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## Uses of Package
de.jstacs.scoringFunctions

Packages that use de.jstacs.scoringFunctions
de.jstacs.classifier.scoringFunctionBased | Provides the classes for `Classifier`s that are based on `ScoringFunction`s.
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.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer
de.jstacs.scoringFunctions | Provides `ScoringFunction`s that can be used in a `ScoreClassifier`.
de.jstacs.scoringFunctions.directedGraphicalModels | Provides `ScoringFunction`s that are equivalent to directed graphical models.
de.jstacs.scoringFunctions.homogeneous | Provides `ScoringFunction`s that are homogeneous, i.e. model probabilities or scores independent of the position within a sequence
de.jstacs.scoringFunctions.mix | Provides `ScoringFunction`s that are mixtures of other `ScoringFunction`s.
de.jstacs.scoringFunctions.mix.motifSearch |

Classes in de.jstacs.scoringFunctions used by de.jstacs.classifier.scoringFunctionBased
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.classifier.scoringFunctionBased.cll
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.classifier.scoringFunctionBased.logPrior
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.motifDiscovery
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.scoringFunctions
AbstractNormalizableScoringFunction This class is the main part of any `ScoreClassifier`.
IndependentProductScoringFunction This class enables the user to model parts of a sequence independent of each other.
MRFScoringFunction This class implements the scoring function for any MRF (Markov Random Field).
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
NormalizedScoringFunction This class makes an unnormalized ScoringFunction to a normalized ScoringFunction.
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.scoringFunctions.directedGraphicalModels
AbstractNormalizableScoringFunction This class is the main part of any `ScoreClassifier`.
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.scoringFunctions.homogeneous
AbstractNormalizableScoringFunction This class is the main part of any `ScoreClassifier`.
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
ScoringFunction This interface is the main part of any `ScoreClassifier`.
VariableLengthScoringFunction This is the main class for all `ScoringFunction`s that allow to score subsequences of arbitrary length.

Classes in de.jstacs.scoringFunctions used by de.jstacs.scoringFunctions.mix
AbstractNormalizableScoringFunction This class is the main part of any `ScoreClassifier`.
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
ScoringFunction This interface is the main part of any `ScoreClassifier`.

Classes in de.jstacs.scoringFunctions used by de.jstacs.scoringFunctions.mix.motifSearch
AbstractNormalizableScoringFunction This class is the main part of any `ScoreClassifier`.
NormalizableScoringFunction The interface for normalizable `ScoringFunction`s.
ScoringFunction This interface is the main part of any `ScoreClassifier`.

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