- calculateNormalDistribution(double, double) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
Calculates not the actual normal distribution N(input|0,sigma) /
N(0|0,sigma)
- calculateSyntacticProbability(Annotation, Annotation, double, JCas) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
See below
- calculateSyntacticProbability(Annotation, Annotation, double, int, int, JCas) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
Calculates a probability (between 0 and 1) that models the confidence
that two annotations belong together given their syntactic distance (the
number of words, sentences and paragraphs in between).
- ClassificationResult - Class in de.unibi.techfak.scie.classifiers.data
-
This is an interface container class for the result of a classifier for a
given DataPoint.
- ClassificationResult(DataPoint, boolean, double) - Constructor for class de.unibi.techfak.scie.classifiers.data.ClassificationResult
-
- Classifier - Interface in de.unibi.techfak.scie.classifiers
-
This is an interface for classifiers that are able to correctly treat our
data structure.
- ClassifierEvaluation - Class in de.unibi.techfak.scie.classifiers
-
- ClassifierEvaluation(Classifier, ArrayList<LabeledDataPoint>, ArrayList<LabeledDataPoint>) - Constructor for class de.unibi.techfak.scie.classifiers.ClassifierEvaluation
-
- ClassifierEvaluation(Classifier, ArrayList<LabeledDataPoint>, ArrayList<LabeledDataPoint>, boolean) - Constructor for class de.unibi.techfak.scie.classifiers.ClassifierEvaluation
-
- ClassifierEvaluation(Classifier, ArrayList<LabeledDataPoint>, ArrayList<LabeledDataPoint>, int) - Constructor for class de.unibi.techfak.scie.classifiers.ClassifierEvaluation
-
- ClassifierEvaluation(Classifier, ArrayList<LabeledDataPoint>, ArrayList<LabeledDataPoint>, int, boolean) - Constructor for class de.unibi.techfak.scie.classifiers.ClassifierEvaluation
-
- ClassifierEvaluation(Reader) - Constructor for class de.unibi.techfak.scie.classifiers.ClassifierEvaluation
-
- ClassifierEvaluation.SetEvaluation - Class in de.unibi.techfak.scie.classifiers
-
This object encapsulates evaluation measures for one set, either training
or test.
- ClassifierEvaluation.SetEvaluation(Classifier, ArrayList<LabeledDataPoint>, int) - Constructor for class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- ClassifierEvaluation.SetEvaluation(Classifier, ArrayList<LabeledDataPoint>, int, boolean) - Constructor for class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- ClassifierEvaluation.SetEvaluation(int, double, double, double, double[], double[], double[], double) - Constructor for class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- ClassifierEvaluation.SetEvaluation(Reader) - Constructor for class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- classify(DataPoint) - Method in interface de.unibi.techfak.scie.classifiers.Classifier
-
Classify the given DataPoint.
- classify(DataPoint) - Method in class de.unibi.techfak.scie.classifiers.LibLinearClassifier
-
Classify the given DataPoint.
- cleanWord(String) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
Cleans the given input word for word identity features.
- CoreDataPoint<C extends de.unibi.techfak.scie.descriptors.Annotation> - Class in de.unibi.techfak.scie.classifiers.data
-
This models the core of some relation with its relevant features.
- CoreDataPoint(C, JCas) - Constructor for class de.unibi.techfak.scie.classifiers.data.CoreDataPoint
-
- CoreDataPoint.CoreTrainingDataReader<C extends de.unibi.techfak.scie.descriptors.Annotation> - Class in de.unibi.techfak.scie.classifiers.data
-
The CoreTrainingDataReader is pretty straightforward and just creates one
DataPoint for each instance of the core class.
- CoreDataPoint.CoreTrainingDataReader(Class<C>, String) - Constructor for class de.unibi.techfak.scie.classifiers.data.CoreDataPoint.CoreTrainingDataReader
-
- CoreSlotCombinationDataPoint<C extends de.unibi.techfak.scie.descriptors.Annotation,S extends de.unibi.techfak.scie.descriptors.Annotation> - Class in de.unibi.techfak.scie.classifiers.data
-
This models as a combination of core and slot for some relation.
