de.jstacs.scoringFunctions.mix
Class MixtureScoringFunction

java.lang.Object
  de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction
      de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction
          de.jstacs.scoringFunctions.mix.MixtureScoringFunction

All Implemented Interfaces:

NormalizableScoringFunction, ScoringFunction, Storable, Cloneable

public class MixtureScoringFunction
extends AbstractMixtureScoringFunction

This class implements a real mixture model.

Author:

Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction

componentScore, dList, function, hiddenParameter, hiddenPotential, iList, isNormalized, logGammaSum, logHiddenNorm, logHiddenPotential, norm, optimizeHidden, paramRef, partNorm, plugIn

Fields inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction

alphabets, length, r

Fields inherited from interface de.jstacs.scoringFunctions.ScoringFunction

UNKNOWN

Constructor Summary

MixtureScoringFunction(int starts, boolean plugIn, NormalizableScoringFunction... component)
This constructor creates a mixture.

MixtureScoringFunction(StringBuffer xml)
This is the constructor for Storable.

Method Summary

protected void	fillComponentScores(Sequence seq, int start) Fills the internal array componentScore with the log scores of the components.
double	getEss() Returns the equivalent sample size of this model, i.e. the equivalent sample size for the class or component that is represented by this model.
double	getHyperparameterForHiddenParameter(int index) This method returns the hyperparameter for the hidden parameter with index index.
String	getInstanceName() Returns a short instance name.
double	getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList partialDer) Returns the log score for the sequence and fills the list with the indices and the partial derivations.
protected double	getNormalizationConstantForComponent(int i) Computes the normalization constant for the component i
double	getPartialNormalizationConstant(int parameterIndex) Returns the partial normalization constant for the parameter with index parameterIndex.
protected void	initializeUsingPlugIn(int index, boolean freeParams, Sample[] data, double[][] weights) This method initializes the function using the data in some way.
String	toString()

Methods inherited from class de.jstacs.scoringFunctions.mix.AbstractMixtureScoringFunction

addGradientOfLogPriorTerm, clone, cloneFunctions, computeHiddenParameter, computeLogGammaSum, extractFurtherInformation, fromXML, getCurrentParameterValues, getFunction, getFunctions, getFurtherInformation, getIndexOfMaximalComponentFor, getIndices, getLogPriorTerm, getLogScore, getMaxIndex, getNormalizationConstant, getNumberOfComponents, getNumberOfParameters, getNumberOfRecommendedStarts, getProbsForComponent, getScoringFunctions, getSizeOfEventSpaceForRandomVariablesOfParameter, getXMLTag, init, initializeFunction, initializeFunctionRandomly, initializeHiddenPotentialRandomly, initializeHiddenUniformly, initWithLength, isInitialized, isNormalized, precomputeNorm, setHiddenParameters, setParameters, setParametersForFunction, toXML

Methods inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction

getAlphabetContainer, getInitialClassParam, getLength, getLogScore, getLogScoreAndPartialDerivation, isNormalized

Methods inherited from class java.lang.Object

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

Constructor Detail

MixtureScoringFunction

public MixtureScoringFunction(int starts,
                              boolean plugIn,
                              NormalizableScoringFunction... component)
                       throws CloneNotSupportedException

This constructor creates a mixture.

Parameters:

starts - the number of starts the should be done in an optimization

plugIn - whether the initial parameters for an optimization should be related to the data or randomly drawn

component - the ScoringFunctions

Throws:

CloneNotSupportedException

MixtureScoringFunction

public MixtureScoringFunction(StringBuffer xml)
                       throws NonParsableException

This is the constructor for Storable.

Parameters:

xml - the xml representation

Throws:

NonParsableException - if the representation could not be parsed.

Method Detail

getNormalizationConstantForComponent

protected double getNormalizationConstantForComponent(int i)

Description copied from class: AbstractMixtureScoringFunction

Computes the normalization constant for the component i

Specified by:

getNormalizationConstantForComponent in class AbstractMixtureScoringFunction

Parameters:

i - the index of the component

Returns:

the normalization constant

getPartialNormalizationConstant

public double getPartialNormalizationConstant(int parameterIndex)
                                       throws Exception

Description copied from interface: NormalizableScoringFunction

Returns the partial normalization constant for the parameter with index parameterIndex. This is the partial derivation of the normalization constant for the parameter with index parameterIndex \frac{\partial Z(\lambda)}{\partial \lambda_{index}}.

Parameters:

parameterIndex - the index of the parameter

Returns:

the partial normalization constant

Throws:

Exception - if something went wrong with the Normalization

getHyperparameterForHiddenParameter

public double getHyperparameterForHiddenParameter(int index)

Description copied from class: AbstractMixtureScoringFunction

This method returns the hyperparameter for the hidden parameter with index index.

Specified by:

getHyperparameterForHiddenParameter in class AbstractMixtureScoringFunction

Parameters:

index - the index

Returns:

the hyperparameter

getEss

public double getEss()

Description copied from interface: NormalizableScoringFunction

Returns the equivalent sample size of this model, i.e. the equivalent sample size for the class or component that is represented by this model.

Returns:

the equivalent sample size.

initializeUsingPlugIn

protected void initializeUsingPlugIn(int index,
                                     boolean freeParams,
                                     Sample[] data,
                                     double[][] weights)
                              throws Exception

Description copied from class: AbstractMixtureScoringFunction

This method initializes the function using the data in some way.

Specified by:

initializeUsingPlugIn in class AbstractMixtureScoringFunction

Parameters:

index - the class index

freeParams - if true, the (reduced) parameterization is used

data - the data

weights - the weights

Throws:

Exception - if the initialization could not be done

See Also:

ScoringFunction.initializeFunction(int, boolean, Sample[], double[][])

getInstanceName

public String getInstanceName()

Description copied from interface: ScoringFunction

Returns a short instance name.

Returns:

a short instance name

fillComponentScores

protected void fillComponentScores(Sequence seq,
                                   int start)

Description copied from class: AbstractMixtureScoringFunction

Fills the internal array componentScore with the log scores of the components.

Specified by:

fillComponentScores in class AbstractMixtureScoringFunction

Parameters:

seq - the sequence

start - the start position

getLogScoreAndPartialDerivation

public double getLogScoreAndPartialDerivation(Sequence seq,
                                              int start,
                                              IntList indices,
                                              DoubleList partialDer)

Description copied from interface: ScoringFunction

Returns the log score for the sequence and fills the list with the indices and the partial derivations.

Parameters:

seq - the sequence

start - the startposition in the sequence

indices - after method invocation the list should contain the indices i where \frac{\partial \log score(seq)}{\partial \lambda_i} is not zero

partialDer - after method invocation the list should contain the corresponding \frac{\partial \log score(seq)}{\partial \lambda_i}

Returns:

the log score

toString

public String toString()

Overrides:

toString in class Object