de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous

Class MultivariateGaussianEmission

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.states.emissions.continuous.MultivariateGaussianEmission

All Implemented Interfaces:

Emission, Storable, Cloneable

public class MultivariateGaussianEmission
extends Object
implements Emission

Multivariate Gaussian emission density for a Hidden Markov Model.

Author:

Michael Seifert, Jens Keilwagen

Field Summary

Fields

Modifier and Type	Field and Description
protected HashMap<Sequence,double[]>	gammas Contains the emission sequences and corresponding gammas (state-posteriors) required for the estimation of the standard deviation.

Constructor Summary

Constructors

Constructor and Description
MultivariateGaussianEmission(double[] mean, double[] sds, double[][] correlation, double scaleMean, double[] aprioriMean, double shapeSd, double[][] scaleSd) Creates a Multivariate Gaussian emission density.
MultivariateGaussianEmission(StringBuffer xml) Creates a MultivariateGaussianEmission from its XML representation.

Method Summary

Modifier and Type	Method and Description
void	addToStatistic(boolean forward, int startPos, int endPos, double weight, Sequence seq) This method adds the weight to the internal sufficient statistic.
MultivariateGaussianEmission	clone()
void	estimateFromStatistic() This method estimates the parameters from the internal sufficient statistic.
protected void	fromXML(StringBuffer xml) Parses the XML representation.
AlphabetContainer	getAlphabetContainer() This method returns the AlphabetContainer of this emission.
double	getLogPriorTerm() Returns a value that is proportional to the log of the prior.
double	getLogProbFor(boolean forward, int startPos, int endPos, Sequence seq) This method computes the logarithm of the likelihood.
String	getNodeLabel(double weight, String name, NumberFormat nf) Returns the graphviz label of the node containing this emission.
String	getNodeShape(boolean forward) Returns the graphviz string for the shape of the node.
void	initializeFunctionRandomly() This method initializes the emission randomly.
void	joinStatistics(Emission... emissions) This method joins the statistics of different instances and sets this joined statistic as statistic of each instance.
void	resetStatistic() This method resets the internal sufficient statistic.
void	setParameters(Emission t) Set values of parameters of the instance to the value of the parameters of the given instance.
String	toString(NumberFormat nf) This method returns a String representation of the instance.
StringBuffer	toXML() This method returns an XML representation as StringBuffer of an instance of the implementing class.

Methods inherited from class java.lang.Object

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

Field Detail

gammas

protected HashMap<Sequence,double[]> gammas

Contains the emission sequences and corresponding gammas (state-posteriors) required for the estimation of the standard deviation.

Constructor Detail

MultivariateGaussianEmission

public MultivariateGaussianEmission(double[] mean,
                                    double[] sds,
                                    double[][] correlation,
                                    double scaleMean,
                                    double[] aprioriMean,
                                    double shapeSd,
                                    double[][] scaleSd)

Creates a Multivariate Gaussian emission density.

Parameters:

mean - mean vector

sds - standard deviation vector

correlation - correlation matrix

scaleMean - scale of a priori mean

aprioriMean - a priori mean

shapeSd - scale for scaleSd (a covariance matrix)

scaleSd - a priori covariance matrix

MultivariateGaussianEmission

public MultivariateGaussianEmission(StringBuffer xml)
                             throws NonParsableException

Creates a MultivariateGaussianEmission from its XML representation.

Parameters:

xml - the XML representation.

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

addToStatistic

public void addToStatistic(boolean forward,
                           int startPos,
                           int endPos,
                           double weight,
                           Sequence seq)
                    throws OperationNotSupportedException

Description copied from interface: Emission

This method adds the weight to the internal sufficient statistic.

Specified by:

addToStatistic in interface Emission

Parameters:

forward - whether to use the forward or the reverse strand

startPos - the start position

endPos - the end position

weight - the weight of the sequence

seq - the sequence

Throws:

OperationNotSupportedException - if forward=false and the reverse complement of the sequence seq is not defined

joinStatistics

public void joinStatistics(Emission... emissions)

Description copied from interface: Emission

This method joins the statistics of different instances and sets this joined statistic as statistic of each instance. This method might be used for instance in a multi-threaded optimization to join partial statistics.

