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488 Commits

Author SHA1 Message Date
Brad ebcc281b50
Merge 1fcf2d0136 into fea2cb4bfa 2025-10-28 22:53:24 +08:00
Joseph Lizier cb12914e7a Changing spiking TE code to return all embeddings with the local TE contributions at each spike 2025-05-02 16:06:52 +10:00
Joseph Lizier d773508cf9 Fixing handling of data normalisation in the KNN computation methods 2025-04-01 23:09:09 +11:00
Joseph Lizier 333a00fc07 Adding method to compute kNN distances for KSG AIS estimator 2025-04-01 22:55:28 +11:00
Joseph Lizier 2ab3ec347c Adding method for KSG TE estimator to return KNN distances 2025-04-01 22:49:45 +11:00
Joseph Lizier 5dc9d00aff Adding univariate calls for KNN distances in KSG MI estimators 2025-04-01 22:33:45 +11:00
Joseph Lizier c08aeb1783 Adding univariate calls for cross CMI 2025-04-01 22:33:02 +11:00
Joseph Lizier fa21f7343a Adding debug methods to KSG estimators to retrieve knn distances 2025-04-01 18:08:38 +11:00
Joseph Lizier 13251a0104 Cleaning up code of the spiking TE estimator 2025-04-01 15:29:20 +11:00
Joseph Lizier 283dcb3b94 Adding a field to the object returned from local TE for spike trains which holds the ISI to previous (selected) source spike 2025-03-28 18:09:28 +11:00
Joseph Lizier cab3de8b07 Bug fix to local TE for spike trains code; forgot to increment the index when computing local values, fixed. 2025-03-28 15:15:30 +11:00
Joseph Lizier efd3943697 Implementing local TE contributions for the spiking estimator 2025-03-21 16:08:39 +11:00
Brad Wootton de44f67d46 Final commit for Brad's thesis. All remaining TODO comments are real TODOs. Support for larger alphabets has been added for entropy and mutual information, lightly tested. The old misleading 'alphabet size' has refactored to 'base'. 2024-12-24 20:40:51 +10:00
Brad Wootton ac8326aecf Discrete entropy is complete I think. Maybe a few more things moved around. No tests yet. 2024-08-22 13:52:19 +10:00
Joseph Lizier a9b6b3e77c Adding property to set random seed for noise addition to EntropyMultiVariate estimators (mimicing that for MI/CMI estimators), extending the fix for issue #99 to Entropy estimators 2024-04-20 18:52:10 +10:00
Joseph Lizier 3d1f3fec86 Gathering common functionality of EntropyMultiVariate estimators into a Common class. Adds some new functionality (e.g. addObservations() for Gaussian and Kernel) 2024-04-20 17:57:38 +10:00
Joseph Lizier 2a18cd0e74 Adding property to allow used to set random seed for noise addition to data in MI, CMI and wrapped estimators. Closes issue #99 2024-04-16 14:08:04 +10:00
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