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481 Commits

Author SHA1 Message Date
Donovan Rynne 914dc171f5 fix bugs where shuffle and rotate strategy where switched 
Also fixed rotate surrogate selection, list was being rotate continuously rather than rotating the initial index list, which nullified the dyncorrexcl setting.
 2024-05-18 14:24:22 +10:00
Donovan Rynne 9643b1ce6b update autoanalyser for new theiler window handling 2024-04-28 14:24:12 +10:00
Donovan Rynne 6bf7954d4e modify generateRotatedSurrogates for theiler window exclusion 2024-04-28 14:23:48 +10:00
Donovan Rynne 484421bf3c refactor to bring DYN_CORR_EXCL from kernel and kraskov into common 2024-04-28 14:23:10 +10:00
Donovan Rynne c1225d67c7 add surrogate type to common getProperty 2024-04-20 15:33:11 +10:00
Donovan Rynne 401df8ee45 add surrogate type to AutoAnalyserMI 2024-04-20 11:09:24 +10:00
Donovan Rynne 2c33e36752 add new surrogate types formatting 2024-04-20 11:09:24 +10:00
Donovan Rynne a3cdcc04b5 add surrogate_type checking into computeSignificance, surrogate property plumbing in interface class 2024-04-20 11:09:23 +10:00
Donovan Rynne 191a81f1bc add generateRotatedSurrogates method in RandomGenerator 2024-04-20 11:09:22 +10:00
Donovan Rynne 037159cf86 rename numPermutationsToCheck to numSurrogatesToCheck 2024-03-24 19:01:30 +11:00
Joseph Lizier 2130985c34 Adding/implementing interfaces for continuous CMI estimators to allow all combinations of univariate/multivariate arrays to be passed for var1/var2/conditional 2023-10-27 10:04:25 +11:00
Joseph Lizier 4b85a7fd46 AIS and TE estimators (for KSG in particular) utilising the underlying NN Searchers holding the different data sets separately. 2023-10-09 13:16:27 +11:00
Joseph Lizier ec8e7f848f CMI common estimators utilising underlying nearest neighbour searchers holding different data sets separately (for dynamic correlation exclusion) 2023-10-09 13:15:56 +11:00
Joseph Lizier 5f87e2018b MI common estimators utilising underlying nearest neighbour searchers holding different data sets separately (for dynamic correlation exclusion) 2023-10-09 13:14:29 +11:00
Joseph Lizier 938dd7c4fb Implementing multiple data sets in the nearest neighbour searches, to facilitate dynamic correlation exclusion only for points within the same data set 2023-10-09 13:12:07 +11:00
Joseph Lizier a554361de9 Adding unit test for no conditional on CMI Gaussian 2023-10-06 12:29:37 +11:00
Joseph Lizier 90baf68ee7 Making AutoAnalyser Python code only start JVM if not already started 2023-08-21 17:55:16 +10:00
Joseph Lizier 817abd1de0 For Autoanalyser Python code adding \ at the end of line for print statement 2023-08-15 16:28:04 +10:00
jlizier 865d82630a Altering AutoAnalyser generated python code to set flag convertStrings=True in JVM start, as per PR #94 2022-09-08 10:20:20 +10:00
jlizier 2b0a5cb943 Updated mixed-continiuous CMI KSG estimator, for the bias correction based on number of continuous variables. This was identified from testing, and aligns with testing so far. 2022-09-05 17:51:49 +10:00
Joseph Lizier d750a737be
Removing what appears to be an old test file from the integrated Spiking TE code from David 2022-09-05 17:08:10 +10:00
Joseph Lizier 27f9cccf65
Don't need code for old way of doing spiking TE estimation 2022-09-05 14:45:50 +10:00
Joseph Lizier 47be5df74b
editing comment on how to implement dynamic correlation exclusions in spiking TE estimator 2022-09-05 14:43:18 +10:00
Joseph Lizier e747e8aa93
Merge pull request #93 from dpshorten/master 
Spike train TE estimation
 2022-09-05 14:38:21 +10:00
jlizier 05248ef105 Extra fixing windows paths generated from AutoAnalyser to be properly escaped in data filename for Python/Matlab 2022-09-01 15:50:27 +10:00
jlizier c233485c90 Fixing windows paths generated from AutoAnalyser to be properly escaped 2022-09-01 15:28:28 +10:00
jlizier 2714650cfa Amending Kraskov (KSG) MI estimators to have an experimental method to provide conditional entropy of the first variable given the second. Works by removing the Kozachenko Leonenko entropy of variable 1 from the MI, using the same kNN radii as the MI estimator. Includes Unit tests to provide some initial validation. 2022-06-16 21:29:29 +10:00
jlizier 25159009ca updating max entropy discretisation to gracefully handle NaNs in the input (which shouldn't be there anyway) 2022-06-09 12:39:59 +10:00
David Shorten c068c8308d improving jittered surrogates 2022-02-25 18:49:12 +11:00
David Shorten 285c95947a integrating artemis changes 2022-02-22 14:39:15 +11:00
David Shorten b4e32727c9 merge 2022-02-22 11:55:09 +11:00
Joseph Lizier 0e33393cdc
Merge pull request #86 from pmediano/master 
Thanks Pedro, and sorry to take so long to attend to this
 2021-11-15 12:08:57 +11:00
Joseph Lizier b02760ddd3 Adding overloads on setObservations and addObservations for MI and TE calculators to handle one variable univariate and one variable multivariate 2021-11-15 10:58:59 +11:00
Joseph Lizier 7d7291fb9d Implementing Analytic null distributions for discrete conditional TE estimator 2021-11-02 23:11:45 +11:00
Joseph Lizier 6f43dfb620 Altering the python-java jpype data conversion in AutoAnalyser to work properly with jpype 0.7 and upwards 2021-10-08 16:03:14 +11:00
Joseph Lizier 21ae0bdeaa Fixing logic error in printing whether GPU calculation was falling back to CPU 2021-10-08 11:28:37 +11:00
Joseph Lizier 650159661d Patching conditional MI calculator to properly allow null or empty conditionals if dimension of conditionals is 0 2021-09-06 10:23:31 +10:00
David Shorten c8d17e9522 functionality allowing specific embedding intervals 2021-08-23 17:50:34 +10:00
Joseph Lizier aa8148eca9 Updates to KL entropy estimator: removing NORMALISE property, and adding method for cross entropy 2021-08-23 09:09:49 +10:00
David Shorten dd215fdfbb spiking surrogates implemented 2021-08-11 09:20:35 +10:00
Joseph Lizier ef7cfbb525 Fixed missing " in comment 2021-08-06 17:43:56 +10:00
David Shorten dc85001ff7 refactoring + conditional processes + radius sharing + euclidean norm working 2021-08-02 22:06:07 +10:00
David Shorten 9a17361cca minor edits 2021-07-26 21:34:22 +10:00
David Shorten dc226be60a minor refactorings 2021-07-25 17:47:27 +10:00
David Shorten 8d7c598022 better testing script and a touch of refactoring 2021-07-25 17:30:30 +10:00
David Shorten cf5f8edf5e confirmed working on canonical ex 2021-07-25 16:29:31 +10:00
David Shorten 4ece80b5ef appear to have 4kl estimator working 2021-07-24 23:32:57 +10:00
David Shorten bb51b09048 converting embedding vectors to arrays for the trees 2021-07-23 17:54:46 +10:00
David Shorten 0e530cdceb history embeddings done 2021-07-23 17:26:18 +10:00
David Shorten deb9d97520 advancing previous indices throughout iteration 2021-07-22 19:06:53 +10:00