Efficient Non-conjugate Gaussian Process Factor Models for Spike Count Data using Polynomial Approximations

Stephen L. Keeley, David M. Zoltowski, Yiyi Yu, Jacob L. Yates, Spencer L. Smith, Jonathan W. Pillow

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Gaussian Process Factor Analysis (GPFA) has been broadly applied to the problem of identifying smooth, low-dimensional temporal structure underlying large-scale neural recordings. However, spike trains are non-Gaussian, which motivates combining GPFA with discrete observation models for binned spike count data. The drawback to this approach is that GPFA priors are not conjugate to count model likelihoods, which makes inference challenging. Here we address this obstacle by introducing a fast, approximate inference method for non-conjugate GPFA models. Our approach uses orthogonal second-order polynomials to approximate the nonlinear terms in the non-conjugate log-likelihood, resulting in a method we refer to as polynomial approximate log-likelihood (PAL) estimators. This approximation allows for accurate closed-form evaluation of marginal likelihoods and fast numerical optimization for parameters and hyperparameters. We derive PAL estimators for GPFA models with binomial, Poisson, and negative binomial observations and find the PAL estimation is highly accurate, and achieves faster convergence times compared to existing state-of-The-Art inference methods. We also find that PAL hyperparameters can provide sensible initialization for black box variational inference (BBVI), which improves BBVI accuracy. We demonstrate that PAL estimators achieve fast and accurate extraction of latent structure from multi-neuron spike train data.1.

Original languageEnglish (US)
Title of host publication37th International Conference on Machine Learning, ICML 2020
EditorsHal Daume, Aarti Singh
PublisherInternational Machine Learning Society (IMLS)
Pages5133-5142
Number of pages10
ISBN (Electronic)9781713821120
StatePublished - 2020
Event37th International Conference on Machine Learning, ICML 2020 - Virtual, Online
Duration: Jul 13 2020Jul 18 2020

Publication series

Name37th International Conference on Machine Learning, ICML 2020
VolumePartF168147-7

Conference

Conference37th International Conference on Machine Learning, ICML 2020
CityVirtual, Online
Period7/13/207/18/20

All Science Journal Classification (ASJC) codes

  • Computational Theory and Mathematics
  • Human-Computer Interaction
  • Software

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