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Packages that use NotTrainedException | |
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de.jstacs.classifiers | This package provides the framework for any classifier. |
de.jstacs.classifiers.differentiableSequenceScoreBased | Provides the classes for Classifier s that are based on SequenceScore s.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.sampling | Provides the classes for AbstractScoreBasedClassifier s that are based on
SamplingDifferentiableStatisticalModel s
and that sample parameters using the Metropolis-Hastings algorithm. |
de.jstacs.sequenceScores.statisticalModels | Provides all StatisticalModel s, which can compute a proper (i.e., normalized) likelihood over the input space of sequences.StatisticalModel s can be further differentiated into TrainableStatisticalModel s,
which can be learned from a single input DataSet , and DifferentiableStatisticalModel s,
which define a proper likelihood but can also compute gradients like DifferentiableSequenceScore s. |
de.jstacs.sequenceScores.statisticalModels.differentiable | Provides all DifferentiableStatisticalModel s, which can compute the gradient with
respect to their parameters for a given input Sequence . |
de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels | Provides DifferentiableStatisticalModel s that are directed graphical models. |
de.jstacs.sequenceScores.statisticalModels.trainable | Provides all TrainableStatisticalModel s, which can
be learned from a single DataSet . |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete | |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous | |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous | This package contains various inhomogeneous models. |
de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared | |
de.jstacs.sequenceScores.statisticalModels.trainable.mixture | This package is the super package for any mixture model. |
de.jstacs.utils | This package contains a bundle of useful classes and interfaces like ... |
Uses of NotTrainedException in de.jstacs.classifiers |
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Methods in de.jstacs.classifiers that throw NotTrainedException | |
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protected void |
AbstractScoreBasedClassifier.check(DataSet s)
This method checks if the given DataSet can be used. |
protected void |
AbstractScoreBasedClassifier.check(Sequence seq)
This method checks if the given Sequence can be used. |
protected double |
MappingClassifier.getScore(Sequence seq,
int i,
boolean check)
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protected abstract double |
AbstractScoreBasedClassifier.getScore(Sequence seq,
int i,
boolean check)
This method returns the score for a given Sequence and a given
class. |
Uses of NotTrainedException in de.jstacs.classifiers.differentiableSequenceScoreBased |
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Methods in de.jstacs.classifiers.differentiableSequenceScoreBased that throw NotTrainedException | |
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protected double |
ScoreClassifier.getScore(Sequence seq,
int i,
boolean check)
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Uses of NotTrainedException in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling |
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Methods in de.jstacs.classifiers.differentiableSequenceScoreBased.sampling that throw NotTrainedException | |
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protected double |
SamplingScoreBasedClassifier.getScore(Sequence seq,
int cls,
boolean check)
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Uses of NotTrainedException in de.jstacs.sequenceScores.statisticalModels |
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Methods in de.jstacs.sequenceScores.statisticalModels that throw NotTrainedException | |
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DataSet |
StatisticalModel.emitDataSet(int numberOfSequences,
int... seqLength)
This method returns a DataSet object containing artificial
sequence(s). |
Uses of NotTrainedException in de.jstacs.sequenceScores.statisticalModels.differentiable |
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Methods in de.jstacs.sequenceScores.statisticalModels.differentiable that throw NotTrainedException | |
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DataSet |
UniformDiffSM.emitDataSet(int numberOfSequences,
int... seqLength)
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DataSet |
MarkovRandomFieldDiffSM.emitDataSet(int numberOfSequences,
int... seqLength)
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DataSet |
IndependentProductDiffSM.emitDataSet(int numberOfSequences,
int... seqLength)
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DataSet |
AbstractDifferentiableStatisticalModel.emitDataSet(int numberOfSequences,
int... seqLength)
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Uses of NotTrainedException in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels |
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Methods in de.jstacs.sequenceScores.statisticalModels.differentiable.directedGraphicalModels that throw NotTrainedException | |
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DataSet |
BayesianNetworkDiffSM.emitDataSet(int numberOfSequences,
int... seqLength)
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Uses of NotTrainedException in de.jstacs.sequenceScores.statisticalModels.trainable |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable that throw NotTrainedException | |
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protected void |
AbstractTrainableStatisticalModel.check(Sequence sequence,
int startpos,
int endpos)
This method checks all parameters before a probability can be computed for a sequence. |
DataSet |
AbstractTrainableStatisticalModel.emitDataSet(int numberOfSequences,
int... seqLength)
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double |
VariableLengthWrapperTrainSM.getLogProbFor(Sequence sequence,
int startpos,
int endpos)
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double |
DifferentiableStatisticalModelWrapperTrainSM.getLogProbFor(Sequence sequence,
int startpos,
int endpos)
|
double |
CompositeTrainSM.getLogProbFor(Sequence sequence,
int startpos,
int endpos)
|
Uses of NotTrainedException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete that throw NotTrainedException | |
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protected void |
DiscreteGraphicalTrainSM.check(Sequence sequence,
int startpos,
int endpos)
Checks some conditions on a Sequence . |
Uses of NotTrainedException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.homogeneous that throw NotTrainedException | |
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protected void |
HomogeneousTrainSM.check(Sequence sequence,
int startpos,
int endpos)
Checks some constraints, these are in general conditions on the AlphabetContainer of a (sub)Sequence
between startpos und endpos . |
DataSet |
HomogeneousTrainSM.emitDataSet(int no,
int... length)
Creates a DataSet of a given number of Sequence s from a
trained homogeneous model. |
double |
HomogeneousTrainSM.getLogProbFor(Sequence sequence,
int startpos,
int endpos)
|
Uses of NotTrainedException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous that throw NotTrainedException | |
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protected void |
InhomogeneousDGTrainSM.check(Sequence sequence,
int startpos,
int endpos)
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DataSet |
MEManager.emitDataSet(int n,
int... lengths)
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DataSet |
DAGTrainSM.emitDataSet(int n,
int... lengths)
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double |
MEManager.getLogProbFor(Sequence sequence,
int startpos,
int endpos)
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double |
DAGTrainSM.getLogProbFor(Sequence sequence,
int startpos,
int endpos)
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String |
MEManager.getStructure()
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abstract String |
InhomogeneousDGTrainSM.getStructure()
Returns a String representation of the underlying graph. |
String |
DAGTrainSM.getStructure()
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Uses of NotTrainedException in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.discrete.inhomogeneous.shared that throw NotTrainedException | |
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String |
SharedStructureMixture.getStructure()
Returns a String representation of the structure of the used
models. |
Uses of NotTrainedException in de.jstacs.sequenceScores.statisticalModels.trainable.mixture |
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Methods in de.jstacs.sequenceScores.statisticalModels.trainable.mixture that throw NotTrainedException | |
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protected Sequence[] |
StrandTrainSM.emitDataSetUsingCurrentParameterSet(int n,
int... lengths)
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double |
AbstractMixtureTrainSM.getScoreForBestRun()
Returns the value of the optimized function from the best run of the last training. |
Uses of NotTrainedException in de.jstacs.utils |
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Methods in de.jstacs.utils that throw NotTrainedException | |
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static DataSet |
DiscreteInhomogenousDataSetEmitter.emitDataSet(StatisticalModel m,
int n)
This method emits a data set with n |
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