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EntRate -- Entropy rate estimators for neuroscience

This library contains Octave/Matlab (>R2016a) functions to compute entropy rate- and Lempel-Ziv complexity-related functions in continuous and discrete data. An example application of LZ complexity to neuroimaging data with a relevant discussion on entropy rate can be found here:

  • Mediano, P., Rosas, F., Timmermann, C., Roseman, L., Nutt, ... Bor, D. & Carhart-Harris, R. L. (2020). Effects of external stimulation on psychedelic state neurodynamics. bioRxiv.

Note: this repository contains a copy of the MVGC2 library, lightly modified to be Octave-compatible. Full credit for the MVGC2 library goes to the original authors, and interested users are referred to the original repository and associated papers for details. It also contains a precompiled (unmodified) jar of the VMM code by Ron Begleiter (see paper for details).

Download and installation

If you intend to use the LZ76 entropy rate estimator, you need to compile it first by running:

mex COPTIMFLAGS="-O3" LZ76.c

Once this is done, you can run LZ76() and call help LZ76 as usual.

Note, however, that if you use Octave you will need to install the statistics package. You can do this simply by running pkg install -forge io statistics.

Tests are provided in the tests/ subfolder. To run them in Matlab, run runtests('tests/') from this repository's root folder.

Usage

This library implements a few entropy rate estimators (via state-space entropy [CSER], context tree-weighted predictor [CTW], and Lempel-Ziv compression) applicable to discrete or continuous data. For example, to compute the entropy rate of a maximum-entropy random sequence of bits, run:

X = 1*(rand([1, 1000]) < 0.5);
H = CTWEntropyRate(X);

Simple example scripts comparing LZ, CTW and CSER can be found in the examples/ folder.

Feature requests and bug reports are warmly welcome. Email Pedro Mediano (see email in the paper above) for any questions or comments.

Use in Python

The CTWEntropyRate and StateSpaceEntropyRate functions in this repository are Octave-friendly, which means they can be easily called from Python through the wholesome oct2py package, as long as you have a functional Octave installation.

You can simply run (from the root folder of the repo):

import numpy.random as rn
from oct2py import Oct2Py

oc = Oct2Py()
oc.StateSpaceEntropyRate(rn.randn(1, 1000))

Note that StateSpaceEntropyRate requires the statistics Octave package (which you can install running pkg install -forge io statistics from Octave), and CTWEntropyRate requires an Octave installation with Java support.

Licence

This software is distributed under the GNU General Public Licence, version 3.

Further reading

  • Barnett, L., & Seth, A. (2015). Granger causality for state-space models. Physical Review E, 91(4), 040101.

  • Begleiter, R., El-Yaniv, R., & Yona, G. (2004). On prediction using variable order Markov models. Journal of Artificial Intelligence Research, 22, 385-421.

  • Kaspar, F., & Schuster, H. G. (1987). Easily calculable measure for the complexity of spatiotemporal patterns. Physical Review A, 36(2), 842.

  • Mediano, P., Rosas, F., Barrett, A., & Bor, D. (2020). Decomposing spectral and phasic differences in non-linear features between datasets. arXiv:2009.10015.

(C) Pedro Mediano, Fernando Rosas and Andrea Luppi, 2019-21