- CoreSlotCombinationDataPoint(C, S, JCas, double) - Constructor for class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint
-
- CoreSlotCombinationDataPoint.CoreSlotTrainingDataReader<C extends de.unibi.techfak.scie.descriptors.Annotation,S extends de.unibi.techfak.scie.descriptors.Annotation> - Class in de.unibi.techfak.scie.classifiers.data
-
The CoreSlotTrainingDataReader has a quadratic search space in nature: It
combines all possible core instances found in the training data with all
possible slot instances.
- CoreSlotCombinationDataPoint.CoreSlotTrainingDataReader(Class<C>, Class<S>, String) - Constructor for class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint.CoreSlotTrainingDataReader
-
- createCombination(C, S, JCas) - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint.CoreSlotTrainingDataReader
-
- createCoreDataPoint(C, JCas) - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
-
This method should create a CoreDataPoint given a core instance.
- createCoreDataPoint(C, JCas) - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
-
This method should create a CoreDataPoint given a core instance.
- createCoreSlotCombinationDataPoint(SlotSpecification, C, Annotation, JCas) - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
-
This method should create a CoreSlotCombination given a
SlotSpecification, a core instance and a Slot instance.
- createCoreSlotCombinationDataPoint(SlotSpecification, C, Annotation, JCas) - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
-
This method should create a CoreSlotCombination given a
SlotSpecification, a core instance and a Slot instance.
- createDataPoint(C, ClassificationResult, SlotCandidate[], JCas) - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
-
This method should create a RelationDataPoint given a core instance,
a core classification and Candidates for all slots (note that the
candidates might be null).
- createDataPoint(C, JCas) - Method in class de.unibi.techfak.scie.classifiers.data.CoreDataPoint.CoreTrainingDataReader
-
- createDataPoint(C, ClassificationResult, SlotCandidate[], JCas) - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
-
This method should create a RelationDataPoint given a core instance,
a core classification and Candidates for all slots (note that the
candidates might be null).
- createRelationObject(C, ClassificationResult, SlotCandidate[], JCas) - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
-
This is only needed to create an empty relation object and to add
relation-specific information.
- crossValidation(ArrayList<LabeledDataPoint>, Classifier, int, int, Comparator<ClassifierEvaluation>, boolean) - Static method in class de.unibi.techfak.scie.classifiers.TrainingUtils
-
Trains the given classifier using crossvalidation and taking the result
with the best evaluation result according to the given comparator.
- crossValidationSweep(ArrayList<LabeledDataPoint>, C, int, int, TrainingUtils.ParameterSweep<C>, Comparator<ClassifierEvaluation>, boolean) - Static method in class de.unibi.techfak.scie.classifiers.TrainingUtils
-
Does the cross validation but does the given parameter sweep in an outer
loop.
- getAccuracy() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- getAnnotation() - Method in class de.unibi.techfak.scie.classifiers.annotators.SlotCandidate
-
- getArea_under_roc() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- getC() - Method in class de.unibi.techfak.scie.classifiers.LibLinearClassifier
-
- getConfidence() - Method in class de.unibi.techfak.scie.classifiers.data.ClassificationResult
-
Returns the confidence that this results DataPoint should have a
positive label.
- getConfidence(Annotation) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
- getCore() - Method in class de.unibi.techfak.scie.classifiers.data.CoreDataPoint
-
- getCore() - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint
-
- getCore() - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint
-
- getCoreClass() - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
-
- getCoreClass() - Method in class de.unibi.techfak.scie.classifiers.data.CoreDataPoint.CoreTrainingDataReader
-
- getCoreClass() - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint.CoreSlotTrainingDataReader
-
- getCoreClass() - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
-
- getCoreClassification() - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint
-
- getCoreClassifier() - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
-
- getCoreClassifier() - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
-
- getData() - Method in class de.unibi.techfak.scie.classifiers.data.ClassificationResult
-
- getData() - Method in class de.unibi.techfak.scie.classifiers.data.LabeledDataPoint
-
- getDictionary() - Method in class de.unibi.techfak.scie.classifiers.data.FeatureMap
-
- getDictionaryID(Annotation) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
- getDistanceInCoveringClass(Class<X>, JCas, Annotation, Annotation) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
This calculates the distance of two annotations counted in the instance
of the given Class.
