Model-free measures of causality

About

Here you can download the source code for the Transfer Entropy based measure of effective connectivity called Generalized Transfer Entropy (GTE) as published in PLoS Computational Biology.

Features

• Compute effective connectivity based on Transfer Entropy or other causality measures (see below).
• Model-free, so you can supply any kind of signal, not just fluorescence.
• Computationally efficient.
• Can auto-detect the optimal bin number and/or the optimal conditioning level.
• Can simulate fluorescence for you, or you supply your own signal. As it is model-free, any kind of signal can be used.
• Easy parameter control via the SimKernel package.
• Actively maintained by a growing group of active users.

What's included?

Primarily, we provide the analysis in a program called te-extended to efficiently calculate GTE for arbitrary Markov order. Also included is a set of simple examples (work in progress), and the script for the NEST simulator that we use to generate spike trains.

Also included are other causality measures for comparison:

• xcorr, time-lagged cross-correlation
• mi, time-lagged Mutual information
• granger, Granger Causality (time domain)

It also contains three methods of estimating TE and GTE without binning:

• te-binless-Leonenko, based on: L.F. Kozachenko and N.N. Leonenko, Sample Estimate of the Entropy of a Random Vector, Problems of Information Transmission, 1987
• te-binless-Kraskov, based on: A. Kraskov et al., Estimating Mutual Information, Physical Review E, 2004
• te-binless-Frenzel, based on: S. Frenzel and B. Pompe, Partial Mutual Information for Coupling Analysis of Multivariate Time Series, Physical Review Letters, 2007

Documentation

A guide to installation and configuration is provided in the Readme in the source repository. As mentioned above, we are also working on a set of minimal examples to get you started.

Questions?

We will be happy to answer them. Please contact us using the Issues tab on GitHub.

Copyright

All of the files can be copied, modified, used for commercial or non-commercial purpose, as long as you keep the following copyright message in the source files:

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.