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459 Commits

Author SHA1 Message Date
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
David Shorten fe0fb2ed49 positioning embeddings start point 2021-07-22 17:55:00 +10:00
David Shorten 56dacc5232 some progress towards PCB spiking estimator 2021-07-22 14:19:36 +10:00
Pedro Mediano 07883af734 Updated printed messages with cross-platform newline character. 2021-02-09 10:23:30 +00:00
Pedro Mediano bc8c233e68 Added KSG implementation of various multivariate IT measures and unit tests. 2021-01-25 12:41:01 +00:00
Pedro Mediano a58a01fbfd Added discrete implementation of various multivariate IT measures and unit tests. 2021-01-24 22:13:15 +00:00
Pedro Mediano b3abd382aa Added abstract parent class for multivariate IT measures on discrete data. 2021-01-24 22:10:14 +00:00
Pedro Mediano f67e274819 Added Gaussian implementation of various multivariate IT measures and unit tests. 2021-01-24 22:06:39 +00:00
Pedro Mediano 403745800e Added abstract parent class for multivariate IT measures on continuous data. 2021-01-24 21:56:26 +00:00
Pedro Mediano 06cc6d649d Added `select*` methods for `int[][]` matrices. 2021-01-24 21:54:42 +00:00
Pedro Mediano b3192e225f Added convenience methods to multiply an array times a constant value. 2021-01-24 21:54:09 +00:00
Joseph Lizier 3222b5a629 Implementation and unit test for KSG MI calculation with new samples (both algorithms 1 and 2) 2020-10-30 16:21:10 +11:00
Joseph Lizier 0606f8ab39 Cleaning up CMI Kraskov for new samples, including fixing some comments, logic of not using GPU for this, and if no conditional counting all point as a conditional match 2020-10-30 16:19:31 +11:00
Joseph Lizier b5a6fa92c2 Fixing min and max of local CMI values 2020-10-29 13:45:25 +11:00
Joseph Lizier 44e53bc846 Updating error messages for kdTree 2020-10-29 13:39:40 +11:00
Joseph Lizier 34161a2e6d Adding non-overloaded method signatures for multivariate arrays, so that the jpype python-java bridge can resolve which method signature to use more directly via these 2020-05-22 14:42:26 +10:00
Joseph Lizier bf207f866e Patched error in computing start and end times for valid observation sequences in conditional TE calculators (with validity booleans) 2020-05-21 00:57:34 +10:00
Joseph Lizier d0a0fca40c Added non-overloaded method calls for conditionalTE continuous' addObservations() method calls with validity booleans - this is for JPype from Python which seems unable to resolve overloads of double[] and double[][], when more than one variable changes in this way 2020-05-16 12:18:57 +10:00
Joseph Lizier cbcca8d0ff fixing addedMoreThanOneObservationSet for the MultiInfoCalculator 2020-05-15 17:35:54 +10:00
Joseph Lizier 510f999d2e Adds addObservations calls with validity arrays for conditional transfer entropy 2020-05-15 17:34:00 +10:00
Joseph Lizier 61ae6fb40b Minor updates to AutoAnalyser to put fixtures in place for array conversion to Python with eventual handling of 2D arrays (code isn't really changed at the moment, but has methods to make this easy later) 2019-07-25 23:56:56 +10:00
Joseph Lizier 2ab3ac01bb Adding non-overloaded method signatures for adding 1D vs 2D observations for common class for continuous MI and CMI estimators, since JPype 0.7 does not seem able to resolve overloaded 1D vs 2D arrays any longer 2019-07-25 23:11:44 +10:00
Joseph Lizier 1667b9fe7a Added utility for subsampling rows from 2D matrix 2019-07-25 14:36:54 +10:00