Joseph Lizier
|
b1437452e4
|
Adding NORMALISE and NOISE_LEVEL_TO_ADD properties to all mutual information calculators for continuous-valued data (extends this capability from only KSG to Gaussian and kernel as well, the latter already had NORMALISE)
|
2019-04-02 12:38:17 +11:00 |
|
Joseph Lizier
|
ecec4d20e3
|
Added unit tests for linear dependency possibilities for issue #16
|
2019-03-31 23:22:55 +11:00 |
|
Joseph Lizier
|
988d32de70
|
Added bug fix within recent changes to MatrixUtils Cholesky decomposition calculation, along with unit testing of the linear dependency combinations for issue #17
|
2019-03-31 23:21:39 +11:00 |
|
Joseph Lizier
|
2a0024ad83
|
Fixes issue #17: Handling sub-cases for linear redundancy within and across variables in the linear-Gaussian mutual information estimator. This is done by detecting such redundancies and either returning 0 or infinity as the requisite result. Mirrors how this is done for conditional MI.
|
2019-03-29 00:01:36 +11:00 |
|
Joseph Lizier
|
66676a2692
|
A rewrite of parts of the linear Gaussian conditional MI estimator, in order to more deftly handle linear dependencies within variables 1 and 2, and between each of them and the conditional. Previously we removed sub-variables of those arbitrarily, now the removal is targetted to those sub-variables that are problematic. Also required some variable name changes to reflect different ordering of how variables and the conditionals are concatenated in arrays.
|
2019-03-28 23:58:53 +11:00 |
|
Joseph Lizier
|
d58c393c53
|
Added methods to MatrixUtils to make a Cholesky decomposition of independent components only (useful for MI and conditional MI calculations), with a required update to the NonPositiveDefiniteMatrixException to include a field defining which row in the matrix was a problem. Also includes code to convert between native int[] arrays and ArrayList<Integers>, and new method signatures for column selection from matricies.
Also added new unit tests for the Cholesky decomposition.
|
2019-03-28 23:52:47 +11:00 |
|
Joseph Lizier
|
1d2c7c42b9
|
Updating javaMatrixToOctave to handle new conversion routine in octave (and be backwards compatible to old)
|
2019-03-21 09:35:41 +11:00 |
|
Joseph Lizier
|
9aed0d4590
|
Merge remote branch 'origin/master'
|
2019-03-11 12:04:18 +11:00 |
|
Joseph Lizier
|
c4349140f1
|
Updating ant javadoc target to use packageset instead of fileset (for JDK >= 8 it seems that fileset is not properly handling the java source code I want the javadocs to ignore; packageset is doing this ok). Fixes Issue #75 (the javadocs part)
|
2019-03-11 11:58:17 +11:00 |
|
David Shorten
|
4985def021
|
fixed weirdness
|
2019-02-01 15:35:26 +11:00 |
|
Joseph Lizier
|
c693b5d57e
|
Edited funding acknowledgements on README.md
|
2019-02-01 13:38:35 +11:00 |
|
David Shorten
|
ea8a322b61
|
end Tues
|
2019-01-29 19:51:21 +11:00 |
|
David Shorten
|
fcbf5e7dac
|
end Thurs
|
2019-01-22 19:17:36 +11:00 |
|
David Shorten
|
8bcf41e572
|
end Wed
|
2018-12-19 17:15:47 +11:00 |
|
David Shorten
|
504c6262f0
|
end Tues
|
2018-12-18 20:32:37 +11:00 |
|
David Shorten
|
23abc021ac
|
modification to calculation for point inclusion
|
2018-12-11 16:15:03 +11:00 |
|
David Shorten
|
064953c584
|
bit of cleaning up
|
2018-12-11 15:18:51 +11:00 |
|
David Shorten
|
b467ea22a1
|
option of using same K for dest history
|
2018-12-11 15:15:26 +11:00 |
|
David Shorten
|
9f51dc284c
|
option of not doing radius trimming
|
2018-12-11 12:21:27 +11:00 |
|
David Shorten
|
6f8ae62fee
|
option of excluding the point itself
|
2018-12-11 12:03:44 +11:00 |
|
David Shorten
|
267796dc83
|
forced inclusion of TransferEntropyCalculatorSpikingIntegration.java
|
2018-12-10 20:29:54 +11:00 |
|
David Shorten
|
ec01683592
|
Incorporated JL code from 21/11/2018
|
2018-12-10 20:22:15 +11:00 |
|
David Shorten
|
fa9a45a9cf
|
added in the original spiking estimator code
|
2018-12-10 17:12:15 +11:00 |
|
Joseph Lizier
|
2ba27f30ac
|
Merge pull request #73 from pmediano/master
Minor updates to GPU tests and examples following v1.5 release.
|
2018-11-26 10:28:15 +11:00 |
|
Pedro Martinez Mediano
|
4908276333
|
GPU tests and example now compute multiple surrogates.
|
2018-11-25 19:45:48 +02:00 |
|
Pedro Martinez Mediano
|
c616ba55d4
|
Added link to wiki in GPU loader error message.
