A B C D E F G H I J K L M N O P Q R S T U V W X

B

backward(ParameterTree[], int[][]) - Method in class de.jstacs.scoringFunctions.directedGraphicalModels.ParameterTree

Computes the backward-part of the normalization constant starting from this ParameterTree.

backwardIntermediate - Variable in class de.jstacs.models.hmm.models.HigherOrderHMM

Helper variable = only for internal use.

BasicHigherOrderTransition - Class in de.jstacs.models.hmm.transitions

This class implements the basic transition that allows to be trained using the viterbi or the Baum-Welch algorithm.

BasicHigherOrderTransition(boolean[], BasicHigherOrderTransition.AbstractTransitionElement...) - Constructor for class de.jstacs.models.hmm.transitions.BasicHigherOrderTransition

The main constructor.

BasicHigherOrderTransition(StringBuffer) - Constructor for class de.jstacs.models.hmm.transitions.BasicHigherOrderTransition

The standard constructor for the interface Storable.

BasicHigherOrderTransition.AbstractTransitionElement - Class in de.jstacs.models.hmm.transitions

This class declares the probability distribution for a given context, i.e. it contains all possible transition and the corresponding probabilities for a given set offset previously visited states.

BasicHigherOrderTransition.AbstractTransitionElement(int[], int[], double[]) - Constructor for class de.jstacs.models.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.

BasicHigherOrderTransition.AbstractTransitionElement(int[], int[], double[], double[]) - Constructor for class de.jstacs.models.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.

BasicHigherOrderTransition.AbstractTransitionElement(StringBuffer) - Constructor for class de.jstacs.models.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

The standard constructor for the interface Storable.

BasicPluginTransitionElement - Class in de.jstacs.models.hmm.transitions.elements

Basic transition element without random initialization of parameters.

BasicPluginTransitionElement(int[], int[], double[], double[]) - Constructor for class de.jstacs.models.hmm.transitions.elements.BasicPluginTransitionElement

Constructor creating a new instance with given context, descendant states, and hyper parameters.

BasicPluginTransitionElement(int[], int[], double[], double[], double[]) - Constructor for class de.jstacs.models.hmm.transitions.elements.BasicPluginTransitionElement

Constructor creating a new instance with given context, descendant states, and hyper parameters.

BasicPluginTransitionElement(StringBuffer) - Constructor for class de.jstacs.models.hmm.transitions.elements.BasicPluginTransitionElement

The standard constructor for the interface Storable.

BasicTransitionElement - Class in de.jstacs.models.hmm.transitions.elements

This class implements the probability distribution for a given context, i.e. it contains all possible transition and the corresponding probabilities for a given set of previously visited states.

BasicTransitionElement(int[], int[], double[]) - Constructor for class de.jstacs.models.hmm.transitions.elements.BasicTransitionElement

This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.

BasicTransitionElement(int[], int[], double[], double[]) - Constructor for class de.jstacs.models.hmm.transitions.elements.BasicTransitionElement

This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.

BasicTransitionElement(StringBuffer) - Constructor for class de.jstacs.models.hmm.transitions.elements.BasicTransitionElement

The standard constructor for the interface Storable.

baumWelch(int, int, double, Sequence) - Method in class de.jstacs.models.hmm.models.HigherOrderHMM

This method computes the likelihood and modifies the sufficient statistics according to the Baum-Welch algorithm.

BaumWelchParameterSet - Class in de.jstacs.models.hmm.training

This class implements an HMMTrainingParameterSet for the Baum-Welch training of an AbstractHMM.

BaumWelchParameterSet() - Constructor for class de.jstacs.models.hmm.training.BaumWelchParameterSet

This is the empty constructor that can be used to fill the parameters after creation.

BaumWelchParameterSet(int, AbstractTerminationCondition) - Constructor for class de.jstacs.models.hmm.training.BaumWelchParameterSet

This constructor can be used to create an instance with specified parameters.

BaumWelchParameterSet(StringBuffer) - Constructor for class de.jstacs.models.hmm.training.BaumWelchParameterSet

The standard constructor for the interface Storable.

BayesianNetworkModel - Class in de.jstacs.models.discrete.inhomogeneous

The class implements a Bayesian network ( StructureLearner.ModelType.BN ) of fixed order.

