Copyright (C) 2012-2014Joseph T. Lizier; 2014-2015Joseph T. Lizier and Ipek Özdemir
JIDT provides a stand-alone, open-source code Java implementation (also usable inMatlab, Octave,Python,R,Julia andClojure) of information-theoretic measures of distributed computation in complex systems: i.e. information storage, transfer and modification.
JIDT includes implementations:
JIDT is distributed under theGNU GPL v3 license (or later).
For further information or announcements:
Pleasecite your use of this toolkit as:
Joseph T. Lizier, "JIDT: An information-theoretic toolkit for studying the dynamics of complex systems",Frontiers in Robotics and AI 1:11, 2014; doi:10.3389/frobt.2014.00011 (pre-print:arXiv:1408.3270)
And pleaselet me know about any publications resulting from its use!
See otherPublicationsUsingThisToolkit.
19/7/2015 - New jar and full distribution files available forrelease v1.3; Changes for v1.3 include:Added AutoAnalyser (Code Generator) GUI demo for MI and TE;Added auto-embedding capability via Ragwitz criteria for AIS and TE calculators (KSG estimators);Added Java demo 9 for showcasing use of Ragwitz auto-embedding;Adding small amount of noise to data in all KSG estimators now by default (may be disabled via setProperty());Added getProperty() methods for all conditional MI and TE calculators;Upgraded Python demos for Python 3 compatibility;Fixed bias correction on mixed discrete-continuous KSG calculators;Updated the tutorial slides to those in use for ECAL 2015 JIDT tutorial.
12/2/2015 - New jar and full distribution files available forrelease v1.2.1; Changes for v1.2.1 include:Added tutorial slides, description of exercises and sample exercise solutions;Made jar target Java 1.6;Added Schreiber TE heart-breath rate with KSG estimator demo code for Python.
28/1/2015 - New jar and full distribution files available forrelease v1.2; Changes for v1.2 include:Dynamic correlation exclusion, or Theiler window, added to all Kraskov estimators;Added univariate MI calculation to simple demo 6;Added Java code for Schreiber TE heart-breath rate with KSG estimator, ready for use as a template in Tutorial;Patch for crashes in KSG conditional MI algorithm 2.
20/11/2014 - New jar and full distribution files available forrelease v1.1; Changes for v1.1 include:Implemented Fast Nearest Neighbour Search for Kraskov-Stögbauer-Grassberger (KSG) estimators for MI, conditional MI, TE, conditional TE, AIS, Predictive info, and multi-information. This includes a general (multivariate) k-d tree implementation;Added multi-threading (using all available processors by default) for the KSG estimators -- code contributed by Ipek Özdemir;Added Predictive information / Excess entropy implementations for KSG, kernel and Gaussian estimators;Added R, Julia, and Clojure demos;Added Windows batch files for the Simple Java Demos;Added property for adding a small amount of noise to data in all KSG estimators;
15/8/2014 JIDT paper finalised and uploaded to the website andarXiv:1408.3270
14/8/2014 - New jar and full distribution files available for ourfirst official release, v1.0; Changes for v1.0 include: Added the draft of the paper on the toolkit to the release;Javadocs made ready for release;Switched source->destination arguments for discrete TE calculators to be with source first in line with continuous calculators;Renamed all discrete calculators to have Discrete suffix -- TE and conditional TE calculators also renamed to remove "Apparent" prefix and change "Complete" to "Conditional";Kraskov estimators now using 4 nearest neighbours by default;Unit test for Gaussian TE against ChaLearn Granger causality measurement;Added Schreiber TE demos; Interregional transfer demos; documentation for Interaction lag demos; added examples 7 and 8 to Simple Java demos;Added property to add noise to data for Kraskov MI;Added derivation of Apache Commons Math code for chi square distribution, and included relevant notices in our release;Inserted translation class for arrays between Octave and Java;Added analytic statistical significance calculation to Gaussian calculators and discrete TE;Corrected Kraskov algorithm 2 for conditional MI to follow equation in Wibral et al. 2014.
20/4/2014 - New jar and full distribution files available for v0.2.0; Moved downloads tohttp://lizier.me/joseph/ since google code has stopped the download facility here :(. Changes for v0.2.0 include: Rearchitected (most) Transfer Entropy and Multivariate TE calculators to use an underlying conditional mutual information calculator, and have arbitrary embedding delay, source-dest delay; this includes moving Kraskov-Grassberger Transfer Entropy calculator to use a single conditional mutual information estimator instead of two mutual information estimators; Rearchitected (most) Active Information Storage calculators to use an underlying mutual information calculator; Added Conditional Transfer Entropy calculators using underlying conditional mutual information calculators; Moved mixed discrete-continuous calculators to a new "mixed" package; bug fixes.
11/9/2013 - New jar and full distribution files available for v0.1.4; added scripts to generate CA figures for 2013 book chapters; added general Java demo code; added Python demo code; made Octave/Matlab demos and CA demos properly compatible for Matlab; added extra Octave/Matlab general demos; added more unit tests for MI and conditional MI calculators, including against results from Wibral's TRENTOOL; bug fixes.
11/9/2013 - New CA demo scripts for several review book chapters we're preparing in 2013 have been uploaded - seeCellularAutomataDemos.
4/6/2013 - Added instructions on how touse in python and severalPythonExamples.
13/01/2013 - New jar and full distribution files available for v0.1.3; existing Octave/Matlab demo code made compatible with Matlab; several bug fixes, including using max norm by default in Kraskov calculator (instead of requiring this to be set explicitly); more unit tests (including against results from Kraskov's own MI implementation)
19/11/2012 - New jar and full distribution files available for v0.1.2, including demo code for two newly submitted papers
31/10/2012 - Jar and full distribution files available for v0.1.1 (first distribution)
7/5/2012 - JIDT project created and code uploaded