A B C D E F G H I L M N P R S T W 

A

ACC_STR - Static variable in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
 
addBooleanFeature(String, boolean) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureMap
This implicitly maps the given feature to the value 1.
addFeature(String) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
 
addNumericFeature(String, double, boolean) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureMap
 
addSpecialFeatures(FeatureMap, boolean) - Method in class de.unibi.techfak.scie.classifiers.data.CoreDataPoint
This is to be implemented by a subclass to add domain-specific features to the mix.
addSpecialFeatures(FeatureMap, boolean) - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint
This is to be implemented by a subclass to add domain-specific features to the mix.
addSpecialFeatures(FeatureMap, boolean) - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint
This is to be implemented by a subclass to add domain-specific features to the mix.
AREA_ROC_STR - Static variable in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
 

B

balanceDataSet(ArrayList<LabeledDataPoint>) - Static method in class de.unibi.techfak.scie.classifiers.TrainingUtils
Preprocesses the given data and enforces balanced classes by inserting data points of the under-represented label multiple times in the given list.

C

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.

D

DataPoint - Interface in de.unibi.techfak.scie.classifiers.data
This is an interface for all kinds of DataPoints.
de.unibi.techfak.scie.classifiers - package de.unibi.techfak.scie.classifiers
 
de.unibi.techfak.scie.classifiers.annotators - package de.unibi.techfak.scie.classifiers.annotators
 
de.unibi.techfak.scie.classifiers.data - package de.unibi.techfak.scie.classifiers.data
 
DEFAULT_DIST_LIMIT - Static variable in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
 
DEFAULT_DIST_LIMIT - Static variable in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
 
DEFAULT_K - Static variable in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
 
DEFAULT_R - Static variable in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
 
DEFAULT_ROC_STEPS - Static variable in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation
 

E

equals(Object) - Method in class de.unibi.techfak.scie.classifiers.annotators.SlotCandidate
 
equals(Object) - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
 
equals(Object) - Method in class de.unibi.techfak.scie.classifiers.data.ClassificationResult
 
equals(Object) - Method in class de.unibi.techfak.scie.classifiers.data.CoreDataPoint
 
equals(Object) - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint
 
equals(Object) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
 
equals(Object) - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint
 
equals(Object) - Method in class de.unibi.techfak.scie.classifiers.Tuple
 

F

F1_STR - Static variable in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
 
FeatureDictionary - Class in de.unibi.techfak.scie.classifiers.data
This dictionary keeps track of which features actually exist in a certain dataset and thus enables us to address features with index notation and name notation alike.
FeatureDictionary() - Constructor for class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
 
FeatureMap - Class in de.unibi.techfak.scie.classifiers.data
This models represents features of a concrete DataPoint in terms of a map of feature names to values to achieve a sparse feature representation in large feature spaces.
FeatureMap(FeatureDictionary) - Constructor for class de.unibi.techfak.scie.classifiers.data.FeatureMap
 
FeatureUtils - Class in de.unibi.techfak.scie.classifiers
This is a collection of static functions to calculate some standard features.
FeatureUtils() - Constructor for class de.unibi.techfak.scie.classifiers.FeatureUtils
 

G

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
 

H

hasFeature(String) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
 
hashCode() - Method in class de.unibi.techfak.scie.classifiers.annotators.SlotCandidate
 
hashCode() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
 
hashCode() - Method in class de.unibi.techfak.scie.classifiers.data.ClassificationResult
 
hashCode() - Method in class de.unibi.techfak.scie.classifiers.data.CoreDataPoint
 
hashCode() - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint
 
hashCode() - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
 
hashCode() - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint
 
hashCode() - Method in class de.unibi.techfak.scie.classifiers.Tuple
 
hasNextParameter(C) - Method in interface de.unibi.techfak.scie.classifiers.TrainingUtils.ParameterSweep
Returns true if the sweep for the given classifier is not yet finished.

I

ids - Variable in class de.unibi.techfak.scie.classifiers.data.RawRelation
 
initializeParameter(C) - Method in interface de.unibi.techfak.scie.classifiers.TrainingUtils.ParameterSweep
Initializes the parameter that shall be swept.
isSilentCorrect() - Method in class de.unibi.techfak.scie.classifiers.LibLinearClassifier
LibLinear has a nasty habit of outputting the wrong confidence.

