de.jstacs.sequenceScores.differentiable

Interface DifferentiableSequenceScore

All Superinterfaces:

Cloneable, SequenceScore, Storable

All Known Subinterfaces:

DifferentiableStatisticalModel, SamplingDifferentiableStatisticalModel, VariableLengthDiffSM

All Known Implementing Classes:

AbstractDifferentiableSequenceScore, AbstractDifferentiableStatisticalModel, AbstractMixtureDiffSM, AbstractVariableLengthDiffSM, BayesianNetworkDiffSM, CyclicMarkovModelDiffSM, DifferentiableHigherOrderHMM, DurationDiffSM, ExtendedZOOPSDiffSM, HomogeneousDiffSM, HomogeneousMM0DiffSM, HomogeneousMMDiffSM, IndependentProductDiffSM, IndependentProductDiffSS, LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder, LogisticDiffSS, MappingDiffSM, MarkovModelDiffSM, MarkovRandomFieldDiffSM, MixtureDiffSM, MixtureDurationDiffSM, MultiDimensionalSequenceWrapperDiffSS, NormalizedDiffSM, PositionDiffSM, SkewNormalLikeDurationDiffSM, StrandDiffSM, UniformDiffSM, UniformDiffSS, UniformDurationDiffSM, UniformHomogeneousDiffSM, VariableLengthMixtureDiffSM

public interface DifferentiableSequenceScore
extends SequenceScore

This interface is the main part of any ScoreClassifier.

Author:

Jens Keilwagen, Jan Grau

Field Summary

Fields

Modifier and Type	Field and Description
static int	UNKNOWN Indicates that the number of parameters of this DifferentiableSequenceScore is not known (yet).

Method Summary

Modifier and Type	Method and Description
DifferentiableSequenceScore	clone() Creates a clone (deep copy) of the current DifferentiableSequenceScore instance.
double[]	getCurrentParameterValues() Returns a double array of dimension getNumberOfParameters() containing the current parameter values.
double	getInitialClassParam(double classProb) Returns the initial class parameter for the class this DifferentiableSequenceScore is responsible for, based on the class probability classProb.
double	getLogScoreAndPartialDerivation(Sequence seq, int start, int end, 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 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, IntList indices, DoubleList partialDer) Returns the logarithmic score for a Sequence seq and fills lists with the indices and the partial derivations.
int	getNumberOfParameters() Returns the number of parameters in this DifferentiableSequenceScore.
int	getNumberOfRecommendedStarts() This method returns the number of recommended optimization starts.
void	initializeFunction(int index, boolean freeParams, DataSet[] data, double[][] weights) This method creates the underlying structure of the DifferentiableSequenceScore.
void	initializeFunctionRandomly(boolean freeParams) This method initializes the DifferentiableSequenceScore randomly.
void	setParameters(double[] params, int start) This method sets the internal parameters to the values of params between start and start + getNumberOfParameters() - 1

Methods inherited from interface de.jstacs.sequenceScores.SequenceScore

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

Methods inherited from interface de.jstacs.Storable

toXML

Field Detail

UNKNOWN

static final int UNKNOWN

Indicates that the number of parameters of this DifferentiableSequenceScore is not known (yet).

See Also:

Constant Field Values

Method Detail

clone

DifferentiableSequenceScore clone()
                           throws CloneNotSupportedException

Creates a clone (deep copy) of the current DifferentiableSequenceScore instance.

Specified by:

clone in interface SequenceScore

Returns:

the cloned instance of the current DifferentiableSequenceScore

Throws:

CloneNotSupportedException - if something went wrong while cloning the DifferentiableSequenceScore

initializeFunction

void initializeFunction(int index,
                        boolean freeParams,
                        DataSet[] data,
                        double[][] weights)
                 throws Exception

This method creates the underlying structure of the DifferentiableSequenceScore.

Parameters:

index - the index of the class the DifferentiableSequenceScore models

freeParams - indicates whether the (reduced) parameterization is used

data - the data sets

weights - the weights of the sequences in the data sets

Throws:

Exception - if something went wrong

initializeFunctionRandomly

void initializeFunctionRandomly(boolean freeParams)
                         throws Exception

This method initializes the DifferentiableSequenceScore randomly. It has to create the underlying structure of the DifferentiableSequenceScore.

Parameters:

freeParams - indicates whether the (reduced) parameterization is used

Throws:

Exception - if something went wrong

getLogScoreAndPartialDerivation

double getLogScoreAndPartialDerivation(Sequence seq,
                                       IntList indices,
                                       DoubleList partialDer)

Returns the logarithmic score for a Sequence seq and fills lists with the indices and the partial derivations.

Parameters:

seq - 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

getLogScoreAndPartialDerivation

double getLogScoreAndPartialDerivation(Sequence seq,
                                       int start,
                                       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.

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

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

getLogScoreAndPartialDerivation

double getLogScoreAndPartialDerivation(Sequence seq,
                                       int start,
                                       int end,
                                       IntList indices,
                                       DoubleList partialDer)
                                throws Exception

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

Parameters:

seq - the Sequence

start - the start position in the Sequence

end - 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

Throws:

Exception - if, for instance, the subsequence length can not be handled

getNumberOfParameters

int getNumberOfParameters()

Returns the number of parameters in this DifferentiableSequenceScore. If the number of parameters is not known yet, the method returns UNKNOWN.

Returns:

the number of parameters in this DifferentiableSequenceScore

See Also:

UNKNOWN

getNumberOfRecommendedStarts

int getNumberOfRecommendedStarts()

This method returns the number of recommended optimization starts. The standard implementation returns 1.

Returns:

the number of recommended optimization starts

getCurrentParameterValues

double[] getCurrentParameterValues()
                            throws Exception

Returns a double array of dimension getNumberOfParameters() containing the current parameter values. If one likes to use these parameters to start an optimization it is highly recommended to invoke initializeFunction(int, boolean, DataSet[], double[][]) before. After an optimization this method can be used to get the current parameter values.

Returns:

the current parameter values

Throws:

Exception - if no parameters exist (yet)

setParameters

void setParameters(double[] params,
                   int start)

This method sets the internal parameters to the values of params between start and start + getNumberOfParameters() - 1

Parameters:

params - the new parameters

start - the start index in params

getInitialClassParam

double getInitialClassParam(double classProb)

Returns the initial class parameter for the class this DifferentiableSequenceScore is responsible for, based on the class probability classProb.

Parameters:

classProb - the class probability

Returns:

the initial class parameter