seqNMF

This package is a Python port of the SeqNMF MATLAB Toolbox. It provides a tool for performing unsupervised discovery of temporal sequences in high-dimensional data.

Credit for MATLAB toolbox: Emily Mackevicius, Andrew Bahle, and the Fee Lab.

This Python toolbox was developed by Jeremy Manning as a hackathon project during the 2018 MIND Summer School.

Description

SeqNMF uses regularized convolutional non-negative matrix factorization to extract repeated sequential patterns from high-dimensional data. The algorithm can discovery of patterns directly from timeseries data without reference to external markers or labels.

For more information please see: -Original MATLAB implementation -preprint;-COSYNE talk; tutorial -video and -materials; and Simons foundation -article

Installing the toolbox

To install the latest official version of this toolbox type

pip install --upgrade --user seqnmf

To install the (bleeding edge) development version type

pip install --upgrade --user git+https://github.com/ContextLab/seqNMF

Using the toolbox

Given a N (number of features) by T (number of timepoints) data matrix, X, the commands below may be used to factorize the data using seqNFM:

from seqnmf import seqnmf

W, H, cost, loadings, power = seqnmf(X, K=20, L=100, Lambda=0.001)

Here K is the (maximum) number of factors, L is (maximum) sequence length, and Lambda is a regularization parameter. The data matrix is factorized into a tensor product of W and H as follows:

according to:

                                    ----------    
                                L  /         /|
                                  /         / |
        ----------------         /---------/  |          ----------------
        |              |         |         |  |          |              |
      N |      X       |   =   N |    W    |  /   (*)  K |      H       |           
        |              |         |         | /           |              |
        ----------------         /----------/            ----------------
               T                      K                         T

where W contains each of the N by L sequence factors and H describes the combination of sequences that are present at each timepoint.

The cost output stores the reconstruction error after each iteration. The loadings variable stores the factor loadings. The power variable provides a measure of how well the original data is captured by the full reconstruction.

The plot function may be used to visualize the discovered structure by calling plot(W, H).

Demo

An example dataset, ported from the MATLAB toolbox, is provided as part of the seqnmf Python toolbox. To access it and apply seqNMF on the example data, run:

from seqnmf import seqnmf, example_data

[W, H, cost, loadings, power] = seqnmf(example_data, K=20, L=100, Lambda=0.001, plot_it=True)