PMTK Documentation
Revision Date: 16-Mar-2009

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Function Name Title Classes Used Functions Used
alarmNetwork Test VarElimInfEng on the Alarm Network VarElimInfEng mkAlarmNetworkDgm
bernoulli_betaSequentialUpdate Sequential Bayesian Updating of a Bernoulli-Beta model. BernoulliDist , Bernoulli_BetaDist , BetaDist sample
bernoulliDistTest Simple Test of the BernoulliDist Class BernoulliDist  
betaPlotDemo Plotting Beta Distributions BetaDist  
binom_betaPostPredDemo Posterior Predictive Distribution for Beta-Binomial model BetaDist , BinomDist , Binom_BetaDist  
binomial_betaPosteriorDemo Example of parameter updating in a Beta-Binomial model. BetaDist , Binom_BetaDist  
binomialPlotDemo Plotting Binomial Distributions BinomDist  
cancerRatesEb Empirical Bayes Missouri Cancer Example BetaBinomDist  
cancerRatesMh Hierarchical Bayesian Estimation of Some Binomial Proportions   mhSample , sigmoid
casinoDemo HMMs and the occasionally Dishonest Casino DiscreteDist , HmmDist maxidx , sample
chainLengthUgmDgmDemo UGM vs DGM Chains of Different Length DgmDist , TabularCPD , TabularFactor , UgmTabularDist normalize , pmf
chainTransformerTest Test the Chain Transformer AddOnesTransformer , ChainTransformer , StandardizeTransformer  
chordalGraphDemo Make a Chordal Graph ChordalGraph , Jtree mkGraphSymmetric , setdiag
clusterMnistDigits Cluster MNIST Digits and Visualize the Cluster Centers DiscreteMixDist placeFigures , sample , setupMnist
compareVarElimToEnum Validate VarElimInfEng against EnumInfEng results EnumInfEng , VarElimInfEng colvec , mkSprinklerDgm , pmf , powerset , sumv
compareVarElimToFwdBack HMM vs DGM Comparing Forwards Backwards to Variable Elimination DiscreteDist , HmmDist , MvnDist pmf , sample
compareVarElimToJtree Test that JtreeInfEng Returns the Same Results as VarElimInfEng JtreeInfEng , VarElimInfEng mkAlarmNetworkDgm , pmf
constDistTest Simple Test of the ConstDist Class ConstDist sample
cooperYooInterventionDemo Verify Marginal Likelihood Equation with Interventional Data DgmDist , TabularCPD mkStochastic
dataTableDemo Simple Demonstration of the DataTable Class DataTable  
dirichletHistPlotDemo Plot Histogram of Samples Generated From a DirichletDist DirichletDist sample
discrete_DirichletDistTest Simple Test of Discrete_DirichletDist DirichletDist , Discrete_DirichletDist sampleDiscrete
discreteDistTest Simple Test of the DiscreteDist Class DiscreteDist sample
gammaPlotDemo Plot a Gamma Distribution GammaDist  
gammaRainfallDemo Rainfall Demo GammaDist  
gauss_NormInvGammDistTest Simple Test of Gauss_NormInvGammaDist Gauss_NormInvGammaDist , NormInvGammaDist  
gaussCVfitDemo Estimate mu/sigma by Cross Validation GaussDist , ModelDist sample
gaussDGMdemo Koller & Friedman Gaussian DGM Example DgmGaussDist , GaussInfEng , LinGaussCPD sample
gaussHeightWeight Height Weight Example GaussDist  
gaussInferMuSigmaDemo Demo of inferring mu and sigma for a 1d Gaussian GaussDist , Gauss_NormInvGammaDist , NormInvGammaDist sample
gaussMixPlot Plot a Mixture of Gaussians DiscreteDist , MvnDist , MvnMixDist sample
gaussPlotDemo Plot a Gaussian GaussDist  
gaussVsToutlierDemo Illustrate the Robustness of the T-Distribution Compared to the Gaussian. GaussDist , StudentDist  
