de.jstacs.sequenceScores.statisticalModels.differentiable

Class AbstractDifferentiableStatisticalModel

java.lang.Object

de.jstacs.sequenceScores.differentiable.AbstractDifferentiableSequenceScore

de.jstacs.sequenceScores.statisticalModels.differentiable.AbstractDifferentiableStatisticalModel

All Implemented Interfaces:

DifferentiableSequenceScore, SequenceScore, DifferentiableStatisticalModel, StatisticalModel, Storable, Cloneable

Direct Known Subclasses:

AbstractMixtureDiffSM, AbstractVariableLengthDiffSM, BayesianNetworkDiffSM, LimitedSparseLocalInhomogeneousMixtureDiffSM_higherOrder, MappingDiffSM, MarkovRandomFieldDiffSM, NormalizedDiffSM, PositionDiffSM

public abstract class AbstractDifferentiableStatisticalModel
extends AbstractDifferentiableSequenceScore
implements DifferentiableStatisticalModel

This class is the main part of any ScoreClassifier. It implements many methods of the interface DifferentiableStatisticalModel.

Author:

Jens Keilwagen, Jan Grau

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

Constructor and Description
AbstractDifferentiableStatisticalModel(AlphabetContainer alphabets, int length) The main constructor.
AbstractDifferentiableStatisticalModel(StringBuffer xml) This is the constructor for Storable.

Method Summary

Modifier and Type	Method and Description
AbstractDifferentiableStatisticalModel	clone() Creates a clone (deep copy) of the current DifferentiableSequenceScore instance.
DataSet	emitDataSet(int numberOfSequences, int... seqLength) This method returns a DataSet object containing artificial sequence(s).
double	getInitialClassParam(double classProb) Returns the initial class parameter for the class this DifferentiableSequenceScore is responsible for, based on the class probability classProb.
double	getLogProbFor(Sequence sequence) Returns the logarithm of the probability of the given sequence given the model.
double	getLogProbFor(Sequence sequence, int startpos) Returns the logarithm of the probability of (a part of) the given sequence given the model.
double	getLogProbFor(Sequence sequence, int startpos, int endpos) Returns the logarithm of the probability of (a part of) the given sequence given the model.
double[]	getLogScoreFor(DataSet data) This method computes the logarithm of the scores of all sequences in the given data set.
void	getLogScoreFor(DataSet data, double[] res) This method computes and stores the logarithm of the scores for any sequence in the data set in the given double-array.
byte	getMaximalMarkovOrder() This method returns the maximal used Markov order, if possible.
boolean	isNormalized() This method indicates whether the implemented score is already normalized to 1 or not.
static boolean	isNormalized(DifferentiableSequenceScore... function) This method checks whether all given DifferentiableStatisticalModels are normalized.

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

fromXML, getAlphabetContainer, getCharacteristics, getLength, getLogScoreAndPartialDerivation, getLogScoreAndPartialDerivation, getLogScoreFor, 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.DifferentiableStatisticalModel

addGradientOfLogPriorTerm, getESS, getLogNormalizationConstant, getLogPartialNormalizationConstant, getLogPriorTerm, getSizeOfEventSpaceForRandomVariablesOfParameter

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

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

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

AbstractDifferentiableStatisticalModel

public AbstractDifferentiableStatisticalModel(AlphabetContainer alphabets,
                                              int length)
                                       throws IllegalArgumentException

The main constructor.

Parameters:

alphabets - the AlphabetContainer of this DifferentiableSequenceScore

length - the length of this DifferentiableSequenceScore, i.e. the length of the modeled sequences

Throws:

IllegalArgumentException - if the length is negative or does not match with AlphabetContainer.getPossibleLength()

AbstractDifferentiableStatisticalModel

public AbstractDifferentiableStatisticalModel(StringBuffer xml)
                                       throws NonParsableException

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

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the XML representation could not be parsed

Method Detail

clone

public AbstractDifferentiableStatisticalModel clone()
                                             throws CloneNotSupportedException

Description copied from interface: DifferentiableSequenceScore

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

Specified by:

clone in interface DifferentiableSequenceScore

Specified by:

clone in interface SequenceScore

Overrides:

clone in class AbstractDifferentiableSequenceScore

Returns:

the cloned instance of the current DifferentiableSequenceScore

Throws:

CloneNotSupportedException - if something went wrong while cloning the DifferentiableSequenceScore

isNormalized

public boolean isNormalized()

Description copied from interface: DifferentiableStatisticalModel

This method indicates whether the implemented score is already normalized to 1 or not. The standard implementation returns false.

Specified by:

isNormalized in interface DifferentiableStatisticalModel

Returns:

true if the implemented score is already normalized to 1, false otherwise

isNormalized

public static boolean isNormalized(DifferentiableSequenceScore... function)

This method checks whether all given DifferentiableStatisticalModels are normalized.

Parameters:

function - the DifferentiableStatisticalModels to be checked

Returns:

true if all DifferentiableStatisticalModels are already normalized, otherwise false

See Also:

DifferentiableStatisticalModel.isNormalized()

getInitialClassParam

public double getInitialClassParam(double classProb)

Description copied from interface: DifferentiableSequenceScore

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

Specified by:

getInitialClassParam in interface DifferentiableSequenceScore

Overrides:

getInitialClassParam in class AbstractDifferentiableSequenceScore

Parameters:

classProb - the class probability

Returns:

the initial class parameter

getLogProbFor

public double getLogProbFor(Sequence sequence)

Description copied from interface: StatisticalModel

Returns the logarithm of the probability of the given sequence given the model. If at least one random variable is continuous the value of density function is returned.

