Gaussian process based nonlinear latent structure discovery in multivariate spike train data

Anqi Wu, Nicholas A. Roy, Stephen Keeley, Jonathan William Pillow

Research output: Contribution to journalConference articlepeer-review

63 Scopus citations


A large body of recent work focuses on methods for extracting low-dimensional latent structure from multi-neuron spike train data. Most such methods employ either linear latent dynamics or linear mappings from latent space to log spike rates. Here we propose a doubly nonlinear latent variable model that can identify low-dimensional structure underlying apparently high-dimensional spike train data. We introduce the Poisson Gaussian-Process Latent Variable Model (P-GPLVM), which consists of Poisson spiking observations and two underlying Gaussian processes - one governing a temporal latent variable and another governing a set of nonlinear tuning curves. The use of nonlinear tuning curves enables discovery of low-dimensional latent structure even when spike responses exhibit high linear dimensionality (e.g., as found in hippocampal place cell codes). To learn the model from data, we introduce the decoupled Laplace approximation, a fast approximate inference method that allows us to efficiently optimize the latent path while marginalizing over tuning curves. We show that this method outperforms previous Laplace-approximation-based inference methods in both the speed of convergence and accuracy. We apply the model to spike trains recorded from hippocampal place cells and show that it compares favorably to a variety of previous methods for latent structure discovery, including variational auto-encoder (VAE) based methods that parametrize the nonlinear mapping from latent space to spike rates with a deep neural network.

Original languageEnglish (US)
Pages (from-to)3497-3506
Number of pages10
JournalAdvances in Neural Information Processing Systems
StatePublished - 2017
Event31st Annual Conference on Neural Information Processing Systems, NIPS 2017 - Long Beach, United States
Duration: Dec 4 2017Dec 9 2017

All Science Journal Classification (ASJC) codes

  • Computer Networks and Communications
  • Information Systems
  • Signal Processing


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