Index

B

build3DdiagFromDiagVector() (in module stats.svGPFA.utils) buildKernelMatrix() (stats.kernels.ExponentialQuadraticKernel method) (stats.kernels.Kernel method) (stats.kernels.PeriodicKernel method) buildKernelMatrixDiag() (stats.kernels.ExponentialQuadraticKernel method) (stats.kernels.Kernel method) (stats.kernels.PeriodicKernel method) buildKernelsMatrices() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.expectedLogLikelihood.PointProcessELL method) (stats.svGPFA.expectedLogLikelihood.PoissonELL method) (stats.svGPFA.kernelMatricesStore.IndPointsLocsAndAllTimesKMS method) (stats.svGPFA.kernelMatricesStore.IndPointsLocsAndAssocTimesKMS method) (stats.svGPFA.kernelMatricesStore.IndPointsLocsKMS method) (stats.svGPFA.kernelMatricesStore.KernelMatricesStore method) (stats.svGPFA.svEmbedding.SVEmbedding method) (stats.svGPFA.svLowerBound.SVLowerBound method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatents method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatentsAllTimes method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatentsAssocTimes method)

buildKSample() (stats.gaussianProcesses.kernels.Kernel method) buildKSampleGrad() (stats.gaussianProcesses.kernels.Kernel method) buildModel() (stats.svGPFA.svGPFAModelFactory.SVGPFAModelFactory static method) buildQSigma() (stats.svGPFA.svPosteriorOnIndPoints.SVPosteriorOnIndPoints method)

C

chol3D() (in module stats.svGPFA.utils) clock() (in module stats.svGPFA.utils) computeMeansAndVars() (stats.svGPFA.svEmbedding.SVEmbedding method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatents method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatentsAllTimes method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatentsAssocTimes method)

computeSVPosteriorOnLatentsStats() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.expectedLogLikelihood.PointProcessELL method) (stats.svGPFA.svEmbedding.SVEmbedding method) (stats.svGPFA.svLowerBound.SVLowerBound method) computeSVPostOnLatentsStats() (stats.svGPFA.expectedLogLikelihood.PoissonELL method)

E

EmbeddingSimulator (class in stats.svGPFA.simulations) eval() (stats.gaussianProcesses.eval.GaussianProcess method) (stats.gaussianProcesses.learn.GPMarginalLogLikelihood method) (stats.svGPFA.svLowerBound.SVLowerBound method) evalELLSumAcrossTrialsAndNeurons() (stats.svGPFA.svLowerBound.SVLowerBound method) evalGradient() (stats.gaussianProcesses.learn.GPMarginalLogLikelihood method) evalSumAcrossLatentsAndTrials() (stats.svGPFA.klDivergence.KLDivergence method)

evalSumAcrossTrialsAndNeurons() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.expectedLogLikelihood.PointProcessELL method) (stats.svGPFA.expectedLogLikelihood.PoissonELL method) evalWithGradient() (stats.gaussianProcesses.learn.GPMarginalLogLikelihood method) evalWithoutInverse() (stats.gaussianProcesses.learn.GPMarginalLogLikelihood method) ExpectedLogLikelihood (class in stats.svGPFA.expectedLogLikelihood) ExponentialLink (in module stats.svGPFA.svGPFAModelFactory) ExponentialQuadraticKernel (class in stats.kernels)

F

flattenListsOfArrays() (in module stats.svGPFA.utils)

G

GaussianProcess (class in stats.gaussianProcesses.eval) getDiagIndicesIn3DArray() (in module stats.svGPFA.utils) getEmbeddingFunctionForNeuronAndTrial() (stats.svGPFA.simulations.EmbeddingSimulator method) getIndPointsLocs() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.kernelMatricesStore.KernelMatricesStore method) (stats.svGPFA.svEmbedding.SVEmbedding method) (stats.svGPFA.svLowerBound.SVLowerBound method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatents method) getKernels() (stats.svGPFA.kernelMatricesStore.KernelMatricesStore method) getKernelsParams() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.kernelMatricesStore.KernelMatricesStore method) (stats.svGPFA.svEmbedding.SVEmbedding method) (stats.svGPFA.svLowerBound.SVLowerBound method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatents method) getKtt() (stats.svGPFA.kernelMatricesStore.IndPointsLocsAndTimesKMS method)

