1. svGPFA package

1.1. Subpackages

• 1.1.1. svGPFA.plot package
  • 1.1.1.1. Submodules
  • 1.1.1.2. svGPFA.plot.plotUtilsPlotly module
    • get3DPlotOrthonormalizedLatentsAcrossTrials()
    • getPlotCIF()
    • getPlotCIFsImageOneNeuronAllTrials()
    • getPlotCIFsOneNeuronAllTrials()
    • getPlotEmbeddingAcrossTrials()
    • getPlotEmbeddingParams()
    • getPlotEstimatedLatentsForTrial()
    • getPlotKernelsParams()
    • getPlotKernelsParamsOneLatent()
    • getPlotLatentAcrossTrials()
    • getPlotLowerBoundHist()
    • getPlotLowerBoundVsOneParam()
    • getPlotLowerBoundVsTwoParamsParam()
    • getPlotMean()
    • getPlotMeanWithCI()
    • getPlotOrthonormalizedEmbeddingParams()
    • getPlotOrthonormalizedLatentAcrossTrials()
    • getPlotOrthonormalizedLatentImageOneNeuronAllTrials()
    • getPlotResKSTestTimeRescalingNumericalCorrection()
    • getPlotResROCAnalysis()
    • getPlotSimulatedAndEstimatedCIFs()
    • getPlotSmoothedSpikes()
    • getPlotSpikesRatesAllTrialsAllNeurons()
    • getPlotTrueAndEstimatedEmbedding()
    • getPlotTrueAndEstimatedEmbeddingParams()
    • getPlotTrueAndEstimatedEmbeddingPropCovered()
    • getPlotTrueAndEstimatedIndPointsCovs()
    • getPlotTrueAndEstimatedIndPointsCovsOneTrialOneLatent()
    • getPlotTrueAndEstimatedIndPointsLocs()
    • getPlotTrueAndEstimatedIndPointsLocsOneTrialOneLatent()
    • getPlotTrueAndEstimatedIndPointsMeans()
    • getPlotTrueAndEstimatedIndPointsMeansOneTrialOneLatent()
    • getPlotTrueAndEstimatedKernelsParams()
    • getPlotTrueAndEstimatedKernelsParamsOneLatent()
    • getPlotTrueAndEstimatedLatents()
    • getPlotTrueAndEstimatedLatentsMeans()
    • getPlotTrueAndEstimatedLatentsOneTrialOneLatent()
    • getPlotTruePythonAndMatlabCIFs()
    • getPlotTruePythonAndMatlabEmbedding()
    • getPlotTruePythonAndMatlabEmbeddingPropCovered()
    • getPlotTruePythonAndMatlabKernelsParams()
    • getPlotTruePythonAndMatlabLatents()
    • getSimulatedEmbeddingPlot()
    • getSimulatedLatentPlot()
    • getSimulatedLatentsPlot()
    • getSimulatedSpikesTimesPlotMultipleTrials()
    • getSpikesTimesPlotOneNeuron()
    • getSpikesTimesPlotOneTrial()
  • 1.1.1.3. Module contents
• 1.1.2. svGPFA.simulations package
  • 1.1.2.1. Submodules
  • 1.1.2.2. svGPFA.simulations.simulations module
    • BaseSimulator
      • BaseSimulator.getCIF()
      • BaseSimulator.simulate()
    • GPFASimulator
      • GPFASimulator.getLatentsSamplesMeansAndSTDs()
    • GPFAwithIndPointsSimulator
      • GPFAwithIndPointsSimulator.getLatentsSamplesMeansAndSTDs()
  • 1.1.2.3. svGPFA.simulations.utils module
    • getTrueVariationalMean()
  • 1.1.2.4. Module contents
• 1.1.3. svGPFA.stats package
  • 1.1.3.1. Submodules
  • 1.1.3.2. svGPFA.stats.expectedLogLikelihood module
    • ExpectedLogLikelihood
      • ExpectedLogLikelihood.buildKernelsMatrices()
      • ExpectedLogLikelihood.computeEmbeddingsMeansAndVarsAtTimes()
      • ExpectedLogLikelihood.computeExpectedPosteriorCIFs()
