Inference of a Mesoscopic Population Model from Population Spike Trains.

Neural Computation
Alexandre RenéJakob H. Macke

Abstract

Understanding how rich dynamics emerge in neural populations requires models exhibiting a wide range of behaviors while remaining interpretable in terms of connectivity and single-neuron dynamics. However, it has been challenging to fit such mechanistic spiking networks at the single-neuron scale to empirical population data. To close this gap, we propose to fit such data at a mesoscale, using a mechanistic but low-dimensional and, hence, statistically tractable model. The mesoscopic representation is obtained by approximating a population of neurons as multiple homogeneous pools of neurons and modeling the dynamics of the aggregate population activity within each pool. We derive the likelihood of both single-neuron and connectivity parameters given this activity, which can then be used to optimize parameters by gradient ascent on the log likelihood or perform Bayesian inference using Markov chain Monte Carlo (MCMC) sampling. We illustrate this approach using a model of generalized integrate-and-fire neurons for which mesoscopic dynamics have been previously derived and show that both single-neuron and connectivity parameters can be recovered from simulated data. In particular, our inference method extracts posterior correlatio...Continue Reading

References

Jan 1, 1972·Biophysical Journal·H R Wilson, J D Cowan
Nov 2, 2004·Neural Computation·Liam PaninskiEero P Simoncelli
Jul 19, 2005·Annual Review of Neuroscience·Tim P VogelsL F Abbott
Mar 21, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Anton V Chizhov, Lyle J Graham
May 17, 2011·PloS One·Edward WallaceJack D Cowan
Nov 30, 2011·PLoS Computational Biology·Joshua H Goldwyn, Eric Shea-Brown
Oct 12, 2012·PLoS Computational Biology·Richard Naud, Wulfram Gerstner
Jul 9, 2013·Journal of Computational Neuroscience·Alexandro D Ramirez, Liam Paninski
Aug 26, 2014·Nature Neuroscience·John P Cunningham, Byron M Yu
Sep 24, 2014·Neural Computation·Gonzalo Mena, Liam Paninski
Feb 26, 2016·Nature Neuroscience·Brent DoironKrešimir Josić
Jun 18, 2016·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Marie KostineJudith V M G Bovée
Jul 7, 2016·Proceedings of the National Academy of Sciences of the United States of America·Michael HawrylyczUNKNOWN MindScope
Jan 28, 2017·Frontiers in Systems Neuroscience·Arne F MeyerManeesh Sahani
Apr 20, 2017·PLoS Computational Biology·Tilo SchwalgerWulfram Gerstner
Jul 3, 2017·Current Opinion in Neurobiology·Omri Barak
Aug 9, 2017·PLoS Computational Biology·Grégory DumontAndré Longtin
Sep 19, 2018·Nature Methods·Chethan PandarinathDavid Sussillo
Oct 8, 2019·Current Opinion in Neurobiology·Tilo Schwalger, Anton V Chizhov
Nov 5, 2019·PLoS Computational Biology·Michael E RuleGuido Sanguinetti

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Citations

Oct 30, 2020·Frontiers in Computational Neuroscience·Camille Gontier, Jean-Pascal Pfister
Jan 6, 2021·Neural Computation·Kyle P Wendling, Cheng Ly
Aug 20, 2021·Current Opinion in Neurobiology·Cole HurwitzMatthias H Hennig

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Software Mentioned

SciPy
Theano
Adam
HamiltonianMC
mesoGIF
PyMC3
Numpy

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