de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions

Class HigherOrderTransition

java.lang.Object

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition

de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.HigherOrderTransition

All Implemented Interfaces:

SamplingComponent, SamplingFromStatistic, DifferentiableTransition, SamplingTransition, TrainableTransition, Transition, TransitionWithSufficientStatistic, Storable, Cloneable

public class HigherOrderTransition
extends BasicHigherOrderTransition
implements DifferentiableTransition, SamplingTransition

This class can be used in any AbstractHMM allowing to use gradient based or sampling training algorithm.

Author:

Jens Keilwagen

Nested Class Summary

Nested classes/interfaces inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition

BasicHigherOrderTransition.AbstractTransitionElement

Field Summary

Fields

Modifier and Type	Field and Description
protected int[]	counter The counter for the sampling steps of each sampling.
protected File[]	paramsFile The files for saving the parameters during the sampling.
protected BufferedReader	reader The reader for the paramsFile after a sampling.
protected int	samplingIndex The index of the current sampling.
protected BufferedWriter	writer The writer for the paramsFile in a sampling.

Fields inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition

isSilent, lookup, maximalMarkovOrder, maxInDegree, transitions

Constructor Summary

Constructors

Constructor and Description
HigherOrderTransition(boolean[] isSilent, TransitionElement... transitions) The main constructor.
HigherOrderTransition(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
void	acceptParameters() This methods accepts the drawn parameters.
void	addGradientForLogPriorTerm(double[] gradient, int start) This method computes the gradient of Transition.getLogPriorTerm() for each parameter of this transition.
protected void	appendFurtherInformation(StringBuffer xml) This method appends further information to the XML representation.
HigherOrderTransition	clone() This method returns a deep clone of the current instance.
void	extendSampling(int sampling, boolean append) This method allows to extend a sampling.
protected void	extractFurtherInformation(StringBuffer xml) This method extracts further information from the XML representation.
void	fillParameters(double[] params) This method allows to fill the parameters of the transition in a given array.
protected void	fillParameters(double[] params, int offset) This method allows to fill the current parameters using a specific offset.
void	fillSamplingGroups(int parameterOffset, LinkedList<int[]> list) Adds the groups of indexes of those parameters of this transition that should be sampled together in one step of a grouped sampling procedure, each as an int[], into list.
protected void	finalize()
double	getLogPosteriorFromStatistic() This method calculates the a-posteriori probability for the current statistics
double	getLogScoreAndPartialDerivation(int layer, int index, int childIdx, IntList indices, DoubleList partDer, Sequence sequence, int sequencePosition) This method allows to compute the logarithm of the score and the gradient for a specific transition.
int	getSizeOfEventSpace(int index) Returns the size of the event space, i.e., the number of possible outcomes, for the random variable of parameter index
TransitionElement[]	getTransisionElements() Returns a clone of the internal transition elements.
protected String	getXMLTag() The method returns the XML tag used during saving and loading the transition.
void	initForSampling(int starts) This method initializes the instance for the sampling.
boolean	isInSamplingMode() This method returns true if the object is currently used in a sampling, otherwise false.
boolean	parseNextParameterSet() This method allows the user to parse the next set of parameters (from a file).
boolean	parseParameterSet(int sampling, int n) This method allows the user to parse the set of parameters with index n of a certain sampling (from a file).
void	samplingStopped() This method is the opposite of the method SamplingComponent.extendSampling(int, boolean).
protected int	setParameterOffset() This method allows to set the parameter offset in each internally used TransitionElement.
int	setParameterOffset(int offset) This method sets the internal offset of the parameter index.
void	setParameters(double[] params, int start) This method allows to set the parameters of the transition.
protected void	setParams(double[] params, int start) This method allows to set the new parameters using a specific offset.

Methods inherited from class de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.BasicHigherOrderTransition

addToStatistic, drawParametersFromStatistic, estimateFromStatistic, fillTransitionInformation, getChildIdx, getGraphizNetworkRepresentation, getLastContextState, getLogGammaScoreFromStatistic, getLogPriorTerm, getLogScoreFor, getMaximalInDegree, getMaximalMarkovOrder, getMaximalNumberOfChildren, getNumberOfChildren, getNumberOfIndexes, getNumberOfStates, getTransitionElementIndex, hasAnySelfTransitions, initializeRandomly, isAbsoring, joinStatistics, resetStatistic, setParameters, toString, toString, toXML

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.TransitionWithSufficientStatistic

addToStatistic, getLogGammaScoreFromStatistic, joinStatistics, resetStatistic

Methods inherited from interface de.jstacs.sequenceScores.statisticalModels.trainable.hmm.transitions.Transition

fillTransitionInformation, getChildIdx, getGraphizNetworkRepresentation, getLastContextState, getLogPriorTerm, getLogScoreFor, getMaximalInDegree, getMaximalMarkovOrder, getMaximalNumberOfChildren, getNumberOfChildren, getNumberOfIndexes, getNumberOfStates, hasAnySelfTransitions, initializeRandomly, isAbsoring, setParameters, toString

Methods inherited from interface de.jstacs.Storable

toXML

Methods inherited from interface de.jstacs.sampling.SamplingFromStatistic

drawParametersFromStatistic

Field Detail

paramsFile

protected File[] paramsFile

The files for saving the parameters during the sampling.

counter

protected int[] counter

The counter for the sampling steps of each sampling.

samplingIndex

protected int samplingIndex

The index of the current sampling.

writer

protected BufferedWriter writer

The writer for the paramsFile in a sampling.

reader

protected BufferedReader reader

The reader for the paramsFile after a sampling.

