Uses of Interface
de.jstacs.scoringFunctions.ScoringFunction

Packages that use ScoringFunction

de.jstacs.classifier.scoringFunctionBased	Provides the classes for Classifiers that are based on ScoringFunctions.
de.jstacs.classifier.scoringFunctionBased.cll	Provides the implementation of the log conditional likelihood as an OptimizableFunction and a classifier that uses log conditional likelihood or supervised posterior to learn the parameters of a set of ScoringFunctions
de.jstacs.classifier.scoringFunctionBased.logPrior	Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors
de.jstacs.scoringFunctions	Provides ScoringFunctions that can be used in a ScoreClassifier.
de.jstacs.scoringFunctions.directedGraphicalModels	Provides ScoringFunctions that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.homogeneous	Provides ScoringFunctions that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.scoringFunctions.mix	Provides ScoringFunctions that are mixtures of other ScoringFunctions.

Uses of ScoringFunction in de.jstacs.classifier.scoringFunctionBased

Fields in de.jstacs.classifier.scoringFunctionBased declared as ScoringFunction

protected ScoringFunction[]

ScoreClassifier.score The internally used scoring functions.

Methods in de.jstacs.classifier.scoringFunctionBased that return ScoringFunction

ScoringFunction	ScoreClassifier.getScoringFunction(int i) Returns the internally used ScoringFunction with index i.
ScoringFunction[]	ScoreClassifier.getScoringFunctions() Returns all internally used ScoringFunctions in the internal order.

Methods in de.jstacs.classifier.scoringFunctionBased with parameters of type ScoringFunction

abstract void

OptimizableFunction.reset(ScoringFunction[] score) Resets the scoringFunctions and all precomputed values.

Constructors in de.jstacs.classifier.scoringFunctionBased with parameters of type ScoringFunction

ScoreClassifier(ScoreClassifierParameterSet params, ScoringFunction... score)
The default constructor.

Uses of ScoringFunction in de.jstacs.classifier.scoringFunctionBased.cll

Methods in de.jstacs.classifier.scoringFunctionBased.cll with parameters of type ScoringFunction

static CLLClassifier[]	CLLClassifier.create(CLLClassifierParameterSet params, LogPrior prior, ScoringFunction[]... functions) This method creates an array of CLLClassifier by using the cross-product of the given ScoringFunctions.
void	NormConditionalLogLikelihood.reset(ScoringFunction[] funs)

Constructors in de.jstacs.classifier.scoringFunctionBased.cll with parameters of type ScoringFunction

CLLClassifier(CLLClassifierParameterSet params, LogPrior prior, ScoringFunction... score)
The default constructor.

CLLClassifier(CLLClassifierParameterSet params, ScoringFunction... score)
The default constructor.

NormConditionalLogLikelihood(ScoringFunction[] score, Sample[] data, double[][] weights, boolean norm, boolean freeParams)
The constructor creates an instance of the log conditional likelihood.

NormConditionalLogLikelihood(ScoringFunction[] score, Sample[] data, double[][] weights, LogPrior prior, boolean norm, boolean freeParams)
The constructor creates an instance using the given prior.

Uses of ScoringFunction in de.jstacs.classifier.scoringFunctionBased.logPrior

Methods in de.jstacs.classifier.scoringFunctionBased.logPrior with parameters of type ScoringFunction

void	SeparateLogPrior.set(boolean freeParameters, ScoringFunction... funs)
void	LogPrior.set(boolean freeParameters, ScoringFunction... funs) Resets all pre-computed values to their initial values using the ScoringFunctions funs

Uses of ScoringFunction in de.jstacs.scoringFunctions

Subinterfaces of ScoringFunction in de.jstacs.scoringFunctions

interface

NormalizableScoringFunction The interface for normalizable ScoringFunctions.

Classes in de.jstacs.scoringFunctions that implement ScoringFunction

class	AbstractNormalizableScoringFunction This class is the main part of any ScoreClassifier.
class	IndependentProductScoringFunction This class enables the user to model parts of the sequence independent of each other.
class	MRFScoringFunction This class implements the scoring function for any MRF.
class	UniformScoringFunction This scoring function does nothing.
class	VariableLengthScoringFunction This is the main class for all ScoringFunctions that allow to score subsequences of arbitrary length.

Methods in de.jstacs.scoringFunctions that return ScoringFunction

ScoringFunction

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

Uses of ScoringFunction in de.jstacs.scoringFunctions.directedGraphicalModels

Classes in de.jstacs.scoringFunctions.directedGraphicalModels that implement ScoringFunction

class

BayesianNetworkScoringFunction This class implements a scoring function that is a moral directed graphical model, i.e. a moral Bayesian network.

Uses of ScoringFunction in de.jstacs.scoringFunctions.homogeneous

Classes in de.jstacs.scoringFunctions.homogeneous that implement ScoringFunction

class	HMM0ScoringFunction This scoring function implements a homogeneous Markov model of order zero (hMM(0)) for a fixed sequence length.
class	HMMScoringFunction This scoring function implements a homogeneous Markov model of arbitrary order for any sequence length.
class	HomogeneousScoringFunction This is the main class for all homogeneous ScoringFunctions.
class	UniformHomogeneousScoringFunction This scoring function does nothing.

Uses of ScoringFunction in de.jstacs.scoringFunctions.mix

Classes in de.jstacs.scoringFunctions.mix that implement ScoringFunction

class	AbstractMixtureScoringFunction This main abstract class for any mixture (e.g.
class	MixtureScoringFunction This class implements a real mixture model.