de.jstacs.scoringFunctions.mix
Class VariableLengthMixtureScoringFunction

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

All Implemented Interfaces:

MotifDiscoverer, MutableMotifDiscoverer, NormalizableScoringFunction, ScoringFunction, VariableLengthScoringFunction, Storable, Cloneable

public class VariableLengthMixtureScoringFunction
extends MixtureScoringFunction
implements VariableLengthScoringFunction

This class implements a mixture of VariableLengthScoringFunction by extending MixtureScoringFunction and implementing the methods of VariableLengthScoringFunction.

Author:

Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer

MotifDiscoverer.KindOfProfile

Field Summary

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

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

Fields inherited from class de.jstacs.scoringFunctions.AbstractNormalizableScoringFunction

alphabets, length, r

Fields inherited from interface de.jstacs.scoringFunctions.ScoringFunction

UNKNOWN

Constructor Summary

VariableLengthMixtureScoringFunction(int starts, boolean plugIn, VariableLengthScoringFunction... component)
This constructor creates a new VariableLengthMixtureScoringFunction.

VariableLengthMixtureScoringFunction(StringBuffer xml)
This is the constructor for the interface Storable.

Method Summary

double	getLogNormalizationConstant(int length) This method returns the logarithm of the normalization constant for a given sequence length.
double	getLogPartialNormalizationConstant(int parameterIndex, int length) This method returns the logarithm of the partial normalization constant for a given parameter index and a sequence length.
double	getLogScore(Sequence seq, int start, int length) This method computes the logarithm of the score for a given subsequence.
double	getLogScoreAndPartialDerivation(Sequence seq, int start, int length, IntList indices, DoubleList partialDer) This method computes the logarithm of the score and the partial derivations for a given subsequence.
void	setStatisticForHyperparameters(int[] length, double[] weight) This method sets the hyperparameters for the model parameters by evaluating the given statistic.

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

adjustHiddenParameters, clone, fillComponentScores, getEss, getGlobalIndexOfMotifInComponent, getHyperparameterForHiddenParameter, getIndexOfMaximalComponentFor, getInstanceName, getLogNormalizationConstantForComponent, getLogPartialNormalizationConstant, getLogScoreAndPartialDerivation, getMotifLength, getNumberOfMotifs, getNumberOfMotifsInComponent, getProfileOfScoresFor, getStrandProbabilitiesFor, initializeMotif, initializeMotifRandomly, initializeUsingPlugIn, modifyMotif, toString

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

addGradientOfLogPriorTerm, cloneFunctions, computeHiddenParameter, computeLogGammaSum, determineIsNormalized, extractFurtherInformation, fromXML, getCurrentParameterValues, getFunction, getFunctions, getFurtherInformation, getIndexOfMaximalComponentFor, getIndices, getLogNormalizationConstant, getLogPriorTerm, getLogScore, 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, getNumberOfStarts, isNormalized

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.jstacs.scoringFunctions.NormalizableScoringFunction

addGradientOfLogPriorTerm, getEss, getInitialClassParam, getLogNormalizationConstant, getLogPartialNormalizationConstant, getLogPriorTerm, getSizeOfEventSpaceForRandomVariablesOfParameter, isNormalized

Methods inherited from interface de.jstacs.scoringFunctions.ScoringFunction

clone, getAlphabetContainer, getCurrentParameterValues, getInstanceName, getLength, getLogScore, getLogScore, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getNumberOfParameters, getNumberOfRecommendedStarts, initializeFunction, initializeFunctionRandomly, isInitialized, setParameters

Methods inherited from interface de.jstacs.Storable

toXML

Methods inherited from interface de.jstacs.motifDiscovery.MotifDiscoverer

getNumberOfComponents

Constructor Detail

VariableLengthMixtureScoringFunction

public VariableLengthMixtureScoringFunction(int starts,
                                            boolean plugIn,
                                            VariableLengthScoringFunction... component)
                                     throws CloneNotSupportedException

This constructor creates a new VariableLengthMixtureScoringFunction.

Parameters:

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

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

component - the VariableLengthScoringFunctions

Throws:

CloneNotSupportedException - if an element of component could not be cloned

VariableLengthMixtureScoringFunction

public VariableLengthMixtureScoringFunction(StringBuffer xml)
                                     throws NonParsableException

This is the constructor for the interface Storable. Creates a new VariableLengthMixtureScoringFunction out of a StringBuffer.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

getLogScore

public double getLogScore(Sequence seq,
                          int start,
                          int length)

Description copied from interface: VariableLengthScoringFunction

This method computes the logarithm of the score for a given subsequence.

Specified by:

getLogScore in interface VariableLengthScoringFunction

Parameters:

seq - the Sequence

start - the start index in the Sequence

length - the length of the Sequence beginning at start

Returns:

the logarithm of the score for the subsequence

See Also:

ScoringFunction.getLogScore(Sequence, int)

getLogScoreAndPartialDerivation

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

Description copied from interface: VariableLengthScoringFunction

This method computes the logarithm of the score and the partial derivations for a given subsequence.

Specified by:

getLogScoreAndPartialDerivation in interface VariableLengthScoringFunction

Parameters:

seq - the Sequence

start - the start index in the Sequence

length - the end index in the Sequence

indices - an IntList of indices, after method invocation the list should contain the indices i where is not zero

partialDer - a DoubleList of partial derivations, after method invocation the list should contain the corresponding that are not zero

Returns:

the logarithm of the score

See Also:

ScoringFunction.getLogScoreAndPartialDerivation(Sequence, int, IntList, DoubleList)

getLogNormalizationConstant

public double getLogNormalizationConstant(int length)

Description copied from interface: VariableLengthScoringFunction

This method returns the logarithm of the normalization constant for a given sequence length.

Specified by:

getLogNormalizationConstant in interface VariableLengthScoringFunction

Parameters:

length - the sequence length

Returns:

the logarithm of the normalization constant

See Also:

NormalizableScoringFunction.getLogNormalizationConstant()

getLogPartialNormalizationConstant

public double getLogPartialNormalizationConstant(int parameterIndex,
                                                 int length)
                                          throws Exception

Description copied from interface: VariableLengthScoringFunction

This method returns the logarithm of the partial normalization constant for a given parameter index and a sequence length.

Specified by:

getLogPartialNormalizationConstant in interface VariableLengthScoringFunction

Parameters:

parameterIndex - the index of the parameter

length - the sequence length

Returns:

the logarithm of the partial normalization constant

Throws:

Exception - if something went wrong

See Also:

NormalizableScoringFunction.getLogPartialNormalizationConstant(int)

setStatisticForHyperparameters

public void setStatisticForHyperparameters(int[] length,
                                           double[] weight)
                                    throws Exception

Description copied from interface: VariableLengthScoringFunction

This method sets the hyperparameters for the model parameters by evaluating the given statistic. The statistic can be interpreted as follows: The model has seen a number of sequences. From these sequences it is only known how long (length) and how often ( weight) they have been seen.

Specified by:

setStatisticForHyperparameters in interface VariableLengthScoringFunction

Parameters:

length - the non-negative lengths of the sequences

weight - the non-negative weight for the corresponding sequence

Throws:

Exception - if something went wrong

See Also:

Mutable