de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements

Class ReferenceBasedTransitionElement

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.BasicTransitionElement

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.elements.ReferenceBasedTransitionElement

All Implemented Interfaces:

Storable, Cloneable

Direct Known Subclasses:

DistanceBasedScaledTransitionElement, ScaledTransitionElement

public class ReferenceBasedTransitionElement
extends BasicTransitionElement

This class implements transition elements that utilize a reference sequence to determine the transition probability. The reference sequence is given as annotation of the original sequence and can be utilized using annotationID.

Author:

Jens Keilwagen, Michael Seifert

See Also:

ReferenceSequenceAnnotation

Field Summary

Fields

Modifier and Type	Field and Description
protected String	annotationID The annotation id used for determining the transition matrix from the ReferenceSequenceAnnotations.
protected int	diagElement The index of the self transition.
protected double	ess The equivalent sample size (ess) used in the prior of this instance.
protected double[]	probabilities Represents the initial the transition probabilities.
protected double[][]	statisticsTransitionProb Represents the gammas required for estimating the transition probabilities not including pseudocounts.

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

context, descendants, hyperParameters, logNorm, parameters, states, statistic

Constructor Summary

Constructors

Constructor and Description
ReferenceBasedTransitionElement(int[] context, int[] states, double ess, double[] probabilities, String annotationID) Creates an ReferenceBasedTransitionElement representing a conditional transition probability distribution of a Hidden Markov TrainableStatisticalModel for the given context.
ReferenceBasedTransitionElement(int[] context, int[] states, double ess, double[] probabilities, String annotationID, double[] weight) Creates an ReferenceBasedTransitionElement representing a conditional transition probability distribution of a Hidden Markov TrainableStatisticalModel for the given context.
ReferenceBasedTransitionElement(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
protected void	appendFurtherInformation(StringBuffer xml) This method appends further information to the XML representation.
ReferenceBasedTransitionElement	clone()
protected void	determineDiagonalElement() This method determines the self transition.
protected void	extractFurtherInformation(StringBuffer xml) This method extracts further information from the XML representation.
double	getLogGammaScoreFromStatistic() This method calculates a score for the current statistics, which is independent from the current parameters In general the gamma-score is a product of gamma-functions parameterized with the current statistics
double	getLogPriorTerm() Returns a value that is proportional to the log of the prior.
protected void	init() This method initializes internal fields.
void	initializeRandomly() This method draws new parameters from the prior.
protected void	precompute() This method precomputes internal fields as for instance the normalization constant.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition.AbstractTransitionElement

addToStatistic, appendGraphvizDescription, appendTransitions, drawParametersFromStatistic, estimateFromStatistic, getArrowOption, getChild, getContext, getDescendant, getGraphvizEdgeWeight, getLabel, getLastContextState, getLogScoreFor, getNextContext, getNumberOfChildren, getNumberOfParameters, getXMLTag, joinStatistics, resetStatistic, setIndexOfDescendantTransitionElement, setParameters, toString, toString, toXML

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

annotationID

protected String annotationID

The annotation id used for determining the transition matrix from the ReferenceSequenceAnnotations.

probabilities

protected double[] probabilities

Represents the initial the transition probabilities.

statisticsTransitionProb

protected double[][] statisticsTransitionProb

Represents the gammas required for estimating the transition probabilities not including pseudocounts.

ess

protected double ess

The equivalent sample size (ess) used in the prior of this instance.

diagElement

protected int diagElement

The index of the self transition.

Constructor Detail

ReferenceBasedTransitionElement

public ReferenceBasedTransitionElement(int[] context,
                                       int[] states,
                                       double ess,
                                       double[] probabilities,
                                       String annotationID)

Creates an ReferenceBasedTransitionElement representing a conditional transition probability distribution of a Hidden Markov TrainableStatisticalModel for the given context.

Parameters:

context - context of states

states - states that can be reached from the context

probabilities - transition probabilities from the context to the states

ess - the equivalent sample size (ess)

annotationID - identifier for decoding transition classes

See Also:

ReferenceBasedTransitionElement(int[], int[], double, double[], String, double[])

ReferenceBasedTransitionElement

public ReferenceBasedTransitionElement(int[] context,
                                       int[] states,
                                       double ess,
                                       double[] probabilities,
                                       String annotationID,
                                       double[] weight)

Creates an ReferenceBasedTransitionElement representing a conditional transition probability distribution of a Hidden Markov TrainableStatisticalModel for the given context.

Parameters:

context - context of states

states - states that can be reached from the context

probabilities - transition probabilities from the context to the states

ess - the equivalent sample size (ess)

annotationID - identifier for decoding transition classes

weight - the weight for plotting the edge in Graphviz, enables to modify the edge length, larger weights imply shorter edges (default: 1)

ReferenceBasedTransitionElement

public ReferenceBasedTransitionElement(StringBuffer xml)
                                throws NonParsableException

The standard constructor for the interface Storable. Constructs a ReferenceBasedTransitionElement out of an XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the ReferenceBasedTransitionElement could not be reconstructed out of the StringBuffer xml

Method Detail

init

protected void init()

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

This method initializes internal fields.

Overrides:

init in class BasicHigherOrderTransition.AbstractTransitionElement

clone

public ReferenceBasedTransitionElement clone()
                                      throws CloneNotSupportedException

Overrides:

clone in class BasicHigherOrderTransition.AbstractTransitionElement

Throws:

CloneNotSupportedException

determineDiagonalElement

protected void determineDiagonalElement()

This method determines the self transition.

See Also:

diagElement

precompute

protected void precompute()

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

This method precomputes internal fields as for instance the normalization constant.

Overrides:

precompute in class BasicHigherOrderTransition.AbstractTransitionElement

See Also:

BasicHigherOrderTransition.AbstractTransitionElement.logNorm

getLogPriorTerm

public double getLogPriorTerm()

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

Returns a value that is proportional to the log of the prior. For maximum likelihood (ML) 0 should be returned.

Overrides:

getLogPriorTerm in class BasicHigherOrderTransition.AbstractTransitionElement

Returns:

a value that is proportional to the log of the prior

See Also:

Transition.getLogPriorTerm()

getLogGammaScoreFromStatistic

public double getLogGammaScoreFromStatistic()

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

This method calculates a score for the current statistics, which is independent from the current parameters In general the gamma-score is a product of gamma-functions parameterized with the current statistics

Overrides:

getLogGammaScoreFromStatistic in class BasicHigherOrderTransition.AbstractTransitionElement

Returns:

the logarithm of the gamma-score for the current statistics

initializeRandomly

public void initializeRandomly()

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

This method draws new parameters from the prior.

Overrides:

initializeRandomly in class BasicHigherOrderTransition.AbstractTransitionElement

appendFurtherInformation

protected void appendFurtherInformation(StringBuffer xml)

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

This method appends further information to the XML representation. It allows subclasses to save further parameters that are not defined in the superclass.

Overrides:

appendFurtherInformation in class BasicTransitionElement

Parameters:

xml - the XML representation

extractFurtherInformation

protected void extractFurtherInformation(StringBuffer xml)
                                  throws NonParsableException

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

This method extracts further information from the XML representation. It allows subclasses to cast further parameters that are not defined in the superclass.

Overrides:

extractFurtherInformation in class BasicTransitionElement

Parameters:

xml - the XML representation

Throws:

NonParsableException - if the information could not be reconstructed out of the StringBuffer xml