      • ExpectedLogLikelihood.computeSVPosteriorOnLatentsStats()
      • ExpectedLogLikelihood.evalSumAcrossTrialsAndNeurons()
      • ExpectedLogLikelihood.getIndPointsLocs()
      • ExpectedLogLikelihood.getKernels()
      • ExpectedLogLikelihood.getKernelsParams()
      • ExpectedLogLikelihood.getSVEmbeddingParams()
      • ExpectedLogLikelihood.getSVPosteriorOnIndPointsParams()
      • ExpectedLogLikelihood.get_svEmbeddingAllTimes()
      • ExpectedLogLikelihood.predictEmbedding()
      • ExpectedLogLikelihood.predictLatents()
      • ExpectedLogLikelihood.sampleCIFs()
      • ExpectedLogLikelihood.setELLCalculationParams()
      • ExpectedLogLikelihood.setIndPointsLocs()
      • ExpectedLogLikelihood.setInitialParams()
      • ExpectedLogLikelihood.setKernels()
      • ExpectedLogLikelihood.setMeasurements()
      • ExpectedLogLikelihood.setPriorCovRegParam()
    • PointProcessELL
      • PointProcessELL.buildKernelsMatrices()
      • PointProcessELL.computeSVPosteriorOnLatentsStats()
      • PointProcessELL.evalSumAcrossTrialsAndNeurons()
      • PointProcessELL.setELLCalculationParams()
      • PointProcessELL.setIndPointsLocs()
      • PointProcessELL.setInitialParams()
      • PointProcessELL.setKernels()
      • PointProcessELL.setMeasurements()
    • PointProcessELLExpLink
    • PointProcessELLQuad
      • PointProcessELLQuad.setELLCalculationParams()
    • PoissonELL
      • PoissonELL.buildKernelsMatrices()
      • PoissonELL.computeSVPostOnLatentsStats()
      • PoissonELL.computeSVPosteriorOnLatentsStats()
      • PoissonELL.evalSumAcrossTrialsAndNeurons()
      • PoissonELL.setELLCalculationParams()
      • PoissonELL.setIndPointsLocs()
      • PoissonELL.setInitialParams()
      • PoissonELL.setKernels()
      • PoissonELL.setMeasurements()
    • PoissonELLExpLink
    • PoissonELLQuad
  • 1.1.3.3. svGPFA.stats.kernels module
    • ExponentialQuadraticKernel
      • ExponentialQuadraticKernel.buildKernelMatrix()
      • ExponentialQuadraticKernel.buildKernelMatrixDiag()
      • ExponentialQuadraticKernel.getNamedParams()
      • ExponentialQuadraticKernel.getScaledParams()
    • Kernel
      • Kernel.buildKernelMatrix()
      • Kernel.buildKernelMatrixDiag()
      • Kernel.getNamedParams()
      • Kernel.getParams()
      • Kernel.setParams()
    • PeriodicKernel
      • PeriodicKernel.buildKernelMatrix()
      • PeriodicKernel.buildKernelMatrixDiag()
      • PeriodicKernel.getNamedParams()
      • PeriodicKernel.getScaledParams()
  • 1.1.3.4. svGPFA.stats.kernelsMatricesStore module
    • IndPointsLocsAndAllTimesKMS
      • IndPointsLocsAndAllTimesKMS.buildKernelsMatrices()
      • IndPointsLocsAndAllTimesKMS.buildKttKernelsMatrices()
    • IndPointsLocsAndAssocTimesKMS
      • IndPointsLocsAndAssocTimesKMS.buildKernelsMatrices()
    • IndPointsLocsAndTimesKMS
      • IndPointsLocsAndTimesKMS.getKtt()
      • IndPointsLocsAndTimesKMS.getKttDiag()
      • IndPointsLocsAndTimesKMS.getKtz()
