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Interpretable neural spike train models with fully-Bayesian inference algorithms
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README.md

PyGLM: Bayesian inference for nonlinear autoregressive models of count data

Neural circuits contain heterogeneous groups of neurons that differ in type, location, connectivity, and basic response properties. However, traditional methods for dimensionality reduction and clustering are ill-suited to recovering the structure underlying the organization of neural circuits. In particular, they do not take advantage of the rich temporal dependencies in multi-neuron recordings and fail to account for the noise in neural spike trains. This repository contains tools for inferring latent structure from simultaneously recorded spike train data using a hierarchical extension of a multi-neuron point process model commonly known as the generalized linear model (GLM). In the statistics and time series analysis communities, these correspond to nonlinear vector autoregressive processes with count observations. We combine the GLM with flexible graph-theoretic priors governing the relationship between latent features and neural connectivity patterns. Fully Bayesian inference via \polyagamma augmentation of the resulting model allows us to classify neurons and infer latent dimensions of circuit organization from correlated spike trains. We demonstrate the effectiveness of our method with applications to synthetic data and multi-neuron recordings in primate retina, revealing latent patterns of neural types and locations from spike trains alone.

References

Scott W. Linderman, Ryan P. Adams, and Jonathan W. Pillow. Bayesian latent structure discovery from multi-neuron recordings. Advances in Neural Information Processing Systems, 2016.

Scott W. Linderman. Bayesian methods for discovering structure in neural spike trains. PhD thesis, Harvard University, 2016.

Example

We provide a number of classes for building and fitting such models. Let's walk through a simple example where we construct a discrete time model with four neurons, as in examples/synthetic. The neurons are connected via a network such that spikes influence the rate of subsequent spikes on post-synaptic (downstream) neurons.

# Create a simple, sparse network of four neurons
T = 10000   # Number of time bins to generate
N = 4       # Number of neurons
B = 1       # Number of "basis functions"
L = 100     # Autoregressive window of influence

# Create a cosine basis to model smooth influence of
# spikes on one neuron on the later spikes of others.
basis = cosine_basis(B=B, L=L) / L

# Generate some data from a model with self inhibition
true_model = SparseBernoulliGLM(N, basis=basis)

# Generate T time bins of events from the the model
# Y is the generated spike train.
# X is the filtered spike train for inference.
X, Y = true_model.generate(T=T, keep=True)

# Plot the model parameters and data
true_model.plot()

You should see something like this:

True Model

Now create a test model and try to infer the network given the spike train.

# Create the test model and add the spike train
test_model = SparseBernoulliGLM(N, basis=basis)
test_model.add_data(Y)

# Initialize the plot
_, _, handles = test_model.plot()

# Run a Gibbs sampler
N_samples = 100
lps = []
for itr in xrange(N_samples):
    test_model.resample_model()
    lps.append(test_model.log_likelihood())
    test_model.plot(handles=handles)

With interactive plotting enabled, you should see something like: Test Model

Finally, we can plot the log likelihood over iterations to assess the convergence of the sampling algorithm, at least in a heuristic way.

plt.plot(lps)
plt.xlabel("Iteration")
plt.ylabel("Log Likelihood")

Log Likelihood

Looks like it has! Now let's look at the posterior mean of the network and firing rates.

Posterior Mean

Installation

PyGLM requires pypolyagamma for its Bayesian inference algorithms. This dependency will automatically be installed if you do not already have it, but by default, pip will not install the parallel version. If you want to use parallel resampling, look at the pypolyagamma homepage for instructions on installing from source with OpenMP.

To install pyglm from source, first clone the repo

git clone git@github.com:slinderman/pyglm.git
cd pyglm

Then install in developer mode:

pip install -e .

Or use the standard install:

python setup.py install
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