Specified by:

joinStatistics in interface Emission

Parameters:

emissions - the emissions to be joined

estimateFromStatistic

public void estimateFromStatistic()

Description copied from interface: Emission

This method estimates the parameters from the internal sufficient statistic.

Specified by:

estimateFromStatistic in interface Emission

getAlphabetContainer

public AlphabetContainer getAlphabetContainer()

Description copied from interface: Emission

This method returns the AlphabetContainer of this emission.

Specified by:

getAlphabetContainer in interface Emission

Returns:

the AlphabetContainer of this emission

getLogPriorTerm

public double getLogPriorTerm()

Description copied from interface: Emission

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

Specified by:

getLogPriorTerm in interface Emission

Returns:

a value that is proportional to the log of the prior

See Also:

StatisticalModel.getLogPriorTerm()

getLogProbFor

public double getLogProbFor(boolean forward,
                            int startPos,
                            int endPos,
                            Sequence seq)
                     throws OperationNotSupportedException

Description copied from interface: Emission

This method computes the logarithm of the likelihood.

Specified by:

getLogProbFor in interface Emission

Parameters:

forward - whether to use the forward or the reverse strand

startPos - the start position

endPos - the end position

seq - the sequence

Returns:

the logarithm of the probability

Throws:

OperationNotSupportedException - if forward=false and the reverse complement of the sequence seq is not defined

getNodeLabel

public String getNodeLabel(double weight,
                           String name,
                           NumberFormat nf)

Description copied from interface: Emission

Returns the graphviz label of the node containing this emission.

Specified by:

getNodeLabel in interface Emission

Parameters:

weight - the weight of the node which is represented by the color of the node, or -1 for no representation, i.e., white background

name - the name of the state using this emission

nf - the NumberFormat for formatting the textual representation of this emission

Returns:

the label

getNodeShape

public String getNodeShape(boolean forward)

Description copied from interface: Emission

Returns the graphviz string for the shape of the node.

Specified by:

getNodeShape in interface Emission

Parameters:

forward - if this emission is used on the forward strand

Returns:

the shape

initializeFunctionRandomly

public void initializeFunctionRandomly()

Description copied from interface: Emission

This method initializes the emission randomly.

Specified by:

initializeFunctionRandomly in interface Emission

resetStatistic

public void resetStatistic()

Description copied from interface: Emission

This method resets the internal sufficient statistic.

Specified by:

resetStatistic in interface Emission

toXML

public StringBuffer toXML()

Description copied from interface: Storable

This method returns an XML representation as StringBuffer of an instance of the implementing class.

Specified by:

toXML in interface Storable

Returns:

the XML representation

fromXML

protected void fromXML(StringBuffer xml)
                throws NonParsableException

Parses the XML representation.

Parameters:

xml - the XML representation

Throws:

NonParsableException - if the XML could not be parsed

toString

public String toString(NumberFormat nf)

Description copied from interface: Emission

This method returns a String representation of the instance.

Specified by:

toString in interface Emission

Parameters:

nf - the NumberFormat for the String representation of parameters or probabilities

Returns:

a String representation of the instance

clone

public MultivariateGaussianEmission clone()
                                   throws CloneNotSupportedException

Overrides:

clone in class Object

Throws:

CloneNotSupportedException

setParameters

public void setParameters(Emission t)
                   throws IllegalArgumentException

Description copied from interface: Emission

Set values of parameters of the instance to the value of the parameters of the given instance. It can be assumed that the given instance and the current instance are from the same class. This method might be used for instance in a multi-threaded optimization to broadcast the parameters.

Specified by:

setParameters in interface Emission

Parameters:

t - the emission with the parameters to be set

Throws:

IllegalArgumentException - if the assumption about the same class for given and current instance is wrong