      • IndPointsLocsAndTimesKMS.setTimes()
    • IndPointsLocsKMS
      • IndPointsLocsKMS.buildKernelsMatrices()
      • IndPointsLocsKMS.getKzz()
      • IndPointsLocsKMS.getRegParam()
      • IndPointsLocsKMS.setRegParam()
      • IndPointsLocsKMS.solveForLatent()
      • IndPointsLocsKMS.solveForLatentAndTrial()
    • IndPointsLocsKMS_Chol
      • IndPointsLocsKMS_Chol.solveForLatent()
      • IndPointsLocsKMS_Chol.solveForLatentAndTrial()
    • IndPointsLocsKMS_CholWithGettersAndSetters
    • IndPointsLocsKMS_PInv
      • IndPointsLocsKMS_PInv.solveForLatent()
      • IndPointsLocsKMS_PInv.solveForLatentAndTrial()
    • IndPointsLocsKMS_PInvWithGettersAndSetters
    • KernelMatricesStoreGettersAndSetters
      • KernelMatricesStoreGettersAndSetters.get_flattened_ind_points_locs()
      • KernelMatricesStoreGettersAndSetters.get_flattened_ind_points_locs_grad()
      • KernelMatricesStoreGettersAndSetters.get_flattened_kernels_params()
      • KernelMatricesStoreGettersAndSetters.get_flattened_kernels_params_grad()
      • KernelMatricesStoreGettersAndSetters.set_ind_points_locs_from_flattened()
      • KernelMatricesStoreGettersAndSetters.set_ind_points_locs_requires_grad()
      • KernelMatricesStoreGettersAndSetters.set_kernels_params_from_flattened()
      • KernelMatricesStoreGettersAndSetters.set_kernels_params_requires_grad()
    • KernelsMatricesStore
      • KernelsMatricesStore.buildKernelsMatrices()
      • KernelsMatricesStore.getIndPointsLocs()
      • KernelsMatricesStore.getKernels()
      • KernelsMatricesStore.getKernelsParams()
      • KernelsMatricesStore.setIndPointsLocs()
      • KernelsMatricesStore.setInitialParams()
      • KernelsMatricesStore.setKernels()
      • KernelsMatricesStore.setKernelsParams()
  • 1.1.3.5. svGPFA.stats.klDivergence module
    • KLDivergence
      • KLDivergence.evalSumAcrossLatentsAndTrials()
      • KLDivergence.get_indPointsLocsKMS()
      • KLDivergence.get_svPosteriorOnIndPoints()
  • 1.1.3.6. svGPFA.stats.svEM module
    • ErrorTerminationInfo
      • ErrorTerminationInfo.error
      • ErrorTerminationInfo.stack_trace
    • SVEM
      • SVEM.maximize()
    • SVEM_PyTorch
      • SVEM_PyTorch.maximize()
    • SVEM_SciPy
      • SVEM_SciPy.maximize()
    • TerminationInfo
      • TerminationInfo.message
  • 1.1.3.7. svGPFA.stats.svEmbedding module
    • LinearSVEmbedding
      • LinearSVEmbedding.getParams()
      • LinearSVEmbedding.sample()
      • LinearSVEmbedding.setInitialParams()
    • LinearSVEmbeddingAllTimes
      • LinearSVEmbeddingAllTimes.computeMeansAndVarsAtTimes()
      • LinearSVEmbeddingAllTimes.predict()
      • LinearSVEmbeddingAllTimes.predictLatents()
      • LinearSVEmbeddingAllTimes.setPriorCovRegParam()
    • LinearSVEmbeddingAllTimesWithParamsGettersAndSetters
      • LinearSVEmbeddingAllTimesWithParamsGettersAndSetters.get_flattened_params()
      • LinearSVEmbeddingAllTimesWithParamsGettersAndSetters.get_flattened_params_grad()