Constructor Detail

HigherOrderTransition

public HigherOrderTransition(boolean[] isSilent,
                             TransitionElement... transitions)
                      throws Exception

The main constructor.

Parameters:

transitions - the TransitionElements for the internal use

isSilent - an array indicating for each state whether it is silent or not

Throws:

Exception - if an error occurs during checking the TransitionElements and creating internal fields

HigherOrderTransition

public HigherOrderTransition(StringBuffer xml)
                      throws NonParsableException

The standard constructor for the interface Storable. Constructs a HigherOrderTransition out of an XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the HigherOrderTransition could not be reconstructed out of the StringBuffer xml

Method Detail

getXMLTag

protected String getXMLTag()

Description copied from class: BasicHigherOrderTransition

The method returns the XML tag used during saving and loading the transition.

Overrides:

getXMLTag in class BasicHigherOrderTransition

Returns:

he XML tag used during saving and loading the transition.

appendFurtherInformation

protected void appendFurtherInformation(StringBuffer xml)

Description copied from class: BasicHigherOrderTransition

This method appends further information to the XML representation. It allows subclasses to save further parameters that are not defined in the superclass.

Overrides:

appendFurtherInformation in class BasicHigherOrderTransition

Parameters:

xml - the XML representation

extractFurtherInformation

protected void extractFurtherInformation(StringBuffer xml)
                                  throws NonParsableException

Description copied from class: BasicHigherOrderTransition

This method extracts further information from the XML representation. It allows subclasses to cast further parameters that are not defined in the superclass.

Overrides:

extractFurtherInformation in class BasicHigherOrderTransition

Parameters:

xml - the XML representation

Throws:

NonParsableException - if the information could not be reconstructed out of the StringBuffer xml

clone

public HigherOrderTransition clone()
                            throws CloneNotSupportedException

Description copied from interface: Transition

This method returns a deep clone of the current instance.

Specified by:

clone in interface Transition

Overrides:

clone in class BasicHigherOrderTransition

Returns:

a deep clone of the current instance.

Throws:

CloneNotSupportedException - if the instance could not be cloned

fillParameters

public void fillParameters(double[] params)

Description copied from interface: DifferentiableTransition

This method allows to fill the parameters of the transition in a given array.

Specified by:

fillParameters in interface DifferentiableTransition

Parameters:

params - the parameters

fillParameters

protected void fillParameters(double[] params,
                              int offset)

This method allows to fill the current parameters using a specific offset.

Parameters:

params - the parameters

offset - the offset indicating the start position

See Also:

fillParameters(double[]), TransitionElement.fillParameters(double[], int)

setParameterOffset

public int setParameterOffset(int offset)

Description copied from interface: DifferentiableTransition

This method sets the internal offset of the parameter index.

Specified by:

setParameterOffset in interface DifferentiableTransition

Parameters:

offset - the offset

Returns:

the offset for the next parameters

setParameterOffset

protected int setParameterOffset()

This method allows to set the parameter offset in each internally used TransitionElement.

Returns:

the new parameter offset

See Also:

setParameterOffset(int), TransitionElement.setParameterOffset(int)

setParameters

public void setParameters(double[] params,
                          int start)

Description copied from interface: DifferentiableTransition

This method allows to set the parameters of the transition.

Specified by:

setParameters in interface DifferentiableTransition

Parameters:

params - the parameters

start - the (global) start position

setParams

protected void setParams(double[] params,
                         int start)

This method allows to set the new parameters using a specific offset.

Parameters:

params - the parameters

start - the offset indicating the start position

See Also:

setParameters(double[], int), TransitionElement.setParameters(double[], int)

addGradientForLogPriorTerm

public void addGradientForLogPriorTerm(double[] gradient,
                                       int start)

Description copied from interface: DifferentiableTransition

This method computes the gradient of Transition.getLogPriorTerm() for each parameter of this transition. The results are added to the array gradient beginning at index start.

Specified by:

addGradientForLogPriorTerm in interface DifferentiableTransition

Parameters:

gradient - the array of gradients

start - the start index in the gradient array, where the partial derivations for the parameters of this Transition shall be entered

getLogScoreAndPartialDerivation

public double getLogScoreAndPartialDerivation(int layer,
                                              int index,
                                              int childIdx,
                                              IntList indices,
                                              DoubleList partDer,
                                              Sequence sequence,
                                              int sequencePosition)

Description copied from interface: DifferentiableTransition

This method allows to compute the logarithm of the score and the gradient for a specific transition.