- getDistLimit() - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
-
Returns the limit (in characters) a core instance may have to a
slot instance.
- getDistLimit() - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
-
- getEpsilon() - Method in class de.unibi.techfak.scie.classifiers.LibLinearClassifier
-
- getF1() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- getFeatureDictionary() - Method in interface de.unibi.techfak.scie.classifiers.Classifier
-
Returns the FeatureDictionary for this Classifier.
- getFeatureDictionary() - Method in class de.unibi.techfak.scie.classifiers.LibLinearClassifier
-
- getFeatureIndex(String) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
-
Returns a unique index for the feature with the given name or -1 if no
such feature exists.
- getFeatureName(int) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
-
Returns the name for the feature with the given index or null if no such
feature is known.
- getFeatureRepresentation(FeatureDictionary, boolean) - Method in class de.unibi.techfak.scie.classifiers.data.CoreDataPoint
-
Returns a FeatureMap representing this CoreDataPoint sparsely.
- getFeatureRepresentation(FeatureDictionary, boolean) - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint
-
Returns a FeatureMap representing this CoreSlotCombination sparsely.
- getFeatureRepresentation(FeatureDictionary, boolean) - Method in interface de.unibi.techfak.scie.classifiers.data.DataPoint
-
Return the FeatureMap for this DataPoint.
- getFeatureRepresentation(FeatureDictionary, boolean) - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint
-
Returns a FeatureMap representing this RelationDataPoint sparsely.
- getFeatures() - Method in class de.unibi.techfak.scie.classifiers.data.FeatureMap
-
Returns a sparse representation of the features for this datapoint using
the feature indices that are part of the FeatureDictionary.
- getFirst() - Method in class de.unibi.techfak.scie.classifiers.Tuple
-
- getIndexMapping() - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
-
It is not recommended to work on this datastructure directly! Please use
this only for reading purposes!
- getInstance(JCas) - Static method in class de.unibi.techfak.scie.classifiers.NonOverlappingCache
-
- getJcas() - Method in class de.unibi.techfak.scie.classifiers.data.CoreDataPoint
-
- getJcas() - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint
-
- getJcas() - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint
-
- getK() - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
-
Returns the number of annotations that may be present on an
overlapping piece of text.
- getLabel() - Method in class de.unibi.techfak.scie.classifiers.data.ClassificationResult
-
- getLabel() - Method in class de.unibi.techfak.scie.classifiers.data.LabeledDataPoint
-
- getN() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- getNameMapping() - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
-
It is not recommended to work on this datastructure directly! Please use
this only for reading purposes!
- getNumberOfFeatures() - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
-
- getPOSTags(Annotation, JCas) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
- getPrecision() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- getR() - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
-
Returns the number of annotations that may be present in the text.
- getRawRelationClass() - Method in class de.unibi.techfak.scie.classifiers.data.CoreDataPoint.CoreTrainingDataReader
-
- getRawRelationClass() - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint.CoreSlotTrainingDataReader
-
- getRawRelationClass() - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
-
- getRecall() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- getRelationClassifier() - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
-
- getRelativeBegin(Annotation, JCas) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
- getRelativeDist(Annotation, Annotation, JCas) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
- getRelativeEnd(Annotation, JCas) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
- getRelativeIndex(int, JCas) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
- getRelativeLength(Annotation, JCas) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
- getResult() - Method in class de.unibi.techfak.scie.classifiers.annotators.SlotCandidate
-
- getRoc_recalls() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- getRoc_specificities() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- getRoc_thresholds() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- getSecond() - Method in class de.unibi.techfak.scie.classifiers.Tuple
-
- getSlot() - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint
-
- getSlotClass() - Method in class de.unibi.techfak.scie.classifiers.annotators.SlotSpecification
-
- getSlotClass() - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint.CoreSlotTrainingDataReader
-
- getSlotClassifier() - Method in class de.unibi.techfak.scie.classifiers.annotators.SlotSpecification
-
- getSlots() - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint
-
- getSlotSpecifications() - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
-
- getSlotSpecifications() - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
-
- getTestEvaluation() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation
-
- getTrainedModel() - Method in class de.unibi.techfak.scie.classifiers.LibLinearClassifier
-
- getTrainEvaluation() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation
-
- getValue(int) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureMap
-
Returns the value for the given feature or null if the feature is
unknown.