      • LinearSVEmbeddingAllTimesWithParamsGettersAndSetters.set_params_from_flattened()
      • LinearSVEmbeddingAllTimesWithParamsGettersAndSetters.set_params_requires_grad()
    • LinearSVEmbeddingAssocTimes
      • LinearSVEmbeddingAssocTimes.setNeuronForSpikeIndex()
    • SVEmbedding
      • SVEmbedding.buildKernelsMatrices()
      • SVEmbedding.computeMeansAndVars()
      • SVEmbedding.computeSVPosteriorOnLatentsStats()
      • SVEmbedding.getIndPointsLocs()
      • SVEmbedding.getKernels()
      • SVEmbedding.getKernelsParams()
      • SVEmbedding.getParams()
      • SVEmbedding.getSVPosteriorOnIndPointsParams()
      • SVEmbedding.setIndPointsLocs()
      • SVEmbedding.setInitialParams()
      • SVEmbedding.setKernels()
      • SVEmbedding.setTimes()
  • 1.1.3.8. svGPFA.stats.svGPFAModelFactory module
    • ExponentialLink
    • Gaussian
    • LinearEmbedding
    • NonExponentialLink
    • PointProcess
    • Poisson
    • SVGPFAModelFactory
      • SVGPFAModelFactory.buildModelPyTorch()
      • SVGPFAModelFactory.buildModelSciPy()
    • indPointsCovChol
    • indPointsCovRank1PlusDiag
    • kernelMatrixInvChol
    • kernelMatrixInvPInv
  • 1.1.3.9. svGPFA.stats.svLBFGS module
    • ErrorTerminationInfo
      • ErrorTerminationInfo.error
    • SVLBFGS
      • SVLBFGS.maximize()
    • TerminationInfo
      • TerminationInfo.message
  • 1.1.3.10. svGPFA.stats.svLowerBound module
    • SVLowerBound
      • SVLowerBound.buildKernelsMatrices()
      • SVLowerBound.computeEmbeddingMeansAndVarsAtTimes()
      • SVLowerBound.computeExpectedPosteriorCIFs()
      • SVLowerBound.computeSVPosteriorOnLatentsStats()
      • SVLowerBound.eval()
      • SVLowerBound.evalELLSumAcrossTrialsAndNeurons()
      • SVLowerBound.getIndPointsLocs()
      • SVLowerBound.getKernels()
      • SVLowerBound.getKernelsParams()
      • SVLowerBound.getSVEmbeddingParams()
      • SVLowerBound.getSVPosteriorOnIndPointsParams()
      • SVLowerBound.predictEmbedding()
      • SVLowerBound.predictLatents()
      • SVLowerBound.sampleCIFs()
      • SVLowerBound.setELLCalculationParams()
      • SVLowerBound.setIndPointsLocs()
      • SVLowerBound.setInitialParams()
      • SVLowerBound.setKernels()
      • SVLowerBound.setMeasurements()
      • SVLowerBound.setParamsAndData()
      • SVLowerBound.setPriorCovRegParam()
    • SVLowerBoundWithParamsGettersAndSetters
      • SVLowerBoundWithParamsGettersAndSetters.get_flattened_indPointsLocs()
      • SVLowerBoundWithParamsGettersAndSetters.get_flattened_indPointsLocs_grad()
      • SVLowerBoundWithParamsGettersAndSetters.get_flattened_kernels_params()
      • SVLowerBoundWithParamsGettersAndSetters.get_flattened_kernels_params_grad()
      • SVLowerBoundWithParamsGettersAndSetters.get_flattened_svEmbedding_params()
      • SVLowerBoundWithParamsGettersAndSetters.get_flattened_svEmbedding_params_grad()
      • SVLowerBoundWithParamsGettersAndSetters.get_flattened_svPosteriorOnIndPoints_params()
