions
- Reconstruction of recurrent synaptic connectivity of thousands of neurons from simulated spiking activity
- Adaptive importance sampling for control and inference
- Inference of multiplicative factors underlying neural variability in calcium imaging data
- Efficient methods for sampling spike trains in networks of coupled neurons
- A mathematical framework for inferring connectivity in probabilistic neuronal networks
- Detecting cell assemblies by NMF-based clustering from calcium imaging data
- Consistent estimation of complete neuronal connectivity in large neuronal populations using sparse ``shotgun neuronal activity sampling
- Special section on statistics in neuroscience
- A Bayesian compressed-sensing approach for reconstructing neural connectivity from subsampled anatomical data
- Title not available (Why is that?)
- On the use of dynamic Bayesian networks in reconstructing functional neuronal networks from spike train ensembles
- Fast state-space methods for inferring dendritic synaptic connectivity
- Extraction of bouton-like structures from neuropil calcium imaging data
- Scalpel: extracting neurons from calcium imaging data
- Modeling the impact of common noise inputs on the network activity of retinal ganglion cells
- Inferring evoked brain connectivity through adaptive perturbation
- Accurate Connection Strength Estimation Based on Variational Bayes for Detecting Synaptic Plasticity
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