├── .gitignore ├── InfoDynamicsToolkit.pdf ├── README.md ├── course ├── Module0-Overview │ └── Lec0a-IntroToCourse.pdf ├── Module1-IntroductionToInformationTheory │ └── Lec1-IntroductionToInformationTheory.pdf ├── Module10-EffectiveNetworkInference │ └── Lec10-EffectiveNetworkInference.pdf ├── Module11-WrapUp │ └── Lec11-InfoTheoryWrapUp.pdf ├── Module2-WhatIsInformation │ └── Lec2-WhatIsInformation.pdf ├── Module3-JIDT │ └── Lec3-IntroToJIDT.pdf ├── Module4-EstimatorsAndJIDT │ └── Lec4-EstimatorsAndJIDT.pdf ├── Module5-StatisticalSignificance │ └── Lec5-StatSignificanceAndUndersampling.pdf ├── Module6-InfoTheoryAndSelfOrganisation │ └── Lec6-SelfOrganisation.pdf ├── Module7-InfoProcessingInComplexSystems │ └── Lec7-InfoProcessing.pdf ├── Module8-InformationStorage │ └── Lec8-InfoStorage.pdf ├── Module9-InformationTransfer │ └── Lec9-InfoTransfer.pdf ├── README-Course.pdf └── README.md ├── cuda ├── FindJNI.mk ├── Makefile ├── MemoryManagement.txt ├── README-GPU.pdf ├── benchmark.sh ├── ctimer.h ├── cub │ ├── LICENSE.TXT │ ├── README.md │ ├── common.mk │ ├── cub │ │ ├── agent │ │ │ ├── agent_histogram.cuh │ │ │ ├── agent_radix_sort_downsweep.cuh │ │ │ ├── agent_radix_sort_upsweep.cuh │ │ │ ├── agent_reduce.cuh │ │ │ ├── agent_reduce_by_key.cuh │ │ │ ├── agent_rle.cuh │ │ │ ├── agent_scan.cuh │ │ │ ├── agent_segment_fixup.cuh │ │ │ ├── agent_select_if.cuh │ │ │ ├── agent_spmv_csrt.cuh │ │ │ ├── agent_spmv_orig.cuh │ │ │ ├── agent_spmv_row_based.cuh │ │ │ └── single_pass_scan_operators.cuh │ │ ├── block │ │ │ ├── block_adjacent_difference.cuh │ │ │ ├── block_discontinuity.cuh │ │ │ ├── block_exchange.cuh │ │ │ ├── block_histogram.cuh │ │ │ ├── block_load.cuh │ │ │ ├── block_radix_rank.cuh │ │ │ ├── block_radix_sort.cuh │ │ │ ├── block_raking_layout.cuh │ │ │ ├── block_reduce.cuh │ │ │ ├── block_scan.cuh │ │ │ ├── block_shuffle.cuh │ │ │ ├── block_store.cuh │ │ │ └── specializations │ │ │ │ ├── block_histogram_atomic.cuh │ │ │ │ ├── block_histogram_sort.cuh │ │ │ │ ├── block_reduce_raking.cuh │ │ │ │ ├── block_reduce_raking_commutative_only.cuh │ │ │ │ ├── block_reduce_warp_reductions.cuh │ │ │ │ ├── block_scan_raking.cuh │ │ │ │ ├── block_scan_warp_scans.cuh │ │ │ │ ├── block_scan_warp_scans2.cuh │ │ │ │ └── block_scan_warp_scans3.cuh │ │ ├── cub.cuh │ │ ├── device │ │ │ ├── device_histogram.cuh │ │ │ ├── device_partition.cuh │ │ │ ├── device_radix_sort.cuh │ │ │ ├── device_reduce.cuh │ │ │ ├── device_run_length_encode.cuh │ │ │ ├── device_scan.cuh │ │ │ ├── device_segmented_radix_sort.cuh │ │ │ ├── device_segmented_reduce.cuh │ │ │ ├── device_select.cuh │ │ │ ├── device_spmv.cuh │ │ │ └── dispatch │ │ │ │ ├── dispatch_histogram.cuh │ │ │ │ ├── dispatch_radix_sort.cuh │ │ │ │ ├── dispatch_reduce.cuh │ │ │ │ ├── dispatch_reduce_by_key.cuh │ │ │ │ ├── dispatch_rle.cuh │ │ │ │ ├── dispatch_scan.cuh │ │ │ │ ├── dispatch_select_if.cuh │ │ │ │ ├── dispatch_spmv_csrt.cuh │ │ │ │ ├── dispatch_spmv_orig.cuh │ │ │ │ └── dispatch_spmv_row_based.cuh │ │ ├── grid │ │ │ ├── grid_barrier.cuh │ │ │ ├── grid_even_share.cuh │ │ │ ├── grid_mapping.cuh │ │ │ └── grid_queue.cuh │ │ ├── host │ │ │ └── mutex.cuh │ │ ├── iterator │ │ │ ├── arg_index_input_iterator.cuh │ │ │ ├── cache_modified_input_iterator.cuh │ │ │ ├── cache_modified_output_iterator.cuh │ │ │ ├── constant_input_iterator.cuh │ │ │ ├── counting_input_iterator.cuh │ │ │ ├── discard_output_iterator.cuh │ │ │ ├── tex_obj_input_iterator.cuh │ │ │ ├── tex_ref_input_iterator.cuh │ │ │ └── transform_input_iterator.cuh │ │ ├── thread │ │ │ ├── thread_load.cuh │ │ │ ├── thread_operators.cuh │ │ │ ├── thread_reduce.cuh │ │ │ ├── thread_scan.cuh │ │ │ ├── thread_search.cuh │ │ │ └── thread_store.cuh │ │ ├── util_allocator.cuh │ │ ├── util_arch.cuh │ │ ├── util_debug.cuh │ │ ├── util_device.cuh │ │ ├── util_macro.cuh │ │ ├── util_namespace.cuh │ │ ├── util_ptx.cuh │ │ ├── util_type.cuh │ │ └── warp │ │ │ ├── specializations │ │ │ ├── warp_reduce_shfl.cuh │ │ │ ├── warp_reduce_smem.cuh │ │ │ ├── warp_scan_shfl.cuh │ │ │ └── warp_scan_smem.cuh │ │ │ ├── warp_reduce.cuh │ │ │ └── warp_scan.cuh │ └── tune │ │ ├── .gitignore │ │ ├── Makefile │ │ └── tune_device_reduce.cu ├── digamma.c ├── digamma.h ├── findComputeCapability.cu ├── gpuCMILibrary.c ├── gpuCMILibrary.h ├── gpuKnnBF_kernel.cu ├── gpuKnnLibrary.c ├── gpuKnnLibrary.h ├── gpuMILibrary.c ├── gpuMILibrary.h ├── helperfunctions.cu ├── kraskovCuda.c ├── lest.hpp ├── perftest.cpp └── unittest.cpp ├── demos ├── AutoAnalyser │ ├── JIDT-logo-watermark.png │ ├── README-AutoAnalyserDemo.pdf │ ├── launchAutoAnalyser.bat │ ├── launchAutoAnalyser.m │ ├── launchAutoAnalyser.py │ ├── launchAutoAnalyser.sh │ ├── runAutoGenerated.bat │ └── runAutoGenerated.sh ├── README-Demos.pdf ├── clojure │ ├── README-ClojureExamples.pdf │ ├── README-UseInClojure.pdf │ ├── deploy │ │ ├── project-template.clj │ │ └── readme.txt │ └── examples │ │ ├── example1TeBinaryData.clj │ │ ├── example2TeMultidimBinaryData.clj │ │ ├── example3TeContinuousDataKernel.clj │ │ ├── example4TeContinuousDataKraskov.clj │ │ └── project.clj ├── data │ ├── 10ColsGaussianSelfDependence2Steps.txt │ ├── 10ColsRandomGaussian-1.txt │ ├── 2coupledBinaryColsUseK2.txt │ ├── 2coupledDiscreteCols-1.txt │ ├── 2coupledRandomCols-1.txt │ ├── 2randomCols-1.txt │ ├── 4ColsPairedDirectDependence-1.txt │ ├── 4ColsPairedNoisyDependence-1.txt │ ├── 4ColsPairedOneStepNoisyDependence-1.txt │ ├── 4randomCols-1.txt │ ├── Network-GaussianLinear-N100-T100-p0.04-b0.50-c0.50-dir-disc-repeat1.txt │ ├── SFI-heartRate_breathVol_bloodOx-extract.txt │ ├── SFI-heartRate_breathVol_bloodOx.txt │ ├── coupledLogisticMapXY.txt │ ├── region1-numCoupled10-coupling0.30-past0.70.txt │ └── region2-numCoupled10-coupling0.30-past0.70.txt ├── java │ ├── README-SimpleJavaDemos.pdf │ ├── SchreiberTransferEntropyExamples │ │ └── heartRateBreathRateKraskov.sh │ ├── example10GPUBenchmark.sh │ ├── example1TeBinaryData.bat │ ├── example1TeBinaryData.sh │ ├── example2TeMultidimBinaryData.bat │ ├── example2TeMultidimBinaryData.sh │ ├── example3TeContinuousDataKernel.bat │ ├── example3TeContinuousDataKernel.sh │ ├── example4TeContinuousDataKraskov.bat │ ├── example4TeContinuousDataKraskov.sh │ ├── example5TeBinaryMultivarTransfer.bat │ ├── example5TeBinaryMultivarTransfer.sh │ ├── example6LateBindingMutualInfo.bat │ ├── example6LateBindingMutualInfo.props │ ├── example6LateBindingMutualInfo.sh │ ├── example7EnsembleMethodTeContinuousDataKraskov.bat │ ├── example7EnsembleMethodTeContinuousDataKraskov.sh │ ├── example8TeContinuousDataByBinning.bat │ ├── example8TeContinuousDataByBinning.sh │ ├── example9TeKraskovAutoEmbedding.bat │ ├── example9TeKraskovAutoEmbedding.sh │ ├── infodynamics │ │ └── demos │ │ │ ├── Example10GPUBenchmark.java │ │ │ ├── Example1TeBinaryData.java │ │ │ ├── Example2TeMultidimBinaryData.java │ │ │ ├── Example3TeContinuousDataKernel.java │ │ │ ├── Example4TeContinuousDataKraskov.java │ │ │ ├── Example5TeBinaryMultivarTransfer.java │ │ │ ├── Example6LateBindingMutualInfo.java │ │ │ ├── Example7EnsembleMethodTeContinuousDataKraskov.java │ │ │ ├── Example8TeContinuousDataByBinning.java │ │ │ ├── Example9TeKraskovAutoEmbedding.java │ │ │ ├── autoanalysis │ │ │ └── package-info.java │ │ │ └── schreiberTransferEntropyExamples │ │ │ └── HeartBreathRateKraskovRunner.java │ ├── interregionalTransfer │ │ ├── README-InterregionalTransferDemo.pdf │ │ ├── interregionalCalc.properties │ │ ├── runSample.sh │ │ ├── sampleOutput1to2.txt │ │ └── sampleOutput2to1.txt │ └── plotExample10BenchmarkResults.py ├── julia │ ├── README-JuliaExamples.pdf │ ├── README-UseInJulia.pdf │ ├── example1TeBinaryData.jl │ ├── example3TeContinuousDataKernel.jl │ ├── example4TeContinuousDataKraskov.jl │ └── example6DynamicCallingMutualInfo.jl ├── matlab │ └── See_octave_folder_for_matlab_demos ├── octave │ ├── CellularAutomata │ │ ├── DemoFrontiersBitsFromBiology2014.m │ │ ├── DirectedMeasuresChapterDemo2013.m │ │ ├── GsoChapterDemo2013.m │ │ ├── README-CellularAutomataDemos.pdf │ │ ├── TeBook2013.m │ │ ├── initialStates │ │ │ ├── DirectedMeasuresChapterDemo2013-initialStates.txt │ │ │ ├── GsoChapterDemo2013-initialState-phipar.txt │ │ │ ├── GsoChapterDemo2013-initialState.txt │ │ │ └── MovingFrameDemo2013-initialState.txt │ │ ├── movingFrame.m │ │ ├── plotLocalInfoMeasureForCA.m │ │ ├── plotLocalInfoValues.m │ │ ├── plotRawCa.m │ │ ├── prepareColourmap.m │ │ ├── runCA.m │ │ └── saveCA.m │ ├── DetectingInteractionLags │ │ ├── README-DetectingInteractionLags.pdf │ │ ├── coupledLogisticMap.m │ │ ├── sampleResults │ │ │ ├── sourceMemory-MIT.png │ │ │ └── sourceMemory-TE.png │ │ └── transferWithSourceMemory.m │ ├── EffectiveNetworkInference │ │ └── greedyInferParents.m │ ├── FlockingAnalysis │ │ ├── NetLogoExample │ │ │ ├── Flocking.nlogo │ │ │ ├── Flocking_withSPEED.nlogo │ │ │ └── loadProperties.m │ │ ├── README-Flocking.pdf │ │ ├── computeAIS.m │ │ ├── computeTE.m │ │ ├── generateObservations.m │ │ ├── loadBasic2d.m │ │ ├── loadseparatexy.m │ │ ├── loadseparatexyz.m │ │ ├── loadxls2d.m │ │ ├── loadxls3d.m │ │ ├── plotLocalTEs.m │ │ ├── processFilenames.m │ │ ├── runAnalysis.m │ │ ├── watchLocalTEs.m │ │ └── watchRawMovement.m │ ├── NullDistributions │ │ ├── README-NullDistributions.pdf │ │ ├── checkMiDiscreteNullDistribution.m │ │ └── sampleResults │ │ │ ├── cdfMiDiscrete-N100-p-0.05-0.05-edited.png │ │ │ ├── cdfMiDiscrete-N100-p-0.50-0.50-edited.png │ │ │ └── cdfMiDiscrete-N10000-p-0.05-0.05-edited.png │ ├── README-OctaveMatlabDemos.pdf │ ├── README-UseInMatlabAndOctave.pdf │ ├── SchreiberTransferEntropyExamples │ │ ├── README-SchreiberTeDemos.pdf │ │ ├── SchreiberExample2.txt │ │ ├── SchreiberExample3.txt │ │ ├── activeInfoStorageHeartBreathRatesKraskov.m │ │ ├── runHeartBreathRateKernel.m │ │ ├── runHeartBreathRateKraskov.m │ │ ├── runTentMap.m │ │ ├── runUlamMap.m │ │ └── sampleResults │ │ │ ├── heartBreathResults-kernel.png │ │ │ ├── heartBreathResults-kraskovAIS.png │ │ │ ├── heartBreathResults-kraskovMI.png │ │ │ ├── heartBreathResults-kraskovTE.png │ │ │ ├── tentMapResultsForWebMatlab.png │ │ │ ├── ulamMapResults-noNorm-dynExc100-r0.2.png │ │ │ └── ulamMapResults-noNorm-dynExc100-r0.3.png │ ├── example10ConditionalTeKraskov.m │ ├── example1TeBinaryData.m │ ├── example2TeMultidimBinaryData.m │ ├── example3TeContinuousDataKernel.m │ ├── example4TeContinuousDataKraskov.m │ ├── example5TeBinaryMultivarTransfer.m │ ├── example6DynamicCallingMutualInfo.m │ ├── example9TeContinuousMultivariateDataKraskov.m │ ├── javaMatrixToOctave.m │ ├── octaveToJavaDoubleArray.m │ ├── octaveToJavaDoubleMatrix.m │ ├── octaveToJavaIntArray.m │ └── octaveToJavaIntMatrix.m ├── python │ ├── EffectiveNetworkInference │ │ └── spiking │ │ │ ├── net_inf.py │ │ │ └── spk_to_pk.py │ ├── README-PythonDemos.pdf │ ├── README-UseInPython.pdf │ ├── SchreiberTransferEntropyExamples │ │ └── runHeartBreathRateKraskov.py │ ├── SpikingTE │ │ └── SpikeTrainTETesting.py │ ├── create_env.bat │ ├── create_env.sh │ ├── example1TeBinaryData.py │ ├── example2TeMultidimBinaryData.py │ ├── example3TeContinuousDataKernel.py │ ├── example4TeContinuousDataKraskov.py │ ├── example5TeBinaryMultivarTransfer.py │ ├── example6DynamicCallingMutualInfo.py │ ├── example7EnsembleMethodTeContinuousDataKraskov.py │ ├── example9TeKraskovAutoEmbedding.py │ ├── readFloatsFile.py │ ├── readIntsFile.py │ ├── start_env.sh │ ├── start_jupyter_env.sh │ ├── writeFloatsFile.py │ └── writeIntsFile.py └── r │ ├── README-R_Demos.pdf │ ├── README-UseInR.pdf │ ├── example1TeBinaryData.r │ ├── example2TeMultidimBinaryData.r │ ├── example3TeContinuousDataKernel.r │ ├── example4TeContinuousDataKraskov.r │ ├── example5TeBinaryMultivarTransfer.r │ └── example6DynamicCallingMutualInfo.r ├── java ├── source │ └── infodynamics │ │ ├── demos │ │ └── autoanalysis │ │ │ ├── AutoAnalyser.java │ │ │ ├── AutoAnalyserAIS.java │ │ │ ├── AutoAnalyserCMI.java │ │ │ ├── AutoAnalyserCTE.java │ │ │ ├── AutoAnalyserChannelCalculator.java │ │ │ ├── AutoAnalyserEntropy.java │ │ │ ├── AutoAnalyserLauncher.java │ │ │ ├── AutoAnalyserMI.java │ │ │ └── AutoAnalyserTE.java │ │ ├── measures │ │ ├── continuous │ │ │ ├── ActiveInfoStorageCalculator.java │ │ │ ├── ActiveInfoStorageCalculatorMultiVariate.java │ │ │ ├── ActiveInfoStorageCalculatorMultiVariateViaMutualInfo.java │ │ │ ├── ActiveInfoStorageCalculatorViaMutualInfo.java │ │ │ ├── ChannelCalculator.java │ │ │ ├── ChannelCalculatorCommon.java │ │ │ ├── ChannelCalculatorMultiVariate.java │ │ │ ├── ConditionalMutualInfoCalculatorMultiVariate.java │ │ │ ├── ConditionalMutualInfoMultiVariateCommon.java │ │ │ ├── ConditionalTransferEntropyCalculator.java │ │ │ ├── ConditionalTransferEntropyCalculatorViaCondMutualInfo.java │ │ │ ├── EntropyCalculator.java │ │ │ ├── EntropyCalculatorMultiVariate.java │ │ │ ├── EntropyCalculatorMultiVariateCommon.java │ │ │ ├── InfoMeasureCalculatorContinuous.java │ │ │ ├── MultiInfoCalculator.java │ │ │ ├── MultiInfoCalculatorCommon.java │ │ │ ├── MultiVariateInfoMeasureCalculatorCommon.java │ │ │ ├── MutualInfoCalculatorMultiVariate.java │ │ │ ├── MutualInfoMultiVariateCommon.java │ │ │ ├── PredictiveInfoCalculator.java │ │ │ ├── PredictiveInfoCalculatorViaMutualInfo.java │ │ │ ├── TransferEntropyCalculator.java │ │ │ ├── TransferEntropyCalculatorMultiVariate.java │ │ │ ├── TransferEntropyCalculatorMultiVariateViaCondMutualInfo.java │ │ │ ├── TransferEntropyCalculatorViaCondMutualInfo.java │ │ │ ├── TransferEntropyCommon.java │ │ │ ├── gaussian │ │ │ │ ├── ActiveInfoStorageCalculatorGaussian.java │ │ │ │ ├── ActiveInfoStorageCalculatorMultiVariateGaussian.java │ │ │ │ ├── ConditionalMutualInfoCalculatorMultiVariateGaussian.java │ │ │ │ ├── ConditionalTransferEntropyCalculatorGaussian.java │ │ │ │ ├── DualTotalCorrelationCalculatorGaussian.java │ │ │ │ ├── EntropyCalculatorGaussian.java │ │ │ │ ├── EntropyCalculatorMultiVariateGaussian.java │ │ │ │ ├── MultiInfoCalculatorGaussian.java │ │ │ │ ├── MultiVariateInfoMeasureCalculatorGaussian.java │ │ │ │ ├── MutualInfoCalculatorMultiVariateGaussian.java │ │ │ │ ├── OInfoCalculatorGaussian.java │ │ │ │ ├── PredictiveInfoCalculatorGaussian.java │ │ │ │ ├── SInfoCalculatorGaussian.java │ │ │ │ ├── TransferEntropyCalculatorGaussian.java │ │ │ │ ├── TransferEntropyCalculatorMultiVariateGaussian.java │ │ │ │ └── package-info.java │ │ │ ├── kernel │ │ │ │ ├── ActiveInfoStorageCalculatorKernel.java │ │ │ │ ├── ActiveInfoStorageCalculatorMultiVariateKernel.java │ │ │ │ ├── EntropyCalculatorKernel.java │ │ │ │ ├── EntropyCalculatorMultiVariateKernel.java │ │ │ │ ├── KernelCount.java │ │ │ │ ├── KernelEstimatorMultiVariate.java │ │ │ │ ├── KernelEstimatorTransferEntropy.java │ │ │ │ ├── KernelEstimatorTransferEntropyMultiVariate.java │ │ │ │ ├── KernelEstimatorUniVariate.java │ │ │ │ ├── MultiInfoCalculatorKernel.java │ │ │ │ ├── MutualInfoCalculatorMultiVariateKernel.java │ │ │ │ ├── PredictiveInfoCalculatorKernel.java │ │ │ │ ├── TransferEntropyCalculatorKernel.java │ │ │ │ ├── TransferEntropyCalculatorKernelPlain.java │ │ │ │ ├── TransferEntropyCalculatorKernelPlainIterators.java │ │ │ │ ├── TransferEntropyCalculatorKernelSeparate.java │ │ │ │ ├── TransferEntropyCalculatorMultiVariateKernel.java │ │ │ │ ├── TransferEntropyCalculatorMultiVariateSingleObservationsKernel.java │ │ │ │ ├── TransferEntropyKernelCounts.java │ │ │ │ └── package-info.java │ │ │ ├── kozachenko │ │ │ │ ├── EntropyCalculatorMultiVariateKozachenko.java │ │ │ │ └── package-info.java │ │ │ ├── kraskov │ │ │ │ ├── ActiveInfoStorageCalculatorKraskov.java │ │ │ │ ├── ActiveInfoStorageCalculatorMultiVariateKraskov.java │ │ │ │ ├── ConditionalMutualInfoCalculatorMultiVariateKraskov.java │ │ │ │ ├── ConditionalMutualInfoCalculatorMultiVariateKraskov1.java │ │ │ │ ├── ConditionalMutualInfoCalculatorMultiVariateKraskov2.java │ │ │ │ ├── ConditionalTransferEntropyCalculatorKraskov.java │ │ │ │ ├── DualTotalCorrelationCalculatorKraskov.java │ │ │ │ ├── MultiInfoCalculatorKraskov.java │ │ │ │ ├── MultiInfoCalculatorKraskov1.java │ │ │ │ ├── MultiInfoCalculatorKraskov2.java │ │ │ │ ├── MultiVariateInfoMeasureCalculatorKraskov.java │ │ │ │ ├── MutualInfoCalculatorMultiVariateKraskov.java │ │ │ │ ├── MutualInfoCalculatorMultiVariateKraskov1.java │ │ │ │ ├── MutualInfoCalculatorMultiVariateKraskov2.java │ │ │ │ ├── OInfoCalculatorKraskov.java │ │ │ │ ├── PredictiveInfoCalculatorKraskov.java │ │ │ │ ├── SInfoCalculatorKraskov.java │ │ │ │ ├── TransferEntropyCalculatorKraskov.java │ │ │ │ ├── TransferEntropyCalculatorMultiVariateKraskov.java │ │ │ │ └── package-info.java │ │ │ ├── package-info.java │ │ │ └── symbolic │ │ │ │ ├── TransferEntropyCalculatorSymbolic.java │ │ │ │ └── package-info.java │ │ ├── discrete │ │ │ ├── ActiveInformationCalculatorDiscrete.java │ │ │ ├── BlockEntropyCalculatorDiscrete.java │ │ │ ├── ChannelCalculatorDiscrete.java │ │ │ ├── CombinedActiveEntRateCalculatorDiscrete.java │ │ │ ├── ConditionalMutualInformationCalculatorDiscrete.java │ │ │ ├── ConditionalTransferEntropyCalculatorDiscrete.java │ │ │ ├── ContextOfPastMeasureCalculatorDiscrete.java │ │ │ ├── DualTotalCorrelationCalculatorDiscrete.java │ │ │ ├── EntropyCalculatorDiscrete.java │ │ │ ├── EntropyRateCalculatorDiscrete.java │ │ │ ├── InfoMeasureCalculatorDiscrete.java │ │ │ ├── MultiInformationCalculatorDiscrete.java │ │ │ ├── MultiVariateInfoMeasureCalculatorDiscrete.java │ │ │ ├── MutualInformationCalculatorDiscrete.java │ │ │ ├── OInfoCalculatorDiscrete.java │ │ │ ├── PredictiveInformationCalculatorDiscrete.java │ │ │ ├── SInfoCalculatorDiscrete.java │ │ │ ├── SeparableInfoCalculatorDiscrete.java │ │ │ ├── SeparableInfoCalculatorDiscreteByAddition.java │ │ │ ├── SingleAgentMeasureDiscrete.java │ │ │ ├── SingleAgentMeasureDiscreteInContextOfPastCalculator.java │ │ │ ├── TransferEntropyCalculatorDiscrete.java │ │ │ └── package-info.java │ │ ├── mixed │ │ │ ├── ConditionalMutualInfoCalculatorMultiVariateWithDiscrete.java │ │ │ ├── ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSource.java │ │ │ ├── ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceCommon.java │ │ │ ├── MutualInfoCalculatorMultiVariateWithDiscrete.java │ │ │ ├── gaussian │ │ │ │ ├── ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSourceGaussian.java │ │ │ │ └── MutualInfoCalculatorMultiVariateWithDiscreteGaussian.java │ │ │ ├── kernel │ │ │ │ └── MutualInfoCalculatorMultiVariateWithDiscreteKernel.java │ │ │ ├── kraskov │ │ │ │ ├── ConditionalMutualInfoCalculatorMultiVariateWithDiscreteKraskov.java │ │ │ │ └── MutualInfoCalculatorMultiVariateWithDiscreteKraskov.java │ │ │ ├── package-info.java │ │ │ └── symbolic │ │ │ │ ├── ConditionalMutualInfoCalculatorMultiVariateWithDiscreteSymbolic.java │ │ │ │ └── MutualInfoCalculatorMultiVariateWithDiscreteSymbolic.java │ │ └── spiking │ │ │ ├── TransferEntropyCalculatorSpiking.java │ │ │ ├── integration │ │ │ ├── TransferEntropyCalculatorSpikingIntegration.java │ │ │ └── package-info.java │ │ │ └── package-info.java │ │ ├── networkinference │ │ └── interregional │ │ │ ├── InterregionalChannelMeasure.java │ │ │ ├── InterregionalMutualInfo.java │ │ │ ├── InterregionalTransferEntropy.java │ │ │ ├── MeasurementDistributionPermutationsOverSubsets.java │ │ │ └── package-info.java │ │ └── utils │ │ ├── AnalyticMeasurementDistribution.java │ │ ├── AnalyticNullDistributionComputer.java │ │ ├── ArrayFileReader.java │ │ ├── ArrayFileWriter.java │ │ ├── ChiSquareMeasurementDistribution.java │ │ ├── EmpiricalMeasurementDistribution.java │ │ ├── EmpiricalNullDistributionComputer.java │ │ ├── EuclideanUtils.java │ │ ├── FirstIndexComparatorDouble.java │ │ ├── FirstIndexComparatorInteger.java │ │ ├── IntArrayWrapper.java │ │ ├── KdTree.java │ │ ├── MathsUtils.java │ │ ├── MatrixUtils.java │ │ ├── MeasurementDistribution.java │ │ ├── NativeUtils.java │ │ ├── NearestNeighbourSearcher.java │ │ ├── NeighbourNodeData.java │ │ ├── NonPositiveDefiniteMatrixException.java │ │ ├── OctaveFileReader.java │ │ ├── OctaveFileWriter.java │ │ ├── OctaveMatrix.java │ │ ├── ParsedProperties.java │ │ ├── RandomGenerator.java │ │ ├── UnivariateNearestNeighbourSearcher.java │ │ ├── commonsmath3 │ │ ├── Field.java │ │ ├── FieldElement.java │ │ ├── RealFieldElement.java │ │ ├── analysis │ │ │ ├── UnivariateFunction.java │ │ │ └── solvers │ │ │ │ ├── AbstractUnivariateSolver.java │ │ │ │ ├── AllowedSolution.java │ │ │ │ ├── BaseAbstractUnivariateSolver.java │ │ │ │ ├── BaseUnivariateSolver.java │ │ │ │ ├── BracketedUnivariateSolver.java │ │ │ │ ├── BrentSolver.java │ │ │ │ ├── UnivariateSolver.java │ │ │ │ └── UnivariateSolverUtils.java │ │ ├── distribution │ │ │ ├── AbstractIntegerDistribution.java │ │ │ ├── AbstractRealDistribution.java │ │ │ ├── BetaDistribution.java │ │ │ ├── BinomialDistribution.java │ │ │ ├── CauchyDistribution.java │ │ │ ├── ChiSquaredDistribution.java │ │ │ ├── ExponentialDistribution.java │ │ │ ├── FDistribution.java │ │ │ ├── GammaDistribution.java │ │ │ ├── HypergeometricDistribution.java │ │ │ ├── IntegerDistribution.java │ │ │ ├── NormalDistribution.java │ │ │ ├── PascalDistribution.java │ │ │ ├── PoissonDistribution.java │ │ │ ├── RealDistribution.java │ │ │ ├── SaddlePointExpansion.java │ │ │ ├── TDistribution.java │ │ │ ├── UniformIntegerDistribution.java │ │ │ ├── WeibullDistribution.java │ │ │ └── ZipfDistribution.java │ │ ├── exception │ │ │ ├── ConvergenceException.java │ │ │ ├── DimensionMismatchException.java │ │ │ ├── MathArithmeticException.java │ │ │ ├── MathIllegalArgumentException.java │ │ │ ├── MathIllegalNumberException.java │ │ │ ├── MathIllegalStateException.java │ │ │ ├── MathInternalError.java │ │ │ ├── MathUnsupportedOperationException.java │ │ │ ├── MaxCountExceededException.java │ │ │ ├── NoBracketingException.java │ │ │ ├── NoDataException.java │ │ │ ├── NonMonotonicSequenceException.java │ │ │ ├── NotANumberException.java │ │ │ ├── NotFiniteNumberException.java │ │ │ ├── NotPositiveException.java │ │ │ ├── NotStrictlyPositiveException.java │ │ │ ├── NullArgumentException.java │ │ │ ├── NumberIsTooLargeException.java │ │ │ ├── NumberIsTooSmallException.java │ │ │ ├── OutOfRangeException.java │ │ │ ├── TooManyEvaluationsException.java │ │ │ ├── ZeroException.java │ │ │ └── util │ │ │ │ ├── ArgUtils.java │ │ │ │ ├── ExceptionContext.java │ │ │ │ ├── ExceptionContextProvider.java │ │ │ │ ├── Localizable.java │ │ │ │ └── LocalizedFormats.java │ │ ├── random │ │ │ ├── AbstractWell.java │ │ │ ├── BitsStreamGenerator.java │ │ │ ├── RandomData.java │ │ │ ├── RandomDataGenerator.java │ │ │ ├── RandomDataImpl.java │ │ │ ├── RandomGenerator.java │ │ │ ├── RandomGeneratorFactory.java │ │ │ └── Well19937c.java │ │ ├── special │ │ │ ├── Beta.java │ │ │ ├── Erf.java │ │ │ └── Gamma.java │ │ └── util │ │ │ ├── ArithmeticUtils.java │ │ │ ├── Combinations.java │ │ │ ├── CombinatoricsUtils.java │ │ │ ├── ContinuedFraction.java │ │ │ ├── DoubleArray.java │ │ │ ├── FastMath.java │ │ │ ├── FastMathCalc.java │ │ │ ├── FastMathLiteralArrays.java │ │ │ ├── IntegerSequence.java │ │ │ ├── MathArrays.java │ │ │ ├── MathUtils.java │ │ │ ├── Precision.java │ │ │ └── ResizableDoubleArray.java │ │ └── package-info.java └── unittests │ └── infodynamics │ ├── measures │ ├── continuous │ │ ├── ConditionalMutualInfoMultiVariateAbstractTester.java │ │ ├── ConditionalTransferEntropyAbstractTester.java │ │ ├── MultiInfoAbstractTester.java │ │ ├── MutualInfoMultiVariateAbstractTester.java │ │ ├── PredictiveInfoAbstractTester.java │ │ ├── TransferEntropyAbstractTester.java │ │ ├── TransferEntropyMultiVariateAbstractTester.java │ │ ├── gaussian │ │ │ ├── ActiveInfoStorageGaussianTester.java │ │ │ ├── ActiveInfoStorageMultiVariateGaussianTester.java │ │ │ ├── ConditionalMutualInfoMultiVariateTester.java │ │ │ ├── ConditionalTransferEntropyGaussianTester.java │ │ │ ├── DualTotalCorrelationCalculatorGaussianTester.java │ │ │ ├── EntropyCalculatorGaussianTest.java │ │ │ ├── MutualInfoMultiVariateTester.java │ │ │ ├── OInfoCalculatorGaussianTester.java │ │ │ ├── SInfoCalculatorGaussianTester.java │ │ │ ├── TransferEntropyGaussianTester.java │ │ │ └── TransferEntropyMultiVariateGaussianTester.java │ │ ├── kernel │ │ │ ├── ActiveInfoStorageCalculatorCorrelationIntegrals.java │ │ │ ├── ActiveInfoStorageCalculatorKernelDirect.java │ │ │ ├── ActiveInfoStorageTester.java │ │ │ ├── EntropyCalculatorKernelTest.java │ │ │ ├── MutualInfoMultiVariateTester.java │ │ │ └── TransferEntropyMultiVariateTester.java │ │ └── kraskov │ │ │ ├── ActiveInfoStorageMultiVariateTester.java │ │ │ ├── ActiveInfoStorageTester.java │ │ │ ├── ConditionalMutualInfoMultiVariateTester.java │ │ │ ├── ConditionalTransferEntropyKraskovTester.java │ │ │ ├── DualTotalCorrelationCalculatorKraskovTester.java │ │ │ ├── GPUCondMutualInfoTester.java │ │ │ ├── GPUMutualInfoTester.java │ │ │ ├── GPUPerformanceTester.java │ │ │ ├── MultiInfoTester.java │ │ │ ├── MutualInfoMultiVariateTester.java │ │ │ ├── OInfoCalculatorKraskovTester.java │ │ │ ├── PredictiveInfoTester.java │ │ │ ├── SInfoCalculatorKraskovTester.java │ │ │ ├── TransferEntropyMultiVariateTester.java │ │ │ └── TransferEntropyTester.java │ ├── discrete │ │ ├── ConditionalMutualInformationTester.java │ │ ├── ConditionalTransferEntropyTester.java │ │ ├── DualTotalCorrelationTester.java │ │ ├── MutualInformationTester.java │ │ ├── OInfoTester.java │ │ ├── PredictiveInformationTester.java │ │ ├── SInfoTester.java │ │ └── TransferEntropyTester.java │ └── mixed │ │ ├── gaussian │ │ └── MutualInfoMultiVariateWithDiscreteTester.java │ │ └── kraskov │ │ ├── ConditionalMutualInfoWithDiscreteKraskovTester.java │ │ └── MutualInfoMultiVariateWithDiscreteKraskovTester.java │ └── utils │ ├── ChiSquareMeasurementDistributionTest.java │ ├── KdTreeTest.java │ ├── MathsUtilsTest.java │ ├── MatrixUtilsTest.java │ ├── RandomGeneratorTest.java │ └── UnivariateNearestNeighbourTest.java ├── license-gplv3.txt ├── notices ├── JAMA │ └── readme.txt ├── commons-math │ ├── ApacheCommons-LICENSE.txt │ ├── ApacheCommons-NOTICE.txt │ └── readme.txt └── octave-java │ └── readme.txt ├── readme-template.txt ├── tutorial ├── JIDT-TutorialSlides.pdf ├── README-TutorialAndExercise.pdf └── sampleExerciseSolutions │ └── matlabOctave │ ├── runHeartBreathRateKraskovMI.m │ └── runHeartBreathRateKraskovMIWithLags.m ├── version-template.txt └── web ├── AutoAnalyser-LauncherGUI.png ├── AutoAnalyserGUI-1-Launch.png ├── AutoAnalyserGUI-2-Compute.png ├── JIDT-logo.png ├── YouTubePlaylist.png └── twitterGadget.xml /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/jlizier/jidt/HEAD/.gitignore -------------------------------------------------------------------------------- /InfoDynamicsToolkit.pdf: 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