de.jstacs.sequenceScores.statisticalModels.differentiable

Class AbstractVariableLengthDiffSM

java.lang.Object

de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

de.jstacs.sequenceScores.statisticalModels.differentiable.AbstractDifferentiableStatisticalModel

de.jstacs.sequenceScores.statisticalModels.differentiable.AbstractVariableLengthDiffSM

All Implemented Interfaces:

DifferentiableSequenceScore, SequenceScore, DifferentiableStatisticalModel, VariableLengthDiffSM, StatisticalModel, Storable, Cloneable

Direct Known Subclasses:

CyclicMarkovModelDiffSM, HomogeneousDiffSM

public abstract class AbstractVariableLengthDiffSM
extends AbstractDifferentiableStatisticalModel
implements VariableLengthDiffSM

This abstract class implements some methods declared in DifferentiableStatisticalModel based on the declaration of methods in VariableLengthDiffSM. It allows to score subsequences of arbitrary length. This DifferentiableStatisticalModel should be the super class for non-motif DifferentiableStatisticalModels like homogeneous Markov models, cyclic Markov models, ... etc.

Author:

Jens Keilwagen

Field Summary

Fields inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

alphabets, length, r

Fields inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore

UNKNOWN

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractVariableLengthDiffSM(AlphabetContainer alphabets) This is the main constructor that creates an instance of a VariableLengthDiffSM that models sequences of arbitrary length.
protected	AbstractVariableLengthDiffSM(AlphabetContainer alphabets, int length) This is the main constructor that creates an instance of a VariableLengthDiffSM that models sequences of a given length.
protected	AbstractVariableLengthDiffSM(StringBuffer source) This is the constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
double	getLogNormalizationConstant() Returns the logarithm of the sum of the scores over all sequences of the event space.
double	getLogPartialNormalizationConstant(int parameterIndex) Returns the logarithm of the partial normalization constant for the parameter with index parameterIndex.
abstract double	getLogScoreAndPartialDerivation(Sequence seq, int startpos, int endpos, IntList indices, DoubleList partialDer) Returns the logarithmic score for a Sequence beginning at position start in the Sequence and fills lists with the indices and the partial derivations.
double	getLogScoreAndPartialDerivation(Sequence seq, int start, IntList indices, DoubleList dList) Returns the logarithmic score for a Sequence beginning at position start in the Sequence and fills lists with the indices and the partial derivations.
double	getLogScoreFor(Sequence seq, int start) Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.
abstract double	getLogScoreFor(Sequence seq, int startpos, int endpos) Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.differentiable.AbstractDifferentiableStatisticalModel

clone, emitDataSet, getInitialClassParam, getLogProbFor, getLogProbFor, getLogProbFor, getLogScoreFor, getLogScoreFor, getMaximalMarkovOrder, isNormalized, isNormalized

Methods inherited from class de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

fromXML, getAlphabetContainer, getCharacteristics, getLength, getLogScoreAndPartialDerivation, getLogScoreFor, getNumberOfRecommendedStarts, getNumberOfStarts, getNumericalCharacteristics, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.differentiable.VariableLengthDiffSM

getLogNormalizationConstant, getLogPartialNormalizationConstant, setStatisticForHyperparameters

Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.differentiable.DifferentiableStatisticalModel

addGradientOfLogPriorTerm, getESS, getLogPriorTerm, getSizeOfEventSpaceForRandomVariablesOfParameter, isNormalized

Methods inherited from interface de.jstacs.sequenceScores.differentiable.DifferentiableSequenceScore

clone, getCurrentParameterValues, getInitialClassParam, getLogScoreAndPartialDerivation, getNumberOfParameters, getNumberOfRecommendedStarts, initializeFunction, initializeFunctionRandomly, setParameters

Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.StatisticalModel

emitDataSet, getLogProbFor, getLogProbFor, getLogProbFor, getMaximalMarkovOrder

Methods inherited from interface de.jstacs.sequenceScores.SequenceScore

getAlphabetContainer, getCharacteristics, getInstanceName, getLength, getLogScoreFor, getLogScoreFor, getLogScoreFor, getNumericalCharacteristics, isInitialized, toString

Methods inherited from interface de.jstacs.Storable

toXML

Constructor Detail

AbstractVariableLengthDiffSM

protected AbstractVariableLengthDiffSM(AlphabetContainer alphabets)

This is the main constructor that creates an instance of a VariableLengthDiffSM that models sequences of arbitrary length.