BayesianNetworkModel(BayesianNetworkModelParameterSet) - Constructor for class de.jstacs.models.discrete.inhomogeneous.BayesianNetworkModel

Creates a new BayesianNetworkModel from a given BayesianNetworkModelParameterSet.

BayesianNetworkModel(StringBuffer) - Constructor for class de.jstacs.models.discrete.inhomogeneous.BayesianNetworkModel

The standard constructor for the interface Storable.

BayesianNetworkModelParameterSet - Class in de.jstacs.models.discrete.inhomogeneous.parameters

The ParameterSet for the class BayesianNetworkModel.

BayesianNetworkModelParameterSet(StringBuffer) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.BayesianNetworkModelParameterSet

The standard constructor for the interface Storable.

BayesianNetworkModelParameterSet() - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.BayesianNetworkModelParameterSet

The simple constructor for an empty BayesianNetworkModelParameterSet for a BayesianNetworkModel.

BayesianNetworkModelParameterSet(AlphabetContainer, int, double, String, StructureLearner.ModelType, byte, StructureLearner.LearningType) - Constructor for class de.jstacs.models.discrete.inhomogeneous.parameters.BayesianNetworkModelParameterSet

This is the constructor of a filled BayesianNetworkModelParameterSet for a BayesianNetworkModel.

BayesianNetworkScoringFunction - Class in de.jstacs.scoringFunctions.directedGraphicalModels

This class implements a scoring function that is a moral directed graphical model, i.e. a moral Bayesian network.

BayesianNetworkScoringFunction(AlphabetContainer, int, double, boolean, Measure) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction

Creates a new BayesianNetworkScoringFunction that has neither been initialized nor trained.

BayesianNetworkScoringFunction(BayesianNetworkScoringFunctionParameterSet) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction

Creates a new BayesianNetworkScoringFunction that has neither been initialized nor trained from a BayesianNetworkScoringFunctionParameterSet.

BayesianNetworkScoringFunction(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunction

The standard constructor for the interface Storable.

BayesianNetworkScoringFunctionParameterSet - Class in de.jstacs.scoringFunctions.directedGraphicalModels

Class for the parameters of a BayesianNetworkScoringFunction.

BayesianNetworkScoringFunctionParameterSet(AlphabetContainer, int, double, boolean, Measure) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunctionParameterSet

Creates a new BayesianNetworkScoringFunctionParameterSet with pre-defined parameter values.

BayesianNetworkScoringFunctionParameterSet() - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunctionParameterSet

Creates a new BayesianNetworkScoringFunctionParameterSet with empty parameter values.

BayesianNetworkScoringFunctionParameterSet(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.BayesianNetworkScoringFunctionParameterSet

Creates a new BayesianNetworkScoringFunctionParameterSet from its XML representation as defined by the Storable interface.

best - Variable in class de.jstacs.models.mixture.AbstractMixtureModel

This field contains the value of objective function of the best start of the training.

beta - Variable in class de.jstacs.classifier.scoringFunctionBased.gendismix.GenDisMixClassifier

The weights that determine a point of the simplex that corresponds to the function that is optimized by this classifier.

beta - Variable in class de.jstacs.classifier.scoringFunctionBased.gendismix.LogGenDisMixFunction

The mixture parameters of the GenDisMix

bgMaxMarkovOrder - Variable in class de.jstacs.models.mixture.motif.SingleHiddenMotifMixture

The order of the background model.

BioJavaAdapter - Class in de.jstacs.data.bioJava

This class provides static methods to convert BioJava datatypes ( SequenceIterator, Sequence) to Samples and vice versa.

BioJavaAdapter() - Constructor for class de.jstacs.data.bioJava.BioJavaAdapter

brentsMethod(OneDimensionalFunction, double, double, double, double, double) - Static method in class de.jstacs.algorithms.optimization.Optimizer

Approximates a minimum (not necessary the global) in the interval [lower,upper].

brentsMethod(OneDimensionalFunction, double, double, double, double) - Static method in class de.jstacs.algorithms.optimization.Optimizer

Approximates a minimum (not necessary the global) in the interval [lower,upper].

