de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior

Class SeparateLogPrior

java.lang.Object

de.jstacs.algorithms.optimization.DifferentiableFunction

de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.LogPrior

de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.SeparateLogPrior

All Implemented Interfaces:

Function, Storable, Cloneable

Direct Known Subclasses:

SeparateGaussianLogPrior, SeparateLaplaceLogPrior

public abstract class SeparateLogPrior
extends LogPrior
implements Cloneable

Abstract class for priors that penalize each parameter value independently and have some variances (and possible means) as hyperparameters. Such priors are e.g. the SeparateGaussianLogPrior or the SeparateLaplaceLogPrior.

Author:

Jan Grau, Jens Keilwagen

Field Summary

Fields

Modifier and Type	Field and Description
protected double[]	classMus The means for the class parameters, as specified by the user.
protected double[]	classVars The variances for the class parameters, as specified by the user.
protected boolean	freeParameters Indicates, if only free parameters shall be used and hence penalized.
protected DifferentiableStatisticalModel[]	funs The DifferentiableSequenceScores using the parameters that shall be penalized.
protected double[]	vars The base variances for the parameters of the DifferentiableSequenceScores of each class, the means of the non-class parameters should be 0.

Fields inherited from class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.LogPrior

UNKNOWN

Constructor Summary

Constructors

Constructor and Description
SeparateLogPrior(double[] vars, double[] classVars, double[] classMus) Creates a new SeparateLogPrior using the class-specific base variances vars, the variances classVars and the means classMus for the class parameters.
SeparateLogPrior(StringBuffer xml) The standard constructor for the interface Storable.

Method Summary

Modifier and Type	Method and Description
SeparateLogPrior	getNewInstance() This method returns an empty new instance of the current prior.
void	set(boolean freeParameters, DifferentiableSequenceScore... funs) Resets all pre-computed values to their initial values using the DifferentiableSequenceScores funs.
StringBuffer	toXML() Encodes the prior as an XML representation.
protected abstract void	unset() Resets all internally pre-computed values, e.g.

Methods inherited from class de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior.LogPrior

addGradientFor, evaluateGradientOfFunction, getInstanceName

Methods inherited from class de.jstacs.algorithms.optimization.DifferentiableFunction

findOneDimensionalMin

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.jstacs.algorithms.optimization.Function

evaluateFunction, getDimensionOfScope

Field Detail

funs

protected DifferentiableStatisticalModel[] funs

The DifferentiableSequenceScores using the parameters that shall be penalized.

vars

protected double[] vars

The base variances for the parameters of the DifferentiableSequenceScores of each class, the means of the non-class parameters should be 0.

classVars

protected double[] classVars

The variances for the class parameters, as specified by the user.

classMus

protected double[] classMus

The means for the class parameters, as specified by the user.

freeParameters

protected boolean freeParameters

Indicates, if only free parameters shall be used and hence penalized.

Constructor Detail

SeparateLogPrior

public SeparateLogPrior(double[] vars,
                        double[] classVars,
                        double[] classMus)

Creates a new SeparateLogPrior using the class-specific base variances vars, the variances classVars and the means classMus for the class parameters.

Parameters:

vars - the base variances for each class

classVars - the variances for the class parameters

classMus - the means for the class parameters

SeparateLogPrior

public SeparateLogPrior(StringBuffer xml)
                 throws NonParsableException

The standard constructor for the interface Storable. Creates a new SeparateLogPrior out of its XML representation.

Parameters:

xml - the XML representation as StringBuffer

Throws:

NonParsableException - if the SeparateLogPrior could not be reconstructed out of the XML representation (the StringBuffer could not be parsed)

See Also:

Storable

Method Detail

set

public void set(boolean freeParameters,
                DifferentiableSequenceScore... funs)
         throws Exception

Description copied from class: LogPrior

Resets all pre-computed values to their initial values using the DifferentiableSequenceScores funs.

Overrides:

set in class LogPrior

Parameters:

freeParameters - the switch for using only the free parameters or all parameters in a DifferentiableSequenceScore

funs - the DifferentiableSequenceScores for the prior

Throws:

Exception - if the DifferentiableSequenceScores could not be set

unset

protected abstract void unset()

Resets all internally pre-computed values, e.g. the hyperparameters for each parameter.

getNewInstance

public SeparateLogPrior getNewInstance()
                                throws CloneNotSupportedException

Description copied from class: LogPrior

This method returns an empty new instance of the current prior. The method works similar to clone, but does not clone DifferentiableSequenceScore s that may be inside the instance. The DifferentiableSequenceScores must be set by an invocation of the method LogPrior.set(boolean, DifferentiableSequenceScore...).

Specified by:

getNewInstance in class LogPrior

Returns:

a new empty instance of the prior

Throws:

CloneNotSupportedException - if something went wrong while cloning

See Also:

LogPrior.set(boolean, DifferentiableSequenceScore...)

toXML

public StringBuffer toXML()

Description copied from class: LogPrior

Encodes the prior as an XML representation. It does not encode all information, since the method LogPrior.set(boolean, DifferentiableSequenceScore...) has to be invoked after decoding.

Specified by:

toXML in interface Storable

Specified by:

toXML in class LogPrior

Returns:

the XML representation;