Parameters:

alphabets - the AlphabetContainer of this VariableLengthDiffSM

See Also:

AbstractVariableLengthDiffSM(AlphabetContainer, int)

AbstractVariableLengthDiffSM

protected AbstractVariableLengthDiffSM(AlphabetContainer alphabets,
                                       int length)

This is the main constructor that creates an instance of a VariableLengthDiffSM that models sequences of a given length.

Parameters:

alphabets - the AlphabetContainer of this VariableLengthDiffSM

length - the length of the modeled sequences

AbstractVariableLengthDiffSM

protected AbstractVariableLengthDiffSM(StringBuffer source)
                                throws NonParsableException

This is the constructor for the interface Storable. Creates a new VariableLengthDiffSM out of its XML representation.

Parameters:

source - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML representation could not be parsed.

Method Detail

getLogNormalizationConstant

public double getLogNormalizationConstant()

Description copied from interface: DifferentiableStatisticalModel

Returns the logarithm of the sum of the scores over all sequences of the event space.

Specified by:

getLogNormalizationConstant in interface DifferentiableStatisticalModel

Returns:

the logarithm of the normalization constant Z

getLogPartialNormalizationConstant

public double getLogPartialNormalizationConstant(int parameterIndex)
                                          throws Exception

Description copied from interface: DifferentiableStatisticalModel

Returns the logarithm of the partial normalization constant for the parameter with index parameterIndex. This is the logarithm of the partial derivation of the normalization constant for the parameter with index parameterIndex,

.

Specified by:

getLogPartialNormalizationConstant in interface DifferentiableStatisticalModel

Parameters:

parameterIndex - the index of the parameter

Returns:

the logarithm of the partial normalization constant

Throws:

Exception - if something went wrong with the normalization

See Also:

DifferentiableStatisticalModel.getLogNormalizationConstant()

getLogScoreFor

public double getLogScoreFor(Sequence seq,
                             int start)

Description copied from interface: SequenceScore

Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.

Specified by:

getLogScoreFor in interface SequenceScore

Parameters:

seq - the Sequence

start - the start position in the Sequence

Returns:

the logarithmic score for the Sequence

getLogScoreAndPartialDerivation

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

Description copied from interface: DifferentiableSequenceScore

Returns the logarithmic score for a Sequence beginning at position start in the Sequence and fills lists with the indices and the partial derivations.

Specified by:

getLogScoreAndPartialDerivation in interface DifferentiableSequenceScore

Parameters:

seq - the Sequence

start - the start position in the Sequence

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

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

Returns:

the logarithmic score for the Sequence

getLogScoreFor

public abstract double getLogScoreFor(Sequence seq,
                                      int startpos,
                                      int endpos)

Description copied from interface: SequenceScore

Returns the logarithmic score for the Sequence seq beginning at position start in the Sequence.

Specified by:

getLogScoreFor in interface SequenceScore

Specified by:

getLogScoreFor in interface VariableLengthDiffSM

Overrides:

getLogScoreFor in class AbstractDifferentiableSequenceScore

Parameters:

seq - the Sequence

startpos - the start position in the Sequence

endpos - the end position (inclusive) in the Sequence

Returns:

the logarithmic score for the Sequence

getLogScoreAndPartialDerivation

public abstract double getLogScoreAndPartialDerivation(Sequence seq,
                                                       int startpos,
                                                       int endpos,
                                                       IntList indices,
                                                       DoubleList partialDer)

Description copied from interface: DifferentiableSequenceScore

Returns the logarithmic score for a Sequence beginning at position start in the Sequence and fills lists with the indices and the partial derivations.

Specified by:

getLogScoreAndPartialDerivation in interface DifferentiableSequenceScore

Specified by:

getLogScoreAndPartialDerivation in interface VariableLengthDiffSM

Overrides:

getLogScoreAndPartialDerivation in class AbstractDifferentiableSequenceScore

Parameters:

seq - the Sequence

startpos - the start position in the Sequence

endpos - the end position (inclusive) 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 logarithmic score for the Sequence