generativeClassifierTest1 Simple Test of the Generative Classifier Class (1) BernoulliDist , Bernoulli_BetaDist , BetaDist , DirichletDist , DiscreteDist , Discrete_DirichletDist , GaussDist , Gauss_NormInvGammaDist , GenerativeClassifierDist , NormInvGammaDist sampleDiscrete
generativeClassifierTest2 Simple Test of the Generative Classifier Class (2) DirichletDist , DiscreteDist , Discrete_DirichletDist , GenerativeClassifierDist , MvnDist , MvnInvWishartDist , Mvn_MvnInvWishartDist sampleDiscrete
ggmBICdemo BIC of GGMs on 4 nodes UgmGaussDist , UndirectedGraph logsumexp , sample
GGMchordalModelSelection Pick best possible GGM on 4 nodes using exhaustive seach Graphlayout , HiwDist , ModelDist , UgmGaussChordalDist , UgmGaussDist , UndirectedGraph sample
ggmDemo Samples from a GGM UgmGaussDist , UndirectedGraph sample
ggmInferDemo Inference in GGMs MvnDist , UgmGaussDist , UndirectedGraph setdiffPMTK
gibbsSprinklerUGM Gibbs Sampling from the prior of the undirected water sprinkler EnumInfEng , GibbsInfEng mkSprinklerDgm , pmf
graphClassDemo Graph Demo Dag , DirectedGraph , UndirectedGraph dfs , mkGraphSymmetric
hmmDistTest A Simple Test of the HmmDist Class DiscreteDist , DiscreteMixDist , HmmDist , MvnDist , MvnMixDist maxidx , normalize , randpd , sample
inheritedDiseaseVarElim Inherited Disease DGM Example - Stat521A Spring 2009 Hw2 Q4 DgmDist , Graph , JtreeInfEng , MvnDist , MvnMixDist , TabularCPD pmf
invGammaPlotDemo Plot Demo InvGammaDist  
invGammaSampleDemo Draw Samples From an InvGammaDist InvGammaDist sample
invWIplot1D Plot Some invchi2 Distributions InvWishartDist  
invWIplot2D plot some IW distributions InvWishartDist cov2cor , randpd
isingImageDenoiseDemo   IsingGridDist , MvnDist  
isolatedWordClassification Classifying a speech signal with an HMM as "four" or "five" DiscreteDist , GenerativeClassifierDist , HmmDist , MvnDist normalize
Knn3ClassHeatMaps Plot Predictive Distribution of a KNN Classifer KnnDist placeFigures
laplacePlotDemo Plot Laplace Distributions LaplaceDist  
lingaussHybridDemo Test linear Gaussian CPD with discrete parents DgmDist , InputCPD , JtreeInfEng , LinGaussHybridCPD , TabularCPD normalize , pmf
linreg_MvnDistTest Simple Test of Linreg_MvnDist AddOnesTransformer , ChainTransformer , Linreg_MvnDist , StandardizeTransformer mse
linreg_MvnInvGammaDistTest Simple Test of Linreg_MvnInvGammaDist AddOnesTransformer , ChainTransformer , Linreg_MvnInvGammaDist , StandardizeTransformer mse
linregAllMethods LinregDist on the Prostate Data Set AddOnesTransformer , ChainTransformer , LinregDist , StandardizeTransformer mse
linregBasis Linear Regression with Various Basis Expansions LinregDist , Linreg_MvnDist , PolyBasisTransformer , RbfBasisTransformer polyDataMake , sample
linregGaussVsNIG Compare Linreg_MvnDist to LinregMvnInvGammaDist Linreg_MvnDist , Linreg_MvnInvGammaDist , PolyBasisTransformer polyDataMake
linregPolyFitDegree Linear Regression with Polynomial Basis Expansions ChainTransformer , LinregDist , PolyBasisTransformer , RescaleTransformer polyDataMake
linregPolyFitErrorBars Linear Regression with a Polynomial Basis Expansion and Error Bars ChainTransformer , Linreg_MvnInvGammaDist , PolyBasisTransformer , RescaleTransformer polyDataMake
linregPolyFitN Fit Linear Regression Models with Various Polynomial Basis Expansions ChainTransformer , LinregDist , PolyBasisTransformer , RescaleTransformer polyDataMake