Specified by:

getLogScoreAndPartialDerivation in interface DifferentiableTransition

Parameters:

layer - the layer of the matrix

index - the index encoding the context

childIdx - the index of the child

indices - a list for the parameter indices

partDer - a list for the partial derivations

sequence - the sequence

sequencePosition - the position within the sequence

Returns:

the logarithm of the score

See Also:

Transition.getLogScoreFor(int, int, int, Sequence, int)

initForSampling

public void initForSampling(int starts)
                     throws IOException

Description copied from interface: SamplingComponent

This method initializes the instance for the sampling. For instance this method can be used to create new files where all parameter sets are stored.

Specified by:

initForSampling in interface SamplingComponent

Parameters:

starts - the number of different sampling starts that will be done

Throws:

IOException - if something went wrong

See Also:

File.createTempFile(String, String, java.io.File )

finalize

protected void finalize()
                 throws Throwable

Overrides:

finalize in class Object

Throws:

Throwable

extendSampling

public void extendSampling(int sampling,
                           boolean append)
                    throws IOException

Description copied from interface: SamplingComponent

This method allows to extend a sampling.

Specified by:

extendSampling in interface SamplingComponent

Parameters:

sampling - the index of the sampling

append - whether to append the sampled parameters to an existing file or to overwrite the file

Throws:

IOException - if the file could not be handled correctly

isInSamplingMode

public boolean isInSamplingMode()

Description copied from interface: SamplingComponent

This method returns true if the object is currently used in a sampling, otherwise false.

Specified by:

isInSamplingMode in interface SamplingComponent

Returns:

true if the object is currently used in a sampling, otherwise false

parseNextParameterSet

public boolean parseNextParameterSet()

Description copied from interface: SamplingComponent

This method allows the user to parse the next set of parameters (from a file).

Specified by:

parseNextParameterSet in interface SamplingComponent

Returns:

true if the parameters could be parsed, otherwise false

See Also:

SamplingComponent.parseParameterSet(int, int)

parseParameterSet

public boolean parseParameterSet(int sampling,
                                 int n)
                          throws IOException

Description copied from interface: SamplingComponent

This method allows the user to parse the set of parameters with index n of a certain sampling (from a file). The internal numbering should start with 0. The parameter set with index 0 is the initial (random) parameter set. It is recommended that a series of parameter sets is accessed by the following lines:

for( sampling = 0; sampling < numSampling; sampling++ )
{
boolean b = parseParameterSet( sampling, n );
while( b )
{
//do something
b = parseNextParameterSet();
}
}


Specified by:

parseParameterSet in interface SamplingComponent

Parameters:

sampling - the index of the sampling

n - the index of the parameter set

Returns:

true if the parameter set could be parsed

Throws:

IOException

See Also:

SamplingComponent.parseNextParameterSet()

samplingStopped

public void samplingStopped()
                     throws IOException

Description copied from interface: SamplingComponent

This method is the opposite of the method SamplingComponent.extendSampling(int, boolean). It can be used for closing any streams of writer, ...

Specified by:

samplingStopped in interface SamplingComponent

Throws:

IOException - if something went wrong

See Also:

SamplingComponent.extendSampling(int, boolean)

acceptParameters

public void acceptParameters()
                      throws IOException

Description copied from interface: SamplingComponent

This methods accepts the drawn parameters. Internally the drawn parameters should be saved (to a file).

Specified by:

acceptParameters in interface SamplingComponent

Throws:

IOException - if the file could not be handled correctly

getLogPosteriorFromStatistic

public double getLogPosteriorFromStatistic()

Description copied from interface: SamplingFromStatistic

This method calculates the a-posteriori probability for the current statistics

Specified by:

getLogPosteriorFromStatistic in interface SamplingFromStatistic

Returns:

the logarithm of the a-posteriori probability

getSizeOfEventSpace

public int getSizeOfEventSpace(int index)

Description copied from interface: DifferentiableTransition

Returns the size of the event space, i.e., the number of possible outcomes, for the random variable of parameter index

Specified by:

getSizeOfEventSpace in interface DifferentiableTransition

Parameters:

index - the index of the parameter

Returns:

the size of the event space

fillSamplingGroups

public void fillSamplingGroups(int parameterOffset,
                               LinkedList<int[]> list)

Description copied from interface: DifferentiableTransition

Adds the groups of indexes of those parameters of this transition that should be sampled together in one step of a grouped sampling procedure, each as an int[], into list. In most cases, one group should contain the parameters that are living on a common simplex, e.g. the parameters of one TransitionElement of this transition. The internal indexes of the parameters are incremeneted by an external parameterOffset

Specified by:

fillSamplingGroups in interface DifferentiableTransition

Parameters:

parameterOffset - the external parameter offset

list - the list of sampling groups

getTransisionElements

public TransitionElement[] getTransisionElements()
                                          throws CloneNotSupportedException

Returns a clone of the internal transition elements.

Returns:

the transition elements

Throws:

CloneNotSupportedException - if the transition elements could not be cloned