|
2018-11-25 19:25:33 +02:00 |
|
jlizier
|
bd6a9a2601
|
Updating links to latest release to v1.5 on front page. Also fixed indenting
|
2018-11-26 00:33:58 +11:00 |
|
jlizier
|
eefe1e1a8b
|
Updating readme-template.txt and ready for release v1.5
|
2018-11-25 23:48:10 +11:00 |
|
jlizier
|
ee1ef4909c
|
Storing executable permissions for jar file, .sh and .bat files in the distribution .zip and now making a .tar.gz distribution also
|
2018-11-25 23:39:44 +11:00 |
|
jlizier
|
a3ec963618
|
Updating demos PDFs again
|
2018-11-25 23:38:49 +11:00 |
|
jlizier
|
603445651c
|
Moving GPU readme from wiki into CUDA folder
|
2018-11-25 23:27:27 +11:00 |
|
jlizier
|
7bd6496a40
|
Removed old .sh and .bat files for running AutoAnalyser for individual measures (now replaced by launchAutoAnalyser)
|
2018-11-25 22:38:08 +11:00 |
|
jlizier
|
cd1d4c2684
|
Adding executable permission to Java demo 10 for GPU
|
2018-11-25 21:57:25 +11:00 |
|
jlizier
|
7910828ad7
|
Added release notes for v1.5 to readme-template.txt
|
2018-11-25 21:52:07 +11:00 |
|
jlizier
|
dc4e59f945
|
Updating tutorial wiki page PDF
|
2018-11-25 21:50:53 +11:00 |
|
jlizier
|
b6a5285b9b
|
Updated version number in build.xml ready for new release
|
2018-11-25 21:48:29 +11:00 |
|
jlizier
|
3c24debea5
|
Updating PDFs of wiki pages of all demos to make sure they are up to date; includes adding the new wiki page for GPU
|
2018-11-25 21:47:41 +11:00 |
|
jlizier
|
16015e0f12
|
Nearest neighbour searchers now return number of points found for findPointsWithinR as well as marking them in input arrays. Also added new method sumDistanceAboveThresholdForPointsWithinRs() for the univariate searcher (to be used in spiking TE estimator under development)
|
2018-11-24 21:16:36 +11:00 |
|
David Shorten
|
af7fbd6c37
|
added spiking measures
|
2018-11-19 15:55:24 +11:00 |
|
jlizier
|
8909c23fcc
|
Incorporated auto-embedding in the TE multivariate via conditional MI common class. Much of the code is moved up from the TE multivariate KSG estimator; now the functionality is provided for multivariate Gaussian as well. Also necessitated adding the max_cor_num_surrogates property to TE multivariate Gaussian, and took the opportunity to make much of the whitespace here consistent, and unit tests added for Gaussian (tweaked slightly for KSG)
|
2018-10-18 00:58:17 +11:00 |
|
jlizier
|
42f8d01e26
|
Adding property of number of dimensions for the AIS multivariate calculator (and implemented in the via MI common class). Needed this to make multivariate TE embedding a bit neater, and it should be there anyway.
|
2018-10-18 00:51:37 +11:00 |
|
jlizier
|
e1bad39e4e
|
Added proper full definitions for the methods of the AIS multivariate interface; much of this is achieved by extending the univariate AIS interface (which mandates that the univariate methods must be supported). No current child classes required any changes as they all supported these already. Removed superfluous documentation in the AIS multivariate via MI class (as well as fixing whitespace inconsistencies therein)
|
2018-10-17 23:37:43 +11:00 |
|
jlizier
|
da418c31a0
|
Added new auto-embedding capability for TE Gaussian into the AutoAnalyser GUI demo. Also added new auto-embedding drop down option of Max corrected AIS + TE for KSG as well, and debugged the getProperty returning of the number of nearest neighbours for Ragwitz criteria now that this occurs in the common superclass instead of in KSG (and gave this a reasonable default of 4)
|
2018-10-17 14:23:20 +11:00 |
|
jlizier
|
a34bce25ba
|
Enabled auto-embedding for TE Gaussian. Did so by bringing up auto-embedding for TE functionality up from the KSG estimator to the via Conditional MI class. Also added new property to Gaussian TE for number of surrogates to use for bias correction in embedding (if not using analytic bias correction), like Gaussian AIS. This also necessitated adding an empty preFinaliseAddObservations() method to the TE Gaussian multivariate estimator, to ensure it did not yet try to autoembed until that is enabled in the multivariate calculator. Unit tests included here as well (included using more samples for TE KSG autoembedding to ensure we get the correct answer more reliably -- should probably add a stronger effect for that too).
|
2018-10-17 13:49:09 +11:00 |
|
jlizier
|
efb8243ed7
|
Altering TE Kraskov to do auto-embedding properly when we have added multiple observations with validity vectors. Also taking the opportunity to re-engineer the internals to lay groundwork for auto-embedding function to be shared with the Gaussian estimator at a later stage. Unit tests added here as well for the above.
|
2018-10-15 20:56:50 +11:00 |
|
jlizier
|
2ff6d8aeec
|
Added getProperty for AIS Kraskov multivariate. Need to re-engineer this class for proper code re-use anyway.
|
2018-10-15 14:38:46 +11:00 |
|
jlizier
|
3aa1493d7f
|
Added addObservations() method with sourceValid and destValid boolean arrays to TransferEntropyCalculatorViacondMutualInfo class
|
2018-09-21 10:34:01 +10:00 |
|
jlizier
|
6cf43db7f5
|
Updating lecture slides for the course all to 2018 versions
|
2018-09-20 14:15:11 +10:00 |
|
jlizier
|
cf83a73bc0
|
Renaming lecture slide files in the course to align with new numbering and naming
|
2018-09-20 14:11:14 +10:00 |
|
jlizier
|
1f8a33b211
|
Changing folder structure for the course modules
|
2018-09-20 14:04:10 +10:00 |