linregPolyFitNoErrorBars Linear Regression with Polynomial Expansion ChainTransformer , LinregDist , PolyBasisTransformer , RescaleTransformer polyDataMake
linregPolyFitRidge Ridge Regression with Polynomial Basis Expansion ChainTransformer , LinregDist , PolyBasisTransformer , RescaleTransformer polyDataMake
linregPolyFitRidgeBIC Ridge Regression using BIC ChainTransformer , LinregDist , PolyBasisTransformer , RescaleTransformer argmax , polyDataMake
linregPolyFitRidgeCV Ridge Regression Using Cross Validation ChainTransformer , LinregDist , PolyBasisTransformer , RescaleTransformer oneStdErrorRule , polyDataMake
linregPolyFitRidgeU Ridge Regression ChainTransformer , LinregDist , PolyBasisTransformer , RescaleTransformer polyDataMake
linregRbf RBF Expansion ChainTransformer , LinregDist , RbfBasisTransformer , RescaleTransformer polyDataMake
logreg_MvnDistTest Simple Test of Logreg_MvnDist Logreg_MvnDist sampleDiscrete
logregCompareOptimizers Compare the Relative Performance of Various Optimizers LogregDist  
logregCompareOptimizers2 Compare various Logreg Optimizers LogregDist  
logregFitCrabs Logistic Regression Crabs Data ChainTransformer , KernelTransformer , LogregDist , Logreg_MvnDist , StandardizeTransformer makeCrabs
logregLaplaceGirolami Logreg Plot Demo LogregDist , Logreg_MvnDist  
logregSAT Binary Classification of SAT Data via Logistic Regression AddOnesTransformer , ChainTransformer , LogregDist , Logreg_MvnDist , StandardizeTransformer sample
logregVisualizePredictive Logistic Regression: Visualizing the Predictive Distribution ChainTransformer , KernelTransformer , LogregDist , ModelSelection , StandardizeTransformer  
mcmcMvn2d MCMC Sampling from a 2d Gaussians MvnDist , SampleDist acf , gaussPlot2d , gibbsSample , mhSample , suptitle
mcmcMvn2dConditioning MCMC Sampling from a multivariate Gaussian conditioned on data GibbsInfEng , MhInfEng , MvnDist acf , randpd , sample , suptitle
mhGmmDemo MH Sampling from a mixture of two 1d Gaussians using a 1d Gaussian proposal DiscreteDist , MvnDist , MvnMixDist mhSample , plotConvDiagnostics , subd
mhMvn2dConditioning MCMC Sampling from a multivariate Gaussian conditioned on data MvnDist , SampleDist acf , gibbsSample , mhSample , randpd , suptitle
misconceptionRank Figure out rank of linear dependencies in misconception Markov network   ind2subv
misconceptionUGMdemo Inference in 'misconception network' (Koller and Friedman p99) JtreeInfEng dispjoint , mkMisconceptionUGM , pmf
mkAlarmNetworkDgm Create the Alarm Network DGM DgmDist , TabularCPD alarmNetwork
mkFluDgm Create the Flu Network DGM DgmDist , Graphlayout , TabularCPD , Treelayout normalize
mkMisconceptionUGM Misconception tabular UGM (Koller and Friemdna p98) TabularFactor , UgmTabularDist mkSymmetric
mkSprinklerDgm Water Sprinkler Bayes Net Example DgmDist , TabularCPD  
mnistClassifyDemo Classify the Mnist Digits Using KNN DirichletDist , KnnDist , PcaTransformer normalize
mnistErrorVsN KNN Mnist Error Rate W.R.T. N KnnDist  
modelSelect1D Selecting Lambda Using the ModelSelection Class AddOnesTransformer , ChainTransformer , LinregDist , ModelSelection , StandardizeTransformer mse
modelSelect2D 2D Model Selection (Searching Over a Grid of Values) ChainTransformer , LinregDist , ModelSelection , PolyBasisTransformer , StandardizeTransformer mse
