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

Class TransitionElement

java.lang.Object

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

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

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

All Implemented Interfaces:

Storable, Cloneable

public class TransitionElement
extends BasicTransitionElement

This class implements an transition element implements method used for training via sampling or gradient based optimization approach.

Author:

Jens Keilwagen

Field Summary

Fields

Modifier and Type	Field and Description
protected int	offset The internally used parameter offset.
protected double[]	probs The precomputed probabilities for each possible transition.

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

context, descendants, hyperParameters, logNorm, parameters, states, statistic

Constructor Summary

Constructors

Constructor and Description
TransitionElement(int[] context, int[] states, double[] hyperParameters) This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.
TransitionElement(int[] context, int[] states, double[] hyperParameters, double[] weight) This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.
TransitionElement(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
void	addGradientForLogPriorTerm(double[] gradient, int start) This method computes the gradient of BasicHigherOrderTransition.AbstractTransitionElement.getLogPriorTerm() for each parameter of this transition element.
TransitionElement	clone()
int	fillParameters(double[] params, int offset) This method fills the current parameters of this TransitionElement into the given array params starting at position offset.
double	getLogPosteriorFromStatistic() This method computes the log posterior from the internal sufficient statistic.
double	getLogScoreAndPartialDerivation(int childIdx, IntList indices, DoubleList partialDer, Sequence sequence, int sequencePosition) Returns the logarithmic score and fills lists with the indices and the partial derivations.
double	getMinimalHyperparameter() This method returns the minimal hyper parameters of this TransitionElement.
protected void	init() This method initializes internal fields.
protected void	precompute() This method precomputes internal fields as for instance the normalization constant.
int	setParameterOffset(int o) This method sets the internal offset used for several methods (cf.
int	setParameters(double[] params, int start) This method sets the internal parameters to the values of params beginning at index start.

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

appendFurtherInformation, extractFurtherInformation

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

addToStatistic, appendGraphvizDescription, appendTransitions, drawParametersFromStatistic, estimateFromStatistic, getArrowOption, getChild, getContext, getDescendant, getGraphvizEdgeWeight, getLabel, getLastContextState, getLogGammaScoreFromStatistic, getLogPriorTerm, getLogScoreFor, getNextContext, getNumberOfChildren, getNumberOfParameters, getXMLTag, initializeRandomly, joinStatistics, resetStatistic, setIndexOfDescendantTransitionElement, setParameters, toString, toString, toXML

Methods inherited from class java.lang.Object

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

Field Detail

probs

protected double[] probs

The precomputed probabilities for each possible transition.

See Also:

getLogScoreAndPartialDerivation(int, IntList, DoubleList, Sequence, int), addGradientForLogPriorTerm(double[], int)

offset

protected int offset

The internally used parameter offset.

See Also:

setParameterOffset(int), getLogScoreAndPartialDerivation(int, IntList, DoubleList, Sequence, int), addGradientForLogPriorTerm(double[], int)

Constructor Detail

TransitionElement

public TransitionElement(int[] context,
                         int[] states,
                         double[] hyperParameters)

This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.

Parameters:

context - the context (=previously visited state indices); last entry corresponds to the last state visited

states - the transitions to all possible states; if null than no transition allowed

hyperParameters - the hyper parameters for the transitions; if null than no prior is used

See Also:

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

TransitionElement

public TransitionElement(int[] context,
                         int[] states,
                         double[] hyperParameters,
                         double[] weight)

This is the main constructor creating a new instance with given context, descendant states, and hyper parameters.

Parameters:

context - the context (=previously visited state indices); last entry corresponds to the last state visited

states - the transitions to all possible states; if null than no transition allowed

hyperParameters - the hyper parameters for the transitions; if null than no prior is used

weight - the weight for plotting the edge in Graphviz, enables to modify the edge length, larger weights imply shorter edges (default: 1)

TransitionElement

public TransitionElement(StringBuffer xml)
                  throws NonParsableException

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

Parameters:

xml - the XML representation as StringBuffer

Throws:

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

Method Detail

clone

public TransitionElement clone()
                        throws CloneNotSupportedException

Overrides:

clone in class BasicHigherOrderTransition.AbstractTransitionElement

Throws:

CloneNotSupportedException

init

protected void init()

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

This method initializes internal fields.

Overrides:

init in class BasicHigherOrderTransition.AbstractTransitionElement

precompute

protected void precompute()

Description copied from class: BasicHigherOrderTransition.AbstractTransitionElement

This method precomputes internal fields as for instance the normalization constant.

Overrides:

precompute in class BasicHigherOrderTransition.AbstractTransitionElement

See Also:

BasicHigherOrderTransition.AbstractTransitionElement.logNorm

getLogScoreAndPartialDerivation

public double getLogScoreAndPartialDerivation(int childIdx,
                                              IntList indices,
                                              DoubleList partialDer,
                                              Sequence sequence,
                                              int sequencePosition)

Returns the logarithmic score and fills lists with the indices and the partial derivations.

Parameters:

childIdx - the index of the child to be visited

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

sequence - the Sequence that can be used to extract SequenceAnnotation

sequencePosition - the position within the sequence

Returns:

the logarithmic score

setParameterOffset

public int setParameterOffset(int o)

This method sets the internal offset used for several methods (cf. see tags).

Parameters:

o - the offset to be set

Returns:

the new offset that can be used for the next TransitionElement

See Also:

offset, getLogScoreAndPartialDerivation(int, IntList, DoubleList, Sequence, int), addGradientForLogPriorTerm(double[], int)

fillParameters

public int fillParameters(double[] params,
                          int offset)

This method fills the current parameters of this TransitionElement into the given array params starting at position offset.

Parameters:

params - the array for filling the parameters

offset - the start index

Returns:

the next start index for further parameter filling

setParameters

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

This method sets the internal parameters to the values of params beginning at index start.

Parameters:

params - the new parameters

start - the start index in params

Returns:

the first index in params that has not been used

addGradientForLogPriorTerm

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

This method computes the gradient of BasicHigherOrderTransition.AbstractTransitionElement.getLogPriorTerm() for each parameter of this transition element. The results are added to the array gradient using the index start.

Parameters:

gradient - the array of gradients

start - the start index in the gradient array used to add partial derivations for the parameters

See Also:

offset

getMinimalHyperparameter

public double getMinimalHyperparameter()

This method returns the minimal hyper parameters of this TransitionElement.

Returns:

the minimal hyper parameters of this TransitionElement

getLogPosteriorFromStatistic

public double getLogPosteriorFromStatistic()

This method computes the log posterior from the internal sufficient statistic.

Returns:

the log posterior from the internal sufficient statistic