David Shorten
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9a17361cca
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minor edits
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2021-07-26 21:34:22 +10:00 |
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David Shorten
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dc226be60a
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minor refactorings
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2021-07-25 17:47:27 +10:00 |
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David Shorten
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8d7c598022
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better testing script and a touch of refactoring
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2021-07-25 17:30:30 +10:00 |
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David Shorten
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cf5f8edf5e
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confirmed working on canonical ex
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2021-07-25 16:29:31 +10:00 |
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David Shorten
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4ece80b5ef
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appear to have 4kl estimator working
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2021-07-24 23:32:57 +10:00 |
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David Shorten
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bb51b09048
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converting embedding vectors to arrays for the trees
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2021-07-23 17:54:46 +10:00 |
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David Shorten
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0e530cdceb
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history embeddings done
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2021-07-23 17:26:18 +10:00 |
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David Shorten
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deb9d97520
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advancing previous indices throughout iteration
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2021-07-22 19:06:53 +10:00 |
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David Shorten
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fe0fb2ed49
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positioning embeddings start point
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2021-07-22 17:55:00 +10:00 |
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David Shorten
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56dacc5232
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some progress towards PCB spiking estimator
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2021-07-22 14:19:36 +10:00 |
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David Shorten
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4985def021
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fixed weirdness
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2019-02-01 15:35:26 +11:00 |
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David Shorten
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ea8a322b61
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end Tues
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2019-01-29 19:51:21 +11:00 |
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David Shorten
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fcbf5e7dac
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end Thurs
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2019-01-22 19:17:36 +11:00 |
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David Shorten
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8bcf41e572
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end Wed
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2018-12-19 17:15:47 +11:00 |
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David Shorten
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504c6262f0
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end Tues
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2018-12-18 20:32:37 +11:00 |
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David Shorten
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23abc021ac
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modification to calculation for point inclusion
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2018-12-11 16:15:03 +11:00 |
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David Shorten
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064953c584
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bit of cleaning up
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2018-12-11 15:18:51 +11:00 |
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David Shorten
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b467ea22a1
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option of using same K for dest history
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2018-12-11 15:15:26 +11:00 |
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David Shorten
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9f51dc284c
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option of not doing radius trimming
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2018-12-11 12:21:27 +11:00 |
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David Shorten
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6f8ae62fee
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option of excluding the point itself
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2018-12-11 12:03:44 +11:00 |
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David Shorten
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267796dc83
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forced inclusion of TransferEntropyCalculatorSpikingIntegration.java
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2018-12-10 20:29:54 +11:00 |
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David Shorten
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ec01683592
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Incorporated JL code from 21/11/2018
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2018-12-10 20:22:15 +11:00 |
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David Shorten
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fa9a45a9cf
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added in the original spiking estimator code
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2018-12-10 17:12:15 +11:00 |
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Pedro Martinez Mediano
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4908276333
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GPU tests and example now compute multiple surrogates.
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2018-11-25 19:45:48 +02:00 |
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Pedro Martinez Mediano
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c616ba55d4
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Added link to wiki in GPU loader error message.
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2018-11-25 19:25:33 +02:00 |
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jlizier
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16015e0f12
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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)
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2018-11-24 21:16:36 +11:00 |
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jlizier
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8909c23fcc
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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)
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2018-10-18 00:58:17 +11:00 |
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jlizier
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42f8d01e26
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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.
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2018-10-18 00:51:37 +11:00 |
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jlizier
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e1bad39e4e
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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)
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2018-10-17 23:37:43 +11:00 |
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jlizier
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da418c31a0
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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)
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2018-10-17 14:23:20 +11:00 |
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jlizier
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a34bce25ba
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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).
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2018-10-17 13:49:09 +11:00 |
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jlizier
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efb8243ed7
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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.
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2018-10-15 20:56:50 +11:00 |
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jlizier
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2ff6d8aeec
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Added getProperty for AIS Kraskov multivariate. Need to re-engineer this class for proper code re-use anyway.