The length and the alphabets define the type of data that can be modeled and therefore both has to be checked.

Specified by:

getLogProbFor in interface StatisticalModel

Parameters:

sequence - the given sequence for which the logarithm of the probability/the value of the density function should be returned

Returns:

the logarithm of the probability or the value of the density function of the part of the given sequence given the model

See Also:

StatisticalModel.getLogProbFor(Sequence, int, int)

getLogProbFor

public double getLogProbFor(Sequence sequence,
                            int startpos)
                     throws Exception

Description copied from interface: StatisticalModel

Returns the logarithm of the probability of (a part of) the given sequence given the model. If at least one random variable is continuous the value of density function is returned.

If the length of the sequences, whose probability should be returned, is fixed (e.g. in a inhomogeneous model) and the given sequence is longer than their fixed length, the start position within the given sequence is given by startpos. E.g. the fixed length is 12. The length of the given sequence is 30 and the startpos=15 the logarithm of the probability of the part from position 15 to 26 (inclusive) given the model should be returned.
The length and the alphabets define the type of data that can be modeled and therefore both has to be checked.

Specified by:

getLogProbFor in interface StatisticalModel

Parameters:

sequence - the given sequence

startpos - the start position within the given sequence

Returns:

the logarithm of the probability or the value of the density function of (the part of) the given sequence given the model

Throws:

Exception - if the sequence could not be handled by the model

NotTrainedException - if the model is not trained yet

See Also:

StatisticalModel.getLogProbFor(Sequence, int, int)

getLogProbFor

public double getLogProbFor(Sequence sequence,
                            int startpos,
                            int endpos)

Description copied from interface: StatisticalModel

Returns the logarithm of the probability of (a part of) the given sequence given the model. If at least one random variable is continuous the value of density function is returned.

It extends the possibility given by the method StatisticalModel.getLogProbFor(Sequence, int) by the fact, that the model could be e.g. homogeneous and therefore the length of the sequences, whose probability should be returned, is not fixed. Additionally, the end position of the part of the given sequence is given and the probability of the part from position startpos to endpos (inclusive) should be returned.
The length and the alphabets define the type of data that can be modeled and therefore both has to be checked.

Specified by:

getLogProbFor in interface StatisticalModel

Parameters:

sequence - the given sequence

startpos - the start position within the given sequence

endpos - the last position to be taken into account

Returns:

the logarithm of the probability or the value of the density function of (the part of) the given sequence given the model

getLogScoreFor

public double[] getLogScoreFor(DataSet data)
                        throws Exception

Description copied from interface: SequenceScore

This method computes the logarithm of the scores of all sequences in the given data set. The values are stored in an array according to the index of the respective sequence in the data set.

The score for any sequence shall be computed independent of all other sequences in the data set. So the result should be exactly the same as for the method SequenceScore.getLogScoreFor(Sequence).

Specified by:

getLogScoreFor in interface SequenceScore

Overrides:

getLogScoreFor in class AbstractDifferentiableSequenceScore

Parameters:

data - the data set of sequences

Returns:

an array containing the logarithm of the score of all sequences of the data set

Throws:

Exception - if something went wrong

See Also:

SequenceScore.getLogScoreFor(Sequence)

getLogScoreFor

public void getLogScoreFor(DataSet data,
                           double[] res)
                    throws Exception

Description copied from interface: SequenceScore

This method computes and stores the logarithm of the scores for any sequence in the data set in the given double-array.

The score for any sequence shall be computed independent of all other sequences in the data set. So the result should be exactly the same as for the method SequenceScore.getLogScoreFor(Sequence).

Specified by:

getLogScoreFor in interface SequenceScore

Overrides:

getLogScoreFor in class AbstractDifferentiableSequenceScore

Parameters:

data - the data set of sequences

res - the array for the results, has to have length data.getNumberOfElements() (which returns the number of sequences in the data set)

Throws:

Exception - if something went wrong

See Also:

SequenceScore.getLogScoreFor(Sequence), SequenceScore.getLogScoreFor(DataSet)

emitDataSet

public DataSet emitDataSet(int numberOfSequences,
                           int... seqLength)
                    throws NotTrainedException,
                           Exception

Description copied from interface: StatisticalModel

This method returns a DataSet object containing artificial sequence(s).

There are two different possibilities to create a data set for a model with length 0 (homogeneous models).

1. emitDataSet( int n, int l ) should return a data set with n sequences of length l.
2. emitDataSet( int n, int[] l ) should return a data set with n sequences which have a sequence length corresponding to the entry in the given array l.

There are two different possibilities to create a data set for a model with length greater than 0 (inhomogeneous models).
emitDataSet( int n ) and emitDataSet( int n, null ) should return a data set with n sequences of length of the model ( SequenceScore.getLength()).

The standard implementation throws an Exception.

Specified by:

emitDataSet in interface StatisticalModel

Parameters:

numberOfSequences - the number of sequences that should be contained in the returned data set

seqLength - the length of the sequences for a homogeneous model; for an inhomogeneous model this parameter should be null or an array of size 0.

Returns:

a DataSet containing the artificial sequence(s)

Throws:

NotTrainedException - if the model is not trained yet

Exception - if the emission did not succeed

See Also:

DataSet

getMaximalMarkovOrder

public byte getMaximalMarkovOrder()
                           throws UnsupportedOperationException

Description copied from interface: StatisticalModel

This method returns the maximal used Markov order, if possible.

Specified by:

getMaximalMarkovOrder in interface StatisticalModel

Returns:

maximal used Markov order

Throws:

UnsupportedOperationException - if the model can't give a proper answer