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893 Commits

Author SHA1 Message Date
jlizier 46a9785da2 In surrogates for MI and CMI also turning adding noise off since this will have been done in the initial calculation already, and will just broaden the noise here. 2018-05-12 22:35:54 +10:00
jlizier 28ba409ff6 Turning off normalisation when computing surrogates in Common CMI and MI calculators, because normalisation has already been carried out (and if one variable had no variance, this will inflate the values back to original scale) 2018-05-12 21:30:39 +10:00
jlizier 0e4455b2fd Corrects the access at one point to the bins for the data points in the multivariate kernel estimator, which should use an IntArray object but did use an int[] object to access . Fixes #69. 2018-05-10 20:20:02 +10:00
jlizier 860d43dbca Adding additional error message for Exception during KSG Active Info Storage auto-embedding 2018-05-07 23:15:33 +10:00
jlizier 1f625b59f0 AutoAnalyser: fixing bug where column numbers for data are all set to zero if the user unclicks the "compute result?" button 2018-05-07 22:57:10 +10:00
jlizier d1bba0e4c1 Adding computeLocalOfPreviousObservations() to continuous Entropy estimator interface and all underlying implementations. Added unit tests that locals should average back ok. Also fixing multivariate Entropy estimator interface to implement the univariate interface also (and fixing underlying implementations to comply) 2018-04-27 11:20:25 +10:00
jlizier bf0062b902 Switching new debug method in KSG conditional MI calculator 1 to be publicly accessible 2018-04-26 11:43:04 +10:00
jlizier 7d76f82bb2 Adding partialNeighbourCountFromObservations() method to KSG conditional MI calculator 1 for debugging investigations into the neighbour counts 2018-04-26 11:24:56 +10:00
Joseph Lizier 5b569c63dc
Merge pull request #68 from pmediano/master 
Added new autoembedding methods to multivariate KSG TE calculator, including new option of optimising source embedding for maximum TE (after target embedding for maximum AIS is done) on both the multivariate and univariate KSG TE calculator.
 2018-04-23 16:22:33 +10:00
Pedro Martinez Mediano c15c643a09 Added tests for new embeddings in univariate KSG TE calculator. 2018-04-22 22:25:40 +01:00
Pedro Martinez Mediano df8eec27cd Added MAX_CORR_AIS_AND_TE embedding to univariate KSG TE calculator. 2018-04-22 22:25:05 +01:00
Pedro Martinez Mediano f8bca3275d Fixed docs for new MAX_CORR_AIS_AND_TE embedding method. 2018-04-22 20:45:06 +01:00
Joseph Lizier 9c40d7fadc
Fixed wiki link on homepage 
Fixed wiki link for ImplementedMeasures on the homepage
 2018-03-16 10:47:45 +11:00
Pedro Martinez Mediano 02dad26a94 Added brief mention of AUTO_EMBED_METHOD_MAX_CORR_AIS_AND_TE to javadocs. 2018-02-27 20:29:39 +00:00
Pedro Martinez Mediano 03d5e2fb2f Added tests for new TE autoembedding methods. 2018-02-27 20:18:28 +00:00
Pedro Martinez Mediano 5f6671aa2b Added AUTO_EMBED_METHOD_MAX_CORR_AIS_AND_TE to multivariate KSG TE. 2018-02-27 20:18:04 +00:00
Pedro Martinez Mediano d4c9b28973 Fixed error in KSG TE multivariate tester. 
Tester was wrongly calling the univariate version of the algorithm using
the first column of the input.
 2018-02-27 20:16:44 +00:00
Pedro Martinez Mediano 550ff793eb Fixed bug in KSG TE multivariate embeddings and setObservations. 2018-02-27 20:14:08 +00:00
Pedro Martinez Mediano 438a88c97c Added unittests for multivariate KSG TE autoembedding. 2018-02-27 17:56:42 +00:00
Pedro Martinez Mediano 8be6a037af Added auto-embedding methods to multivariate KSG TE calculator. 2018-02-25 19:23:09 +00:00
Pedro Martinez Mediano ce4b1599c6 Added MAX_CORR_AIS embedding method to multivariate KSG AIS. 2018-02-25 18:57:15 +00:00
Pedro Martinez Mediano 75bb2c814a Added addObservations-related methods to multivariate TE calculators. 
This is needed to implement auto-embedding methods later.