      • SVLowerBoundWithParamsGettersAndSetters.get_flattened_svPosteriorOnIndPoints_params_grad()
      • SVLowerBoundWithParamsGettersAndSetters.set_indPointsLocs_from_flattened()
      • SVLowerBoundWithParamsGettersAndSetters.set_indPointsLocs_requires_grad()
      • SVLowerBoundWithParamsGettersAndSetters.set_kernels_params_from_flattened()
      • SVLowerBoundWithParamsGettersAndSetters.set_kernels_params_requires_grad()
      • SVLowerBoundWithParamsGettersAndSetters.set_svEmbedding_params_from_flattened()
      • SVLowerBoundWithParamsGettersAndSetters.set_svEmbedding_params_requires_grad()
      • SVLowerBoundWithParamsGettersAndSetters.set_svPosteriorOnIndPoints_params_from_flattened()
      • SVLowerBoundWithParamsGettersAndSetters.set_svPosteriorOnIndPoints_params_requires_grad()
  • 1.1.3.11. svGPFA.stats.svPosteriorOnIndPoints module
    • SVPosteriorOnIndPoints
      • SVPosteriorOnIndPoints.buildCov()
      • SVPosteriorOnIndPoints.getMean()
      • SVPosteriorOnIndPoints.getParams()
      • SVPosteriorOnIndPoints.setInitialParams()
    • SVPosteriorOnIndPointsChol
      • SVPosteriorOnIndPointsChol.buildCov()
      • SVPosteriorOnIndPointsChol.getMean()
      • SVPosteriorOnIndPointsChol.getParams()
      • SVPosteriorOnIndPointsChol.setInitialParams()
    • SVPosteriorOnIndPointsCholWithGettersAndSetters
      • SVPosteriorOnIndPointsCholWithGettersAndSetters.get_flattened_params()
      • SVPosteriorOnIndPointsCholWithGettersAndSetters.get_flattened_params_grad()
      • SVPosteriorOnIndPointsCholWithGettersAndSetters.set_params_from_flattened()
      • SVPosteriorOnIndPointsCholWithGettersAndSetters.set_params_requires_grad()
    • SVPosteriorOnIndPointsRank1PlusDiag
      • SVPosteriorOnIndPointsRank1PlusDiag.buildCov()
      • SVPosteriorOnIndPointsRank1PlusDiag.getMean()
      • SVPosteriorOnIndPointsRank1PlusDiag.getParams()
      • SVPosteriorOnIndPointsRank1PlusDiag.setInitialParams()
  • 1.1.3.12. svGPFA.stats.svPosteriorOnLatents module
    • SVPosteriorOnLatents
      • SVPosteriorOnLatents.buildKernelsMatrices()
      • SVPosteriorOnLatents.computeMeansAndVars()
      • SVPosteriorOnLatents.getIndPointsLocs()
      • SVPosteriorOnLatents.getKernels()
      • SVPosteriorOnLatents.getKernelsParams()
      • SVPosteriorOnLatents.getSVPosteriorOnIndPointsParams()
      • SVPosteriorOnLatents.setIndPointsLocs()
      • SVPosteriorOnLatents.setInitialParams()
      • SVPosteriorOnLatents.setKernels()
      • SVPosteriorOnLatents.setPriorCovRegParam()
      • SVPosteriorOnLatents.setTimes()
    • SVPosteriorOnLatentsAllTimes
      • SVPosteriorOnLatentsAllTimes.buildKernelsMatrices()
      • SVPosteriorOnLatentsAllTimes.computeMeansAndVars()
      • SVPosteriorOnLatentsAllTimes.computeMeansAndVarsAtTimes()
      • SVPosteriorOnLatentsAllTimes.predict()
      • SVPosteriorOnLatentsAllTimes.sample()
      • SVPosteriorOnLatentsAllTimes.setIndPointsLocs()
      • SVPosteriorOnLatentsAllTimes.setInitialParams()