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2018-10-15 14:38:46 +11:00 |
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jlizier
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3aa1493d7f
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Added addObservations() method with sourceValid and destValid boolean arrays to TransferEntropyCalculatorViacondMutualInfo class
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2018-09-21 10:34:01 +10:00 |
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jlizier
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af1173ba5b
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Patching local MI discrete computation when we have a time difference of > 0 (we were getting an ArrayIndexOutOfBoundsException before)
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2018-09-05 13:43:21 +10:00 |
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jlizier
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9dbe2f8578
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Added to AutoAnalyser GUI for AIS surrogate-based bias correction (parameter being the number of surrogates) for max AIS corrected auto embedding, for kernel estimator as well as Gaussian (as an alternative to analytic). Also includes the implementing code for AIS Gaussian (was already committed for kernel)
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2018-08-27 14:24:05 +10:00 |
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jlizier
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ad31af03a7
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Added throws Exception for computeSignificance() on multivariate Gaussian AIS calculator, because of throws clause introduced on underlying MI estimator
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2018-08-27 13:21:29 +10:00 |
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jlizier
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f502497256
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Added bias correction option to AutoAnalyser GUI for Gaussian AIS, TE and CTE estimators
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2018-08-27 13:19:00 +10:00 |
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jlizier
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7f9b1c0812
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Patching bias correction for Guassian MI and CMI (some for MI was in line with previous work for CMI, which required extending here). Unit tests included.
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2018-08-27 13:17:58 +10:00 |
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jlizier
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fdec72aeff
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Added tracking of bias correction to ChiSquaredMeasurementDistribution, so the distribution is adjusted with bias correction. Should have been sent with previous commit for patch to CMI Gaussian bias correction
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2018-08-27 00:29:59 +10:00 |
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jlizier
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c32b8de8b0
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Fixed a hanging issue with analytic bias correction for Guassian CMI, and added to AutoAnalyser GUI
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2018-08-27 00:22:02 +10:00 |
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jlizier
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b1a02be7db
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Adding sanity check that discrete ContextOfPastMeasure (and child classes, including AIS and TE) have k >= 0.
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2018-08-26 22:48:37 +10:00 |
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jlizier
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dc08e1c372
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Catching OutOfMemoryError in Discrete calculator creation for all other discrete calculators (only MI was done in the previous commit). Also simplified constructor calls (with code re-use) for conditional TE.
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2018-08-25 22:27:29 +10:00 |
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jlizier
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93c767999e
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Catching OutOfMemoryError in Discrete MI calculator creation
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2018-08-25 20:59:05 +10:00 |
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jlizier
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908cf675a8
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Added new constructor for TE Kraskov to pass in KSG algorithm number as an integer (It's not likely that it will be needed, but is there for completeness to match the AIS one)
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2018-08-24 14:48:11 +10:00 |
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jlizier
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373ebbdd56
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Enabling AIS KSG calculator to have underlying KSG algorithm changed via the "ALG_NUM" property
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2018-08-24 14:47:21 +10:00 |
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jlizier
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7f4dfa7970
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Added bias correction property for Gaussian MI to AutoAnalyser GUI
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2018-08-22 16:00:52 +10:00 |
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jlizier
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323ef47475
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Adding auto-embedding properies to AutoAnalyser GUI Active Info Storage for all continuous calculators (was only in KSG before)
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2018-08-22 15:53:09 +10:00 |
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jlizier
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4b6fc39c72
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Fixed tool tip pop-ups for Discrete and Binned estimators in AutoAnalyser GUI (they were using spurious values from a continuous calculator before)
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2018-08-21 20:56:58 +10:00 |
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jlizier
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8c5aa51f57
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AutoAnalyser: Added drop-down menus (aka comboboxes) for parameters whose values are amenable to selection in this way. All child classes updated to be compatible. GUI size adjusted here also.
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2018-06-26 12:22:05 +10:00 |