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934 Commits

Author SHA1 Message Date
joseph.lizier b20d103b56 Continuing (2) to make CA demo scripts have full Matlab compatibility, including loading initial state of CAs from file (since octave and matlab generate different initial states) 2013-09-10 15:27:02 +00:00
joseph.lizier 23bffaf688 Continuing to make CA demo scripts have full Matlab compatibility, including loading initial state of CAs from file (since octave and matlab generate different initial states) 2013-09-10 15:12:03 +00:00
joseph.lizier 6cd0e522fa Patching CA demo scripts for full Matlab compatibility, including loading initial state of CAs from file (since octave and matlab generate different initial states) 2013-09-10 14:37:28 +00:00
joseph.lizier 28911ef2f4 Made octave/examples 4 to 6 Matlab compatible 2013-09-05 05:03:42 +00:00
joseph.lizier 46a5cb208f Made octave/example3 Matlab compatible 2013-09-05 04:57:36 +00:00
joseph.lizier c159cc51b8 Fixed ordering of CA plots in demo script to generate CA plots in my book chapter in the "Directed information measures in neurosciences" book (2013) 2013-08-25 15:12:42 +00:00
joseph.lizier c20546bd55 Adding demo script to generate CA plots in my book chapter in the "Directed information measures in neurosciences" book (2013) 2013-08-25 15:10:19 +00:00
joseph.lizier baf66c713a Added script to reproduce results from the GSO 2013 book chapter on CA results. Several updates to CA scripts associated with this are also uploaded, including ability to save PDF images, nonlinear colour scaling, and alignment of image plot with cell boundaries 2013-08-15 06:59:13 +00:00
joseph.lizier 9c03691c09 Predictive information calculator unit tests added 2013-08-13 04:33:45 +00:00
joseph.lizier 7f48066b57 Predictive information calculator implementation made from active information storage 2013-08-13 04:33:18 +00:00
joseph.lizier 1c0e9098cc Extra unit test for Issue 16 2013-07-06 18:36:03 +00:00
joseph.lizier 68b0233e28 Extended fix to handle zero-covariance conditionals for handling linear redundancies amongst variables properly in ConditionalMICalculatorMultivariateGaussian - this contributes to resolution (closed) for Issue 16 2013-07-06 18:24:13 +00:00
joseph.lizier ce1a3b4b31 Extended fix to local cond MI values for handling linear redundancies amongst variables properly in ConditionalMICalculatorMultivariateGaussian - this resolves Issue 16 2013-07-06 13:54:02 +00:00
joseph.lizier 0907ed495e Handle linear redundancies amongst variables properly in ConditionalMICalculatorMultivariateGaussian. Still need to extend this to the local conditional MI values 2013-07-06 11:11:56 +00:00
joseph.lizier 34c9d31018 Renaming lateBindingMutualInfo to example6LateBindingMutualInfo (4) - completing internal name changes and comments 2013-06-18 12:08:06 +00:00
joseph.lizier 1656ba8730 Renaming lateBindingMutualInfo to example6LateBindingMutualInfo (3) 2013-06-18 11:57:58 +00:00
joseph.lizier f6f41afdba Renaming lateBindingMutualInfo to example6LateBindingMutualInfo (2 - 1 more to come ...) 2013-06-18 11:57:21 +00:00
joseph.lizier b9aa85055d Renaming lateBindingMutualInfo to example6LateBindingMutualInfo 2013-06-18 11:55:52 +00:00
joseph.lizier 6554180b98 Adding Java simple demo 5 2013-06-18 11:28:06 +00:00
joseph.lizier 63f9da620e Adding sample data file 10ColsRandomGaussian-1.txt 2013-06-18 07:37:16 +00:00
joseph.lizier 524b277b54 Adding minor utility functions 2013-06-18 07:31:18 +00:00
joseph.lizier f0dee75f18 Added Java example 4 2013-06-18 06:32:46 +00:00
joseph.lizier bc677030da Adding Java simple demo 3 and shell script to run it 2013-06-14 08:02:10 +00:00
joseph.lizier 06fa1567ab Adding Java demo examples 1 and 2 2013-06-12 00:33:09 +00:00
joseph.lizier f006c53e46 Adding python examples 5 and 6. Minor tweaks to octave examples 5 and 6 to clarify comments or minor conflicts. Error corrected in comment of python example 2 2013-06-07 05:58:47 +00:00
joseph.lizier 88b33308c6 Tweaked python example 2 to add minor comment 2013-06-05 05:39:39 +00:00
