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Uses of Package
de.jstacs.algorithms.optimization

Packages that use de.jstacs.algorithms.optimization
de.jstacs.algorithms.optimization Provides classes for different types of algorithms that are not directly linked to the modelling components of Jstacs: Algorithms on graphs, algorithms for numerical optimization, and a basic alignment algorithm. 
de.jstacs.classifiers.differentiableSequenceScoreBased Provides the classes for Classifiers that are based on SequenceScores.
It includes a sub-package for discriminative objective functions, namely conditional likelihood and supervised posterior, and a separate sub-package for the parameter priors, that can be used for the supervised posterior. 
de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix Provides an implementation of a classifier that allows to train the parameters of a set of DifferentiableStatisticalModels by a unified generative-discriminative learning principle. 
de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior Provides a general definition of a parameter log-prior and a number of implementations of Laplace and Gaussian priors. 
de.jstacs.motifDiscovery This package provides the framework including the interface for any de novo motif discoverer. 
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous This package contains various inhomogeneous models. 
 

Classes in de.jstacs.algorithms.optimization used by de.jstacs.algorithms.optimization
DifferentiableFunction
          This class is the framework for any (at least) one time differentiable function $f: \mathbb{R}^n \to \mathbb{R}$.
DimensionException
          This class is for Exceptions depending on wrong dimensions of vectors for a given function.
EvaluationException
          This class indicates that there was a problem to evaluate a function or the gradient of the function.
Function
          This interface is the framework for any mathematical function $f: \mathbb{R}^n \to \mathbb{R}$.
OneDimensionalFunction
          This class implements the interface Function for an one-dimensional function.
StartDistanceForecaster
          This interface is used to determine the next start distance that will be used in a line search.
TerminationException
          This class is for an Exception that is thrown if something with a termination was not correct.
 

Classes in de.jstacs.algorithms.optimization used by de.jstacs.classifiers.differentiableSequenceScoreBased
DifferentiableFunction
          This class is the framework for any (at least) one time differentiable function $f: \mathbb{R}^n \to \mathbb{R}$.
DimensionException
          This class is for Exceptions depending on wrong dimensions of vectors for a given function.
EvaluationException
          This class indicates that there was a problem to evaluate a function or the gradient of the function.
Function
          This interface is the framework for any mathematical function $f: \mathbb{R}^n \to \mathbb{R}$.
 

Classes in de.jstacs.algorithms.optimization used by de.jstacs.classifiers.differentiableSequenceScoreBased.gendismix
DifferentiableFunction
          This class is the framework for any (at least) one time differentiable function $f: \mathbb{R}^n \to \mathbb{R}$.
DimensionException
          This class is for Exceptions depending on wrong dimensions of vectors for a given function.
EvaluationException
          This class indicates that there was a problem to evaluate a function or the gradient of the function.
Function
          This interface is the framework for any mathematical function $f: \mathbb{R}^n \to \mathbb{R}$.
 

Classes in de.jstacs.algorithms.optimization used by de.jstacs.classifiers.differentiableSequenceScoreBased.logPrior
DifferentiableFunction
          This class is the framework for any (at least) one time differentiable function $f: \mathbb{R}^n \to \mathbb{R}$.
DimensionException
          This class is for Exceptions depending on wrong dimensions of vectors for a given function.
EvaluationException
          This class indicates that there was a problem to evaluate a function or the gradient of the function.
Function
          This interface is the framework for any mathematical function $f: \mathbb{R}^n \to \mathbb{R}$.
 

Classes in de.jstacs.algorithms.optimization used by de.jstacs.motifDiscovery
DifferentiableFunction
          This class is the framework for any (at least) one time differentiable function $f: \mathbb{R}^n \to \mathbb{R}$.
StartDistanceForecaster
          This interface is used to determine the next start distance that will be used in a line search.
 

Classes in de.jstacs.algorithms.optimization used by de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous
DifferentiableFunction
          This class is the framework for any (at least) one time differentiable function $f: \mathbb{R}^n \to \mathbb{R}$.
DimensionException
          This class is for Exceptions depending on wrong dimensions of vectors for a given function.
Function
          This interface is the framework for any mathematical function $f: \mathbb{R}^n \to \mathbb{R}$.
 

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