Uses of Interface
de.jstacs.sampling.SamplingComponent

Packages that use SamplingComponent

Package	Description
de.jstacs.classifiers.differentiableSequenceScoreBased.sampling	Provides the classes for AbstractScoreBasedClassifiers that are based on SamplingDifferentiableStatisticalModels and that sample parameters using the Metropolis-Hastings algorithm.
de.jstacs.sampling	This package contains many classes that can be used while a sampling.
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous	This package contains various inhomogeneous models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states	The package provides all interfaces and classes for states used in hidden Markov models.
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete
de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions	The package provides all interfaces and classes for transitions used in hidden Markov models.

Uses of SamplingComponent in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling

Classes in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling that implement SamplingComponent

Modifier and Type	Class and Description
protected class	SamplingScoreBasedClassifier.DiffSMSamplingComponent The SamplingComponent that handles storing and loading sampled parameters values to and from files.

Uses of SamplingComponent in de.jstacs.sampling

Subinterfaces of SamplingComponent in de.jstacs.sampling

Modifier and Type	Interface and Description
interface	GibbsSamplingModel This is the interface that any AbstractTrainableStatisticalModel has to implement if it should be used in a sampling.
interface	SamplingFromStatistic This is the interface for sampling based on a sufficient statistic.

Uses of SamplingComponent in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous

Classes in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous that implement SamplingComponent

Modifier and Type	Class and Description
class	FSDAGModelForGibbsSampling This is the class for a fixed structure directed acyclic graphical model (see FSDAGTrainSM) that can be used in a Gibbs sampling.

Uses of SamplingComponent in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states

Subinterfaces of SamplingComponent in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states

Modifier and Type	Interface and Description
interface	SamplingState

Classes in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states that implement SamplingComponent

Modifier and Type	Class and Description
class	SimpleSamplingState This class implements a state that can be used for a HMM that obtains its parameters from sampling.

Uses of SamplingComponent in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions

Subinterfaces of SamplingComponent in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions

Modifier and Type	Interface and Description
interface	SamplingEmission

Classes in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions that implement SamplingComponent

Modifier and Type	Class and Description
class	SilentEmission This class implements a silent emission which is used to create silent states.

Uses of SamplingComponent in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete

Classes in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.discrete that implement SamplingComponent

Modifier and Type	Class and Description
class	AbstractConditionalDiscreteEmission The abstract super class of discrete emissions.
class	DiscreteEmission This class implements a simple discrete emission without any condition.
class	PhyloDiscreteEmission Phylogenetic discrete emission This class uses a phylogenetic tree to describe multidimensional data It implements Felsensteins model for nucleotide substitution (F81)
class	ReferenceSequenceDiscreteEmission This class implements a discrete emission that depends on some ReferenceSequenceAnnotation at a certain reference position.

Uses of SamplingComponent in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions

Subinterfaces of SamplingComponent in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions

Modifier and Type	Interface and Description
interface	SamplingTransition This interface declares all method used during a sampling.

Classes in de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions that implement SamplingComponent

Modifier and Type	Class and Description
class	HigherOrderTransition This class can be used in any AbstractHMM allowing to use gradient based or sampling training algorithm.