joseph.lizier 15647840f8 Tweaked python example 2 to keep print statement thin 2013-06-05 05:38:12 +00:00
joseph.lizier 7336780b2b Added python example 2. Patched octave example 2 comments and python example 1 comments 2013-06-05 05:33:49 +00:00
joseph.lizier c767ae929f Added python example 4 2013-06-04 02:00:52 +00:00
joseph.lizier d818db1351 Added python example 3; plotLocalInfoMeasureForCA now allows initial states to be provided. 2013-06-04 01:50:21 +00:00
joseph.lizier 15af54e395 Minor updates 2013-04-26 04:21:32 +00:00
joseph.lizier 75c36dc13a Adding common parent implementation of Conditional MI calculator from continuous to discrete variable, plus a linear-Gaussian implementation of it 2013-03-18 06:08:12 +00:00
joseph.lizier b17ba9b05c Minor alterations to utilities, including adding exceptions and adding to-do notes. 2013-03-18 05:55:43 +00:00
joseph.lizier a00b24019c Making linear-Gaussian implementation of Conditional MI calculator not normalise the data by default (after having made it a child class of the common conditional MI implementation, this had been switched on by default) 2013-03-18 05:52:36 +00:00
joseph.lizier ddf4aaecc5 Reconditioned Conditional MI with Discrete calculator Kraskov as a child class of Conditional MI with Discrete calculator Common 2013-03-18 05:49:00 +00:00
joseph.lizier 4bd22a0984 Reconditioned Conditional MI calculator Kraskov as a child class of Conditional MI calculator Common 2013-03-11 12:55:29 +00:00
joseph.lizier bc218e291c Added new unit test for Kraskov MI calculator against MILCA for large 10000 data points of dimension 5 in each x and y; added unit tests for digamma 2013-03-07 12:50:03 +00:00
joseph.lizier 16cc8e3db2 Patched digamma function for large k; added extra debug prints to Kraskov MI calculator 2 2013-03-07 12:46:52 +00:00
joseph.lizier cb2e0a2588 New unit tests for covariance calculation (inside conditional MI linear Gaussian), making analytic linear Gaussian signficance tests take the number of observations into account 2013-03-04 06:11:43 +00:00
joseph.lizier dcb15ead1d Added new demos regarding dynamic binding of implementations to abstract calculator objects (in java and matlab) 2013-03-04 06:09:26 +00:00
joseph.lizier cd67da53a4 Patching linear Gaussian estimators to give empirical statistical significance given a certain number of observations. 
Changed implementation of our conditional MI calculators Kraskov via algorithm 2 to my current interpretation of how this should be done.

Added a utility for lagged covariance in MatrixUtils
 2013-03-04 06:08:38 +00:00
joseph.lizier 64f6986d45 Added single array addObservations routines for Complete TE calculator discrete. Removed duplicate copyIntoMatrix method from MatrixUtils (duplicated arrayCopy) 2013-01-23 00:45:01 +00:00
joseph.lizier 318778c914 Added example 5 for Matlab/Octave re computation with multivariates and discrete data 2013-01-22 23:39:36 +00:00
joseph.lizier 4671b15d61 Added more unit tests for Kraskov conditional MI against TRENTOOL (here for multivariate data, run with TRENTOOL as univariate TE but with history lengths k=2, l=2) 2013-01-22 03:37:42 +00:00
joseph.lizier afe224ab11 Added MatrixUtils.copyIntoMatrix utility function to copy part of one 2D matrix into another 2013-01-22 03:36:11 +00:00
joseph.lizier cd5073c98e Added comment to matlab example 2 clarifying non-periodic boundary conditions 2013-01-22 03:35:30 +00:00
joseph.lizier efc7b13440 Added new data files for unit tests for Kraskov Conditional MI 2013-01-16 11:55:48 +00:00
joseph.lizier 111055fc81 Added unit tests for Kraskov Conditional MI against TEs computed by Wibral et al.'s TRENTOOL 2013-01-16 11:54:13 +00:00
joseph.lizier 6196cb5710 Switched coupled logistic map example for TE Delays paper with Wibral et al to use Kraskov type 1 estimator (this is much simpler for TE and conditional MI) as per TRENTOOL 2013-01-16 01:30:04 +00:00
joseph.lizier 9d36e5d9a6 Bug fix to debug prints in Kraskov Conditional MI calculators 2013-01-15 01:29:57 +00:00