 2018-02-25 18:54:36 +00:00
Joseph Lizier fa0bc96a6f
Merge pull request #67 from pmediano/master 
Add new set- and addObservations overloadings in KSG mixed calculator
 2018-01-29 12:13:51 +11:00
Pedro Martinez Mediano 08f25beee6 Add tests for new overloadings in KSG mixed calc. 2018-01-12 22:23:12 +00:00
Pedro Martinez Mediano b0fc309d6a Add overloadings for 1d continuous variables in KSG mixed calc. 2018-01-12 22:22:46 +00:00
jlizier b32d9443eb Including the new "course" folder in the distribution produced by ant 2018-01-09 11:41:41 +11:00
jlizier 9feff283c4 First versions of Lecture slides for information theory course uploaded. Tutorial activities and sample code to come later. 2018-01-09 11:39:46 +11:00
jlizier 0278f95ae9 Enabled use of USE_GPU property for KSG calculators in the AutoAnalysers for CMI, TE, CTE and AIS 2017-12-30 12:03:17 +11:00
Joseph Lizier 6b5e3237ed
Merge pull request #65 from pmediano/master 
Added GPU implementation of KSG CMI calculator
 2017-12-21 12:01:10 +11:00
Pedro Martinez Mediano 92f1154e3d Added smoke junit tests for GPU CMI reordering. 2017-12-19 20:43:25 +00:00
Pedro Martinez Mediano 64f1142b40 Added argument to choose which variable to reorder in GPU CMI code. 2017-12-19 20:42:58 +00:00
Pedro Martinez Mediano 65ac0e9ff8 Removed unnecesary overloaded method in KSG CMI calc. 2017-12-19 20:41:11 +00:00
Pedro Martinez Mediano 2c518ab436 Merge branch 'master' into gpu 2017-12-18 18:53:57 +00:00
Pedro Martinez Mediano 76e7277e95 Removed unnecessary prints in GPU C unit tests. 2017-12-18 18:43:01 +00:00
Pedro Martinez Mediano 82593e1db2 Refactored gpuKnn functions for digamma calculation. 2017-12-18 18:27:05 +00:00
Pedro Martinez Mediano 4949a1079d Added junit KSG GPU CMI tests. 2017-12-18 17:51:03 +00:00
Pedro Martinez Mediano 2f1cd192b8 Fixed small typo in Java KSG CMI calculator. 2017-12-18 17:50:37 +00:00
Pedro Martinez Mediano 39fb538945 Added C CMI unit tests. 2017-12-18 17:49:50 +00:00
Pedro Martinez Mediano fc40c279cd Added final code to call gpuCMI functions from JNI. 2017-12-18 17:49:32 +00:00
Pedro Martinez Mediano 75a303875d Replaced stub functions in gpuCMILibrary with correct code. 2017-12-18 17:48:57 +00:00
Pedro Martinez Mediano f1bd757dc0 Added versions of gpuKnn functions adapted for CMI. Refactoring needed. 2017-12-18 17:47:53 +00:00
Pedro Martinez Mediano 1fb4015df5 Remove debug mode from junit GPU MI tests. 2017-12-18 17:43:15 +00:00
Joseph Lizier a9dac705a8
Merge pull request #64 from pmediano/master 
Improvements to Kozachenko multivariate entropy calculator.

Looks great, thanks Pedro. Fixes issue #56, will close it
 2017-12-18 15:56:22 +11:00
Pedro Martinez Mediano d0304ae0c4 Added Java-side JNI functions and ensureKdTreesConstructed to KSG CMI. 2017-12-12 11:19:40 +00:00
Pedro Martinez Mediano 9248005de5 Added stub JNI function for KSG CMI. 2017-12-12 11:18:27 +00:00
Pedro Martinez Mediano 6a13b80531 Added stub gpuCMILibrary and updated Makefile. 2017-12-12 11:17:48 +00:00
Pedro Martinez Mediano b7dd2fca5f Moved common defs from gpuMILibrary to gpuKnnLibrary. 
In preparation for gpuCMILibrary.
 2017-12-12 11:16:03 +00:00
Pedro Martinez Mediano f4ca442de4 Now KSG MI calc does not build KdTrees if GPU is going to be used. 2017-12-12 11:10:50 +00:00
Pedro Martinez Mediano d010f32635 Updated getProperty and removed spurious dependency in KSG MI calc. 2017-12-12 11:04:32 +00:00
Pedro Martinez Mediano eabd7f3701 Fixed typo in Kozachenko entropy calculator. 2017-11-28 16:58:13 +00:00