joseph.lizier
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32c062f880
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Inlining norms in Nearest Neighbour search classes, and adding methods to return Collections of points within ranges
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2014-10-31 12:02:54 +00:00 |
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joseph.lizier
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2a56301b75
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Kraskov multi-info calculators use fast neighbour search and common multi-info class.
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2014-10-30 04:21:12 +00:00 |
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joseph.lizier
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ed6150c6a3
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Additional operations added to multi-info interface for continuous data, and pulled common operations into a common class (revamped Kernel calculator rewritten to use this)
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2014-10-30 04:18:04 +00:00 |
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joseph.lizier
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6ade6d4311
|
Adding fast nearest neighbour searcher for univariate data (uses only a sorted array rather than whole k-d tree). Adds an abstract nearest neighbour searcher so calling classes don't necessarily need to know whether they're dealing with uni or multi-variates. MI and conditional MI Kraskov altered to use this where possible.
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2014-10-30 04:04:16 +00:00 |
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joseph.lizier
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bf94191282
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Fixes issue 34 -- adds predictive information calculators for continuous variables; interface definition, common code via abstract mutual information calculator, and implementations for Gaussian, kernel and KSG estimators.
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2014-10-16 00:31:41 +00:00 |
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joseph.lizier
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9c05f4693a
|
Fixes issue 32 -- adds fast neighbour search to Kraskov conditional MI calculators (and by implication to TE calculators). Requires adding a neighbour search within different radii for each variable to the k-d tree class.
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2014-10-15 10:36:58 +00:00 |
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joseph.lizier
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1fb3735e58
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Bug fix re issue 31 -- ensuring that kd trees get rebuilt for surrogate TE calculations.
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2014-10-15 05:06:30 +00:00 |
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joseph.lizier
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bc2783b971
|
Fixes issue 31 -- implementing fast nearest neighbour search for Kraskov MI using a k-d tree structure.
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2014-10-15 04:48:09 +00:00 |
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joseph.lizier
|
feb0f320ae
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Minor updates to javadocs regarding Active Info Storage Calculators.
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2014-09-16 03:27:28 +00:00 |
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joseph.lizier
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5d16028f5b
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Fixes issue 13 -- by adding normalise option to Kraskov multi-information. Also Fixes issue 26 -- by adding a property for adding noise to the data (which was already done for Kraskov MI and conditional MI)
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2014-09-16 01:55:22 +00:00 |
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joseph.lizier
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70bcc7c922
|
Mirrors multi-threading from Kraskov MI calculators to Kraskov conditional MI calculators, and so fixes issue 29. Also adds some minor modifications to multithreading code for Kraskov MI calculators.
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2014-09-16 01:36:39 +00:00 |
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joseph.lizier
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0db37c9160
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Making multithreading on Kraskov MI calculators the default (using all available processors), and also adding some more debug statements.
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2014-09-12 12:10:42 +00:00 |
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joseph.lizier
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957adeccd5
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Fixes issue 28 - achieves multithreading on Kraskov MI calculators, merging code from Ipek and altering the design. Also partially addresses issue 24 by switching digamma for large arguments over to commons.math
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2014-09-12 07:35:05 +00:00 |
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joseph.lizier
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6e100c65d0
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Added property for Kraskov Conditional MI calculator to add a small amount of noise to the input data. For Kraskov MI calculator, changed this to add the noise in after the data is (potentially) normalised, so the magnitude corresponds to a number of standard deviations of the original data.
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2014-09-11 03:43:40 +00:00 |
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joseph.lizier
|
0767e2e57e
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Tweaks to javadocs
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2014-08-14 06:26:06 +00:00 |
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joseph.lizier
|
916b6d5c34
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Small javadoc modification
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2014-08-14 05:57:20 +00:00 |
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joseph.lizier
|
76a274094f
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Appending suffix "Discrete" to all discrete calculators. Step 3 -- refactoring java files for Separable info. All done for source code now
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2014-08-14 03:05:28 +00:00 |
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joseph.lizier
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f2c5ba4771
|
Appending suffix "Discrete" to all discrete calculators. Step 2 -- refactoring java files, which has flow on effects to other java files. All fixed here.
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2014-08-14 03:00:15 +00:00 |
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joseph.lizier
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752b2fdb23
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Appending suffix "Discrete" to all discrete calculators. Step 1 -- just changing file names
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2014-08-14 02:43:31 +00:00 |
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joseph.lizier
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e7b8958fda
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Adding package-info.java files for Javadocs for the various packages
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2014-08-13 15:36:10 +00:00 |
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joseph.lizier
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4f8137b449
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Minor corrections to Javadocs for the continuous package
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2014-08-13 15:20:00 +00:00 |
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joseph.lizier
|
b68d77e18e
|
Rudimentary Javadocs completed for the utils package
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2014-08-13 15:18:47 +00:00 |
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joseph.lizier
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b916ac08e8
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Javadocs noted as incomplete, and indeed the code itself experimental, for mixed package.
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2014-08-13 14:53:57 +00:00 |
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joseph.lizier
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8ea3368224
|
Javadocs finalised for discrete package. Also added some new methods to ChannelCalculator, SingleAgentMeasure, EntropyRateCalculator, ActiveInfoStorageCalculator made to inherit/extend from SingleAgentMeasureInContextOfPastCalculator.
