natas_hw
/
jidt
mirror of https://github.com/jlizier/jidt
0
0
Fork 0
Code Issues Packages Projects Releases Wiki Activity
756 Commits 5 Branches 6 Tags 66 MiB
Commit Graph

756 Commits

Author SHA1 Message Date
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
joseph.lizier 6761de7e02 Added debug prints to Kraskov Conditional MI calculators 2013-01-15 01:14:13 +00:00
joseph.lizier 40e7d4b211 Added common unit tests for conditional MI calculators, and added implementations of the tests for Kraskov and Gaussian conditional MI calculators 2013-01-14 12:57:01 +00:00
joseph.lizier f466012556 Made Kraskov Conditional MI calculator implement the common Conditional MI interface 2013-01-14 12:51:34 +00:00
joseph.lizier a06efba6e0 Added first python code example using JIDT 2013-01-14 12:49:16 +00:00
joseph.lizier 9b9abda733 Bug fix of computation of epsilon (box width) on conditional variable in Kraskov conditional MI calculator 2 2013-01-14 11:13:58 +00:00
joseph.lizier 3ff564237e Updating distribution version in ant file 2013-01-12 13:47:15 +00:00
joseph.lizier 3167944875 Adding interface for conditional mutual information (continuous) calculator, common methods for it, and implementation for Gaussian variables. 2013-01-12 13:43:43 +00:00
joseph.lizier 69b59403b4 Made the CellularAutomata demos compatible with Matlab 2013-01-12 13:37:34 +00:00
joseph.lizier fc8986d0ab Made the DetectingInteractionLags demos compatible with Matlab 2013-01-12 12:38:19 +00:00
joseph.lizier eb76d4a733 updated info about automatic Matlab matrix to java format conversion in this example's comments. 2013-01-12 11:15:31 +00:00
joseph.lizier b6aece6d51 Fixed main demo scripts to be compatible with Matlab (fixed printf -> printf, rows -> size(x, 1), and not specifically converting matlab arrays to java and back) 2013-01-12 10:57:11 +00:00
joseph.lizier 220f4a8857 Added data for unit test for covariance 2013-01-08 05:39:07 +00:00
joseph.lizier 74ba272f41 Added unit test for covariance 2013-01-08 05:38:22 +00:00
joseph.lizier 030a172d82 Patched covariance calculation, added utils, patched analytic computation of distribution of MI with linear Gaussians, altered comments 2013-01-08 05:37:48 +00:00
joseph.lizier ef6e426c36 Adding bit values to the outputs for our logistic maps example in the detecting interaction lags demo 2013-01-03 12:22:44 +00:00
joseph.lizier 8fe32003ab Adding more unit testing on Kraskov MI, including for dependent data sets 2012-12-20 13:23:52 +00:00
joseph.lizier d95f04ec70 Adding new sample data for more unit testing on Kraskov MI 2012-12-20 13:20:52 +00:00
joseph.lizier b0bc89dcb1 Made the unit tests for Kraskov MI more streamlined; added unit test for multivariate MI 2012-12-20 10:40:42 +00:00
joseph.lizier 617880f9f5 Making Kraskov MI and higher order calculators use MAX_NORM in the marginal spaces by default (previously this had to be supplied via a property - it was the standard choice made, but was not the default). This aligns with the default specified in the Kraskov paper. 2012-12-20 10:38:03 +00:00
joseph.lizier 87f7be56a5 Adding new test data set of 4 random columns 2012-12-18 11:32:55 +00:00
joseph.lizier 13816b9adc Making ant junit call avoid running the abstract Junit tests 2012-12-18 10:59:40 +00:00
joseph.lizier 90c0f5a105 Renaming abstract unit test classes inside java files (missed these in previous commit) 2012-12-18 10:57:44 +00:00
joseph.lizier 74ebf27fa0 Renaming abstract unit test classes inside java files 2012-12-18 10:53:03 +00:00
joseph.lizier 653b511c24 Renaming abstract unit test classes as first step to avoid ant file running them (next commit will update names inside java files) 2012-12-18 10:51:30 +00:00
joseph.lizier 4d4c021be9 Added data for unit testing of MI Kraskov calculator 2012-12-18 10:35:22 +00:00
joseph.lizier 23f7f84eaa Added common functionality for unit testing multivariate MI calculators into an abstract class. 
Added basic tester for Kraskov multivariate MI, including verifying against Kraskov MILCA tool
 2012-12-18 10:34:41 +00:00
joseph.lizier a6e09c7fc4 Pulled some common functionality for testing multivariate TE calculators into an abstract class. 
Added basic tester for Kraskov multivariate TE
 2012-12-13 14:50:33 +00:00
joseph.lizier e789acd4dc Adding various comments 
Patched bug in TECalculatorMultiVariateSingleObservationsKernel whereby only k*destDimensions dimensions of destPast were being considered (this is a problem where one wants to surreptitiously condition on extra variables).
 2012-12-13 14:42:40 +00:00