getKtz() (stats.svGPFA.kernelMatricesStore.IndPointsLocsAndTimesKMS method) getKzz() (stats.svGPFA.kernelMatricesStore.IndPointsLocsKMS method) getKzzChol() (stats.svGPFA.kernelMatricesStore.IndPointsLocsKMS method) getParams() (stats.kernels.Kernel method) (stats.svGPFA.svEmbedding.LinearSVEmbedding method) (stats.svGPFA.svEmbedding.SVEmbedding method) (stats.svGPFA.svPosteriorOnIndPoints.SVPosteriorOnIndPoints method) getQMu() (stats.svGPFA.svPosteriorOnIndPoints.SVPosteriorOnIndPoints method) getSVEmbeddingParams() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.svLowerBound.SVLowerBound method) getSVPosteriorOnIndPointsParams() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.svEmbedding.SVEmbedding method) (stats.svGPFA.svLowerBound.SVLowerBound method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatents method) GPFASimulator (class in stats.svGPFA.simulations) GPMarginalLogLikelihood (class in stats.gaussianProcesses.learn)

I

IndPointsLocsAndAllTimesKMS (class in stats.svGPFA.kernelMatricesStore) IndPointsLocsAndAssocTimesKMS (class in stats.svGPFA.kernelMatricesStore)

IndPointsLocsAndTimesKMS (class in stats.svGPFA.kernelMatricesStore) IndPointsLocsKMS (class in stats.svGPFA.kernelMatricesStore)

K

Kernel (class in stats.gaussianProcesses.kernels) (class in stats.kernels)

KernelMatricesStore (class in stats.svGPFA.kernelMatricesStore) KLDivergence (class in stats.svGPFA.klDivergence)

L

LinearEmbedding (in module stats.svGPFA.svGPFAModelFactory) LinearSVEmbedding (class in stats.svGPFA.svEmbedding)

LinearSVEmbeddingAllTimes (class in stats.svGPFA.svEmbedding) LinearSVEmbeddingAssocTimes (class in stats.svGPFA.svEmbedding)

M

maximize() (stats.svGPFA.svEM.SVEM method)

mean() (stats.gaussianProcesses.eval.GaussianProcess method)

O

OtherLink (in module stats.svGPFA.svGPFAModelFactory)

P

PeriodicKernel (class in stats.kernels) PeriodicRandomFunctionKernel (class in stats.gaussianProcesses.kernels) plot (module) plot.svGPFA (module) plot.svGPFA.plotUtils (module) plotEstimatedLatents() (in module plot.svGPFA.plotUtils) plotLowerBoundHist() (in module plot.svGPFA.plotUtils) plotTrueAndEstimatedLatents() (in module plot.svGPFA.plotUtils) PointProcess (in module stats.svGPFA.svGPFAModelFactory) PointProcessELL (class in stats.svGPFA.expectedLogLikelihood)

PointProcessELLExpLink (class in stats.svGPFA.expectedLogLikelihood) PointProcessELLQuad (class in stats.svGPFA.expectedLogLikelihood) Poisson (in module stats.svGPFA.svGPFAModelFactory) PoissonELL (class in stats.svGPFA.expectedLogLikelihood) PoissonELLExpLink (class in stats.svGPFA.expectedLogLikelihood) PoissonELLQuad (class in stats.svGPFA.expectedLogLikelihood) predict() (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatentsAllTimes method) predictLatents() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.svEmbedding.LinearSVEmbeddingAllTimes method) (stats.svGPFA.svLowerBound.SVLowerBound method)