mvnCondition2D Conditioning a 2D MVN MvnDist gaussPlot2d , normalize
mvnHeightWeight MVN Height Weight Demo MvnDist gaussPlot2d
mvnImputationDemo Imputation for an MVN MvnDist sample
mvnImputationEmDemo Imputation for an MVN MvnDist mse , sample
mvnImputationPima   MvnDist mse , suptitle
mvnInferMuSigma1D Demo of inferring mu and sigma for a 1d Gaussian MvnDist , MvnInvWishartDist , Mvn_MvnInvWishartDist sample
mvnInferParamsMean1d MVN Infer Mean 1D with fixed sigma MvnDist , Mvn_MvnDist  
mvnInferParamsMean2d Bayesian inference of Mean of a 2D MVN with fixed Sigma MvnDist , Mvn_MvnDist sample
mvnInferParamsSigma2d Demo of inferrring 2d MVN covariance given fixed mean InvWishartDist , MvnDist , Mvn_InvWishartDist gaussPlot2d , sample , suplabel
mvnInvWIplotDemo Plot Demo MvnInvWishartDist  
mvnMixDistTest Simple Test of MvnMixDist MvnMixDist sample
mvnPlot2Ddemo Plot an MVN in 2D MvnDist  
mvnSeqlUpdateMuSigma1D Sequential Bayesian updating of (mu,sigma) for a 1D gaussian MvnDist , MvnInvWishartDist , Mvn_MvnInvWishartDist sample
mvnSeqUpdateMu1d Sequential Updating of mu for fixed sigma MvnDist , Mvn_MvnDist sample
mvnSeqUpdateSigma1d Sequential Updating of Sigma in 1d given fixed mean InvWishartDist , MvnDist , Mvn_InvWishartDist sample , suptitle
mvnSoftCondition Soft Conditioning Demo MvnDist , Mvn_MvnDist sample
mvtPlotDemo MVT Plot Demo MvnDist , MvtDist  
naiveBayesBernoulliExample Classify Mnist Digits Using a Naive Bayes Classifier DiscreteDist , GenerativeClassifierDist normalize , setupMnist
numericalIntNIGdemo Demo of computing posterior moments of NIG using numerical integration GaussDist , Gauss_NormInvGammaDist , NormInvGammaDist sample
oldFaithfulDemo Fit a Mixture of Gaussians to the Old Faithful Data Set MvnMixDist  
plotMFCC Plot a spectogram and its MFCC representation    
poissonPlotDemo Poisson Plot Demo PoissonDist  
postModelsExhaustiveDemo UgmGaussDist Exhaustive Search of the Model Space HiwDist , MvnDist , UgmGaussChordalDist , UgmGaussDist , UndirectedGraph hintonDiagram , sample , suptitle
rainyDayDemo Rainy Day DGM Example Dag , DgmDist , TabularCPD mkStochastic , normalize
SAcoolingSchedule Illustration of cooling schedule for simulated annealing    
SAdemoCamel     simAnneal
SAdemoHisto Anneal a histogram to illustrate the effect of temperature    
SAdemoMOG     SA
SAdemoPeaks     print_pdf , simAnneal
sampleDistDemo Sample Dist Example MvnDist , SampleDist sample
sampleHIWdemo Example of sampling from the HIW distribution ChordalGraph , HiwDist randpd , sample , setdiag
sprinklerDGMdemo Example of inference in water sprinkler DGM   ind2subv , mkSprinklerDgm , pmf , xticklabelRot
sprinklerUGMdemo Inference in undirected version of sprinkler network   mkSprinklerDgm , pmf
sprinklerUGMvarelim Variable Elimination in an Undirected Model EnumInfEng , VarElimInfEng mkSprinklerDgm , pmf
studentVSGauss Student T vs Gaussian GaussDist , StudentDist  
undirectedChainFwdBackDemo Run Forwards Backwards on an Undirected Chain TabularFactor , UgmTabularDist , VarElimInfEng hmmFwdBack , mkSymmetric , pmf
WIplotDemo Plot Some Wishart Distributions WishartDist cov2cor , randpd , suptitle
wordSegmentation Train an HMM on the word "four" and then find the Viterbi parse of a test signal into phones DiscreteDist , HmmDist , MvnDist , MvnMixDist maximizeFigure , normalize