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2014-08-13 14:42:56 +00:00 |
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joseph.lizier
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1ecdd8829f
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Extra imports to fix Javadoc references
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2014-08-13 03:48:54 +00:00 |
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joseph.lizier
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0e598bf81e
|
In mixed.kraskov estimators switched to use 4 nearest neighbours by default (as recommended by Kraskov et al.), and Kraskov2 algorithm for conditional MI fixed to match Wibral et al. equation (as per the continuous calculator)
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2014-08-13 02:57:54 +00:00 |
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joseph.lizier
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bc40fb4125
|
Kraskov estimators switched to use 4 nearest neighbours by default (as recommended by Kraskov et al.)
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2014-08-13 02:41:25 +00:00 |
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joseph.lizier
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77680c04ad
|
Javadocs made release-ready in the continuous.symbolic package.
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2014-08-13 02:37:02 +00:00 |
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joseph.lizier
|
786784e83c
|
Javadocs made release-ready in the continuous.kraskov package.
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2014-08-13 02:36:09 +00:00 |
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joseph.lizier
|
df196f115d
|
Javadocs made release-ready in the continuous.kozachenko package.
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2014-08-13 02:31:24 +00:00 |
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joseph.lizier
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4e676a1122
|
Javadocs made release-ready in the continuous.kernel package. Also renamed any "epsilon" variables to "kernelWidth" in most classes.
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2014-08-13 02:30:39 +00:00 |
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joseph.lizier
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fb4d6c423c
|
Javadocs made release-ready in the continuous.gaussian package.
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2014-08-13 02:24:02 +00:00 |
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joseph.lizier
|
edbe595032
|
Javadocs made release-ready in the continuous package. Also added computeLocalUsingPreviousObservations into ChannelCalculator and ChannelCalculatorMultiVariate (removed from MutualInfoMultivarate), and made the ViaCondMutualInfo classes not be abstract anymore, and moved embedding properties up into the main TransferEntropyCalculator interface
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2014-08-13 02:18:33 +00:00 |
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joseph.lizier
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26c98df75c
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Correcting Conditional MI Calculator Kraskov algorithm 2 in line with Wibral et al.'s equation correcting how this should be done.
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2014-08-12 05:24:54 +00:00 |
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joseph.lizier
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a22c0d7629
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Removing MultiInfoCalculatorWithMarginals since it's not used anywhere and may simply be confusing for users.
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2014-08-12 01:57:38 +00:00 |
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joseph.lizier
|
5432d902f1
|
Removing MutualInfoCalculatorMultiVariateWithMarginals since it's not used anywhere and may simply be confusing for users.
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2014-08-11 06:06:44 +00:00 |
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joseph.lizier
|
22883aa575
|
Interregional Transfer demo code: Correcting printing of parameter settings to happen only once
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2014-08-07 02:15:14 +00:00 |
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joseph.lizier
|
4a3532b25b
|
Adding GPLv3 license statement to all code headers in the infodymamics.measures.mixed, utils and networkinference packages.
|
2014-08-06 06:31:24 +00:00 |
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joseph.lizier
|
6709163afd
|
Adding GPLv3 license statement to all code headers in the infodymamics.measures.continuous.kraskov, symbolic and discrete packages (continuing ...)
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2014-08-06 05:43:16 +00:00 |
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joseph.lizier
|
7803966168
|
Adding GPLv3 license statement to all code headers in the infodymamics.measures.continuous.gaussian, kernel and kozachenko packages (continuing ...)
|
2014-08-06 05:37:59 +00:00 |
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joseph.lizier
|
98d5373d62
|
Adding GPLv3 license statement to all code headers in the infodymamics.measures.continuous package (for starters)
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2014-08-06 05:31:37 +00:00 |
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joseph.lizier
|
6a1bacba42
|
Adding notices about derived works from the JAMA project to source files
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2014-08-06 05:20:17 +00:00 |
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joseph.lizier
|
90707379b1
|
Adding derived works from Apache Commons Math library in the JIDT source tree; using these from MathsUtils to compute chi^2 CDF.
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2014-08-06 04:16:15 +00:00 |
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joseph.lizier
|
6c0d2f4e99
|
Refactoring discrete conditional TE calculator to take source as first argument before destination (to match continuous calculators)
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2014-08-06 00:32:54 +00:00 |
|
joseph.lizier
|
8b0de7e9fa
|
Refactoring discrete TE calculator to take source as first argument before destination (to match continuous calculators)
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2014-08-05 12:44:05 +00:00 |
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joseph.lizier
|
9d85a78cc2
|
Renaming Complete TE discrete calculator to Conditional -- step 2 of 2 the file name change
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2014-08-05 06:54:31 +00:00 |
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joseph.lizier
|
a48da3dc42
|
Renaming Complete TE discrete calculator to Conditional -- step 1 of 2, just refactoring class names, file name change to come
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2014-08-05 06:53:48 +00:00 |
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joseph.lizier
|
76d4dc73a6
|
Renaming ApparentTransferEntropyCalculator to TransferEntropyCalculator for simplicity -- step 2 of 2, renaming the actual file
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2014-08-05 04:59:31 +00:00 |
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joseph.lizier
|
7e27c0d4ed
|
Renaming ApparentTransferEntropyCalculator to TransferEntropyCalculator for simplicity -- step 1 of 2
|
2014-08-05 04:58:32 +00:00 |
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joseph.lizier
|
ab916e2253
|
Adding analytic null distribution computation to discrete TE calculator
|
2014-08-05 04:29:37 +00:00 |