S

sampleInhomogeneousPP_thinning() (stats.sampler.Sampler method) sampleInhomogeneousPP_timeRescaling() (stats.sampler.Sampler method) Sampler (class in stats.sampler) setIndPointsLocs() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.expectedLogLikelihood.PointProcessELL method) (stats.svGPFA.expectedLogLikelihood.PoissonELL method) (stats.svGPFA.kernelMatricesStore.KernelMatricesStore method) (stats.svGPFA.svEmbedding.SVEmbedding method) (stats.svGPFA.svLowerBound.SVLowerBound method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatents method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatentsAllTimes method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatentsAssocTimes method) setInitialParams() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.expectedLogLikelihood.PointProcessELL method) (stats.svGPFA.expectedLogLikelihood.PoissonELL method) (stats.svGPFA.kernelMatricesStore.KernelMatricesStore method) (stats.svGPFA.svEmbedding.LinearSVEmbedding method) (stats.svGPFA.svEmbedding.SVEmbedding method) (stats.svGPFA.svLowerBound.SVLowerBound method) (stats.svGPFA.svPosteriorOnIndPoints.SVPosteriorOnIndPoints method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatents method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatentsAllTimes method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatentsAssocTimes method) setKernels() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.expectedLogLikelihood.PointProcessELL method) (stats.svGPFA.expectedLogLikelihood.PoissonELL method) (stats.svGPFA.kernelMatricesStore.KernelMatricesStore method) (stats.svGPFA.svEmbedding.SVEmbedding method) (stats.svGPFA.svLowerBound.SVLowerBound method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatents method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatentsAllTimes method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatentsAssocTimes method) setMeasurements() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.expectedLogLikelihood.PointProcessELL method) (stats.svGPFA.expectedLogLikelihood.PoissonELL method) (stats.svGPFA.svLowerBound.SVLowerBound method) setMiscParams() (stats.svGPFA.expectedLogLikelihood.PoissonELL method) setNeuronForSpikeIndex() (stats.svGPFA.svEmbedding.LinearSVEmbeddingAssocTimes method)

setParams() (stats.kernels.Kernel method) setQuadParams() (stats.svGPFA.expectedLogLikelihood.ExpectedLogLikelihood method) (stats.svGPFA.expectedLogLikelihood.PointProcessELL method) (stats.svGPFA.expectedLogLikelihood.PointProcessELLQuad method) (stats.svGPFA.svLowerBound.SVLowerBound method) setTimes() (stats.svGPFA.kernelMatricesStore.IndPointsLocsAndTimesKMS method) (stats.svGPFA.svEmbedding.SVEmbedding method) (stats.svGPFA.svPosteriorOnLatents.SVPosteriorOnLatents method) simulate() (stats.svGPFA.simulations.GPFASimulator method) SquaredExponentialKernel (class in stats.gaussianProcesses.kernels) stats (module) stats.gaussianProcesses (module) stats.gaussianProcesses.eval (module) stats.gaussianProcesses.kernels (module) stats.gaussianProcesses.learn (module) stats.kernels (module) stats.sampler (module) stats.svGPFA (module) stats.svGPFA.expectedLogLikelihood (module) stats.svGPFA.kernelMatricesStore (module) stats.svGPFA.klDivergence (module) stats.svGPFA.simulations (module) stats.svGPFA.svEM (module) stats.svGPFA.svEmbedding (module) stats.svGPFA.svGPFAModelFactory (module) stats.svGPFA.svLowerBound (module) stats.svGPFA.svPosteriorOnIndPoints (module) stats.svGPFA.svPosteriorOnLatents (module) stats.svGPFA.utils (module) std() (stats.gaussianProcesses.eval.GaussianProcess method) SVEM (class in stats.svGPFA.svEM) SVEmbedding (class in stats.svGPFA.svEmbedding) SVGPFAModelFactory (class in stats.svGPFA.svGPFAModelFactory) SVLowerBound (class in stats.svGPFA.svLowerBound) SVPosteriorOnIndPoints (class in stats.svGPFA.svPosteriorOnIndPoints) SVPosteriorOnLatents (class in stats.svGPFA.svPosteriorOnLatents) SVPosteriorOnLatentsAllTimes (class in stats.svGPFA.svPosteriorOnLatents) SVPosteriorOnLatentsAssocTimes (class in stats.svGPFA.svPosteriorOnLatents)