Fitting and simulation of Poisson generalized linear model for single and multi-neuron spike trains (Pillow et al 2008).
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README.md

GLMspiketools

Fitting and simulation of Poisson generalized linear model for single and multi-neuron spike trains (Pillow et al 2008).

Description: Simulates and computes maximum likelihood estimates for the parameters of a Poisson GLM spike train model. Parameters consist of a bank of stimulus filters ("receptive fields"), spike-history filters, and coupling filters that capture dependencies between neurons. The stimulus filter can be parametrized linearly or bi-linearly, and the nonlinearity can be selected from a class ensuring convexity of the negative log-likelihood, or parametrized using using cubic splines. This model is a generalization of the "Linear-Nonlinear-Poisson" model that incorporates spike-history effects and correlations between neurons.

Relevant publication: Pillow et al, Nature 2008

Download

  1. Either clone the repository from github (git clone git@github.com:pillowlab/GLMspiketools.git) or download as zip and then unzip the archive.

Basic Usage

  1. From the main code directory (e.g., ~/Downloads/GLMspiketools/), run the setpaths script to add relevant sub-directories to the matlab path.
  2. Examine demo scripts in sub-directory demos/ to see simple scripts illustrating how to simulate and fit the GLM to spike train data.

Demo Scripts:

  1. demo1_GLM_temporalStim.m - simulates and fits GLM with 1D (purely temporal) stimulus.
  2. demo2_GLM_spatialStim.m - simulates and fits GLM with 2D (space x time) stimulus, and illustrates both linear and bilinear parametrization of stimulus filter.
  3. demo3_GLM_coupled.m - simulates and fits GLM with two coupled neurons

Notes

  • The code allows for two discretizations of time: dtStim specifies the size of time bins representing a single frame of the stimulus, and dtSp specifies the size of time bins for spikes (both in units of seconds). The code requires dtSp to evenly divide dtStim. Thus, for example, if the stimulus has a refresh rate of 100 Hz and spikes are represented with 1ms precision, then dtStim=.01 and dtSp=.001.

  • fitting code relies on the matlab optimization toolbox function "fminunc".

  • An older release of this code (now sitting in branch old_v1) had functionality that is no longer supported. Namely: cubic spline parametrization of the nonlinearity, and a smart "chunking" of the design matrix that was more memory efficient (albeit slightly slower). If memory issues are a problem, due to large stimulus or coupling from many neurons, we suggest checking out version v1. (In the shell usegit checkout old_v1, or download directly: GLMspiketools-old_v1.zip).