BTExplainingAwayResidual - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Structure learning Measure that computes a maximum spanning tree based on the explaining away residual and uses the resulting tree structure as structure of a Bayesian tree (special case of a Bayesian network) in a BayesianNetworkScoringFunction .

BTExplainingAwayResidual(double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual

Creates a new explaining away residual Bayesian tree Measure.

BTExplainingAwayResidual(BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual

Creates a new BTExplainingAwayResidual from the corresponding InstanceParameterSet parameters.

BTExplainingAwayResidual(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual

The standard constructor for the interface Storable.

BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Class for the parameters of a BTExplainingAwayResidual structure Measure.

BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet() - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet

Creates a new BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet with empty parameter values.

BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet(double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet

Creates a new BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet with the parameter for the equivalent sample sizes set to ess.

BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTExplainingAwayResidual.BTExplainingAwayResidualParameterSet

The standard constructor for the interface Storable .

BTMutualInformation - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Structure learning Measure that computes a maximum spanning tree based on mutual information and uses the resulting tree structure as structure of a Bayesian tree (special case of a Bayesian network) in a BayesianNetworkScoringFunction .

BTMutualInformation(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation

The standard constructor for the interface Storable.

BTMutualInformation(BTMutualInformation.DataSource, double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation

Creates a new mutual information Bayesian tree Measure.

BTMutualInformation(BTMutualInformation.BTMutualInformationParameterSet) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation

Creates a new BTMutualInformation from the corresponding InstanceParameterSet parameters.

BTMutualInformation.BTMutualInformationParameterSet - Class in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Class for the parameters of a BTMutualInformation structure Measure.

BTMutualInformation.BTMutualInformationParameterSet() - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation.BTMutualInformationParameterSet

Creates a new BTMutualInformation.BTMutualInformationParameterSet with empty parameter values.

BTMutualInformation.BTMutualInformationParameterSet(BTMutualInformation.DataSource, double[]) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation.BTMutualInformationParameterSet

Creates a new BTMutualInformation.BTMutualInformationParameterSet with the parameter for the BTMutualInformation.DataSource set to clazz and the parameter for the equivalent sample sizes (ess) set to ess.

BTMutualInformation.BTMutualInformationParameterSet(StringBuffer) - Constructor for class de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures.BTMutualInformation.BTMutualInformationParameterSet

The standard constructor for the interface Storable .

BTMutualInformation.DataSource - Enum in de.jstacs.scoringFunctions.directedGraphicalModels.structureLearning.measures.btMeasures

Enum defining the possible sources of data to compute the mutual information.

burnInTest - Variable in class de.jstacs.classifier.scoringFunctionBased.sampling.SamplingScoreBasedClassifier

The BurnInTest, may be null for no test

burnInTest - Variable in class de.jstacs.models.hmm.models.SamplingHigherOrderHMM

This variable holds the BurnInTest used for training the model

burnInTest - Variable in class de.jstacs.models.mixture.AbstractMixtureModel

The BurnInTest that is used to stop the sampling.

BurnInTest - Interface in de.jstacs.sampling

This is the abstract super class for any test of the length of the burn-in phase.

bwdMatrix - Variable in class de.jstacs.models.hmm.AbstractHMM

matrix for all backward-computed variables; bwdMatrix[l][c] = log P(x_{l+1},...

ByteSequence - Class in de.jstacs.data.sequences

This class is for sequences with the alphabet symbols encoded as bytes and can therefore be used for discrete AlphabetContainers with alphabets that use only few symbols.

ByteSequence(AlphabetContainer, byte[]) - Constructor for class de.jstacs.data.sequences.ByteSequence

Creates a new ByteSequence from an array of byte- encoded alphabet symbols.

ByteSequence(AlphabetContainer, String) - Constructor for class de.jstacs.data.sequences.ByteSequence

Creates a new ByteSequence from a String representation using the default delimiter.

ByteSequence(AlphabetContainer, SequenceAnnotation[], String, String) - Constructor for class de.jstacs.data.sequences.ByteSequence

Creates a new ByteSequence from a String representation using the delimiter delim.

ByteSequence(AlphabetContainer, SequenceAnnotation[], SymbolExtractor) - Constructor for class de.jstacs.data.sequences.ByteSequence

Creates a new ByteSequence from a SymbolExtractor.