- getValue(String) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureMap
-
Returns the value for the given feature or null if the feature is
unknown.
- getWordsInBetween(Annotation, Annotation, JCas) - Static method in class de.unibi.techfak.scie.classifiers.FeatureUtils
-
- RawRelation - Class in de.unibi.techfak.scie.classifiers.data
-
This represents relations for training purposes.
- RawRelation(String) - Constructor for class de.unibi.techfak.scie.classifiers.data.RawRelation
-
- readParameters(Reader, Reader) - Method in interface de.unibi.techfak.scie.classifiers.Classifier
-
Override the current parameters with the ones given in the Reader.
- readParameters(Reader, Reader) - Method in class de.unibi.techfak.scie.classifiers.LibLinearClassifier
-
Override the current parameters with the ones given in the Reader.
- readRawRelations(File) - Static method in class de.unibi.techfak.scie.classifiers.data.RawRelation
-
This reads all RawRelations from the given .rel file.
- readTrainingData(JCas, Collection<RawRelation>, Collection<LabeledDataPoint>) - Method in class de.unibi.techfak.scie.classifiers.data.CoreDataPoint.CoreTrainingDataReader
-
This constructs training data for the given combination of XCAS document
and RawRelations and writes them to the given collection of
LabeledDataPoints.
- readTrainingData(JCas, Collection<RawRelation>, Collection<LabeledDataPoint>) - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint.CoreSlotTrainingDataReader
-
This constructs training data for the given combination of XCAS document
and RawRelations and writes them to the given collection of
LabeledDataPoints.
- readTrainingData(JCas, Collection<RawRelation>, Collection<LabeledDataPoint>) - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
-
This constructs training data for the given combination of XCAS document
and RawRelations and writes them to the given collection of
LabeledDataPoints.
- readTrainingData(JCas, Collection<RawRelation>, Collection<LabeledDataPoint>) - Method in interface de.unibi.techfak.scie.classifiers.data.TrainingDataReader
-
This constructs training data for the given combination of XCAS document
and RawRelations and writes them to the given collection of
LabeledDataPoints.
- RECALL_STR - Static variable in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- RelationAnnotator<C extends de.unibi.techfak.scie.descriptors.Annotation,R extends de.unibi.techfak.scie.descriptors.Aggregated> - Class in de.unibi.techfak.scie.classifiers.annotators
-
This is an abstract super class for annotators of relations according to the
following architecture:
There is a core or trigger element that needs to
be present for a relation to be annotated.
There are S slot elements that may be present.
The base set of viable candidates for core and slots is defined by an
annotation class (e.g.
- RelationAnnotator(Class<C>, Classifier, Classifier) - Constructor for class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
-
- relationClass - Variable in class de.unibi.techfak.scie.classifiers.data.RawRelation
-
- RelationDataPoint<C extends de.unibi.techfak.scie.descriptors.Annotation> - Class in de.unibi.techfak.scie.classifiers.data
-
This defines a relation instance with one specific instance for the core and
each slot.
- RelationDataPoint(C, ClassificationResult, SlotCandidate[], JCas) - Constructor for class de.unibi.techfak.scie.classifiers.data.RelationDataPoint
-
- RelationDataPoint.RelationTrainingDataReader<C extends de.unibi.techfak.scie.descriptors.Annotation> - Class in de.unibi.techfak.scie.classifiers.data
-
Thre RelationTrainingDataReader is a highly complex TrainingDataReader to
construct training DataPoints for a RelationClassifier.
- RelationDataPoint.RelationTrainingDataReader(Class<C>, Classifier, String) - Constructor for class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
-
- removeFeature(String) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
-
Removes the feature with the given name and returns its former index.
- removeFeature(int) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
-
Removes the feature with the given index and returns its former name.
- ROC_REC_STR - Static variable in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- ROC_SPEC_STR - Static variable in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-
- ROC_THR_STR - Static variable in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
-