      • SVPosteriorOnLatentsAllTimes.setKernels()
    • SVPosteriorOnLatentsAssocTimes
      • SVPosteriorOnLatentsAssocTimes.buildKernelsMatrices()
      • SVPosteriorOnLatentsAssocTimes.computeMeansAndVars()
      • SVPosteriorOnLatentsAssocTimes.setIndPointsLocs()
      • SVPosteriorOnLatentsAssocTimes.setInitialParams()
      • SVPosteriorOnLatentsAssocTimes.setKernels()
  • 1.1.3.13. Module contents
• 1.1.4. svGPFA.utils package
  • 1.1.4.1. Submodules
  • 1.1.4.2. svGPFA.utils.configUtils module
    • getIndPointsMeans()
    • getKernels()
    • getLatentsMeansFuncs()
    • getScaledKernels()
    • getVariationalMean0FromList()
  • 1.1.4.3. svGPFA.utils.initUtils module
    • buildEquidistantIndPointsLocs0()
    • buildFloatListFromStringRep()
    • buildUniformIndPointsLocs0()
    • flatToHierarchicalOptimParams()
    • getArgsInfo()
    • getConstantIndPointsMeans()
    • getDefaultParamsDict()
    • getDiffAcrossLatentsAndTrialsIndPointsLocs0()
    • getDiffAcrossLatentsAndTrialsVariationalCov0()
    • getDiffAcrossLatentsAndTrialsVariationalMean0()
    • getIndPointsLocs0()
    • getIndPointsLocs0InDict()
    • getKernelsParams0()
    • getKernelsParams0AndTypes()
    • getKernelsParams0AndTypesInDict()
    • getKernelsScaledParams0()
    • getKzzChol0()
    • getLinearEmbeddingParam0()
    • getLinearEmbeddingParam0InDict()
    • getLinearEmbeddingParams0()
    • getOptimParams()
    • getParam()
    • getParamsAndKernelsTypes()
    • getParamsDictFromArgs()
    • getParamsDictFromStringsDict()
    • getSVPosteriorOnIndPointsParams0()
    • getSameAcrossLatentsAndTrialsIndPointsLocs0()
    • getSameAcrossLatentsAndTrialsVariationalCov0()
    • getSameAcrossLatentsAndTrialsVariationalMean0()
    • getScaledIdentityQSigma0()
    • getUniformIndPointsMeans()
    • getVariationalCov0()
    • getVariationalCov0InDict()
    • getVariationalMean0()
    • getVariationalMean0InDict()
    • strTo1DDoubleTensor()
    • strTo1DIntTensor()
    • strTo1DTensor()
    • strTo2DDoubleTensor()
    • strTo2DIntTensor()
    • strTo2DTensor()
  • 1.1.4.4. svGPFA.utils.miscUtils module
    • build3DdiagFromDiagVector()
    • buildCovsFromCholVecs()
    • buildKernels()
    • buildQSigmaFromQSVecAndQSDiag()
    • chol3D()
    • clock()
    • computeSpikeClassificationROC()
    • computeSpikeRates()
    • getCIFs()
    • getCholFromVec()
    • getDiagIndicesIn3DArray()
    • getEmbeddingMeans()
    • getEmbeddingSTDs()
    • getEmbeddingSamples()
    • getLatentsMeansAndSTDs()
    • getLatentsSTDs()
    • getLatentsSamplesMeansAndSTDsFromSampledMeans()
    • getLegQuadPointsAndWeights()
    • getPropSamplesCovered()
    • getQSVecsAndQSDiagsFromQSCholVecs()
    • getSRQSigmaVec()
    • getSRQSigmaVecsFromKzz()
    • getTrialsTimes()
    • getVectorRepOfLowerTrianMatrices()
    • orthonormalizeLatentsMeans()
    • pinv3D()
    • saveDataForMatlabEstimations()
    • separateNeuronsSpikeTimesByTrials()
  • 1.1.4.5. Module contents

1.2. Module contents