L

LabeledDataPoint - Class in de.unibi.techfak.scie.classifiers.data
This maps a DataPoint to a label for training purposes.
LabeledDataPoint(boolean, DataPoint) - Constructor for class de.unibi.techfak.scie.classifiers.data.LabeledDataPoint
 
LibLinearClassifier - Class in de.unibi.techfak.scie.classifiers
This is a wrapper for Benedikt Waldvogels liblinear implementation for Java.
LibLinearClassifier(SolverType) - Constructor for class de.unibi.techfak.scie.classifiers.LibLinearClassifier
 
load(Reader) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
Loads the content from the given reader to fill this FeatureDictionary.

M

MAX_NUM_INSTANCES - Static variable in class de.unibi.techfak.scie.classifiers.NonOverlappingCache
 
MAX_SLOT_CANDIDATES - Static variable in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
 
MAXCHARDISTANCE - Static variable in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint.CoreSlotTrainingDataReader
 

N

N_STR - Static variable in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
 
NonOverlappingCache - Class in de.unibi.techfak.scie.classifiers
This is a helper class to retrieve all annotations in a certain section of the text.
NonOverlappingCache.AnnotationCache<X extends org.apache.uima.jcas.tcas.Annotation> - Class in de.unibi.techfak.scie.classifiers
This stores all instances of X in a document according to their starting position.
NonOverlappingCache.AnnotationCache() - Constructor for class de.unibi.techfak.scie.classifiers.NonOverlappingCache.AnnotationCache
 
noteOptimal(C) - Method in interface de.unibi.techfak.scie.classifiers.TrainingUtils.ParameterSweep
This is called if the current value of the parameter is considered optimal.

P

PRECISION_STR - Static variable in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
 
process(JCas) - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
Annotates a given document in its JCas form.

R

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
 

S

selectBetween(Class<X>, int, int) - Method in class de.unibi.techfak.scie.classifiers.NonOverlappingCache
 
setC(double) - Method in class de.unibi.techfak.scie.classifiers.LibLinearClassifier
 
setData(DataPoint) - Method in class de.unibi.techfak.scie.classifiers.data.LabeledDataPoint
 
setDistLimit(int) - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
Sets the limit (in characters) a core instance may have to a slot instance.
setDistLimit(int) - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint.RelationTrainingDataReader
 
setEpsilon(double) - Method in class de.unibi.techfak.scie.classifiers.LibLinearClassifier
 
setFirst(A) - Method in class de.unibi.techfak.scie.classifiers.Tuple
 
setK(int) - 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.
setLabel(boolean) - Method in class de.unibi.techfak.scie.classifiers.data.LabeledDataPoint
 
setNextParameter(C) - Method in interface de.unibi.techfak.scie.classifiers.TrainingUtils.ParameterSweep
Sets the next parameter for the given classifier.
setR(int) - Method in class de.unibi.techfak.scie.classifiers.annotators.RelationAnnotator
Sets the number of annotations that may be present in the text.
setSecond(B) - Method in class de.unibi.techfak.scie.classifiers.Tuple
 
setSilentCorrect(boolean) - Method in class de.unibi.techfak.scie.classifiers.LibLinearClassifier
LibLinear has a nasty habit of outputting the wrong confidence.
simpleParameterSweep(ArrayList<LabeledDataPoint>, C, double, TrainingUtils.ParameterSweep<C>, int, Comparator<ClassifierEvaluation>, boolean) - Static method in class de.unibi.techfak.scie.classifiers.TrainingUtils
Does the simple training but does the given parameter sweep in an outer loop.
simpleTraining(ArrayList<LabeledDataPoint>, Classifier, double, int, Comparator<ClassifierEvaluation>, boolean) - Static method in class de.unibi.techfak.scie.classifiers.TrainingUtils
Chooses randomly testRatio datapoints for testing, trains the classifier with the rest and reports precision, recall and accuracy for the test set.
SlotCandidate<S extends de.unibi.techfak.scie.descriptors.Annotation> - Class in de.unibi.techfak.scie.classifiers.annotators
This is a model for a slot candidate of a relation.
SlotCandidate(S, ClassificationResult) - Constructor for class de.unibi.techfak.scie.classifiers.annotators.SlotCandidate
 
SlotSpecification<S extends org.apache.uima.jcas.tcas.Annotation> - Class in de.unibi.techfak.scie.classifiers.annotators
This specifies a slot of a relation.
SlotSpecification(Class<S>, Classifier) - Constructor for class de.unibi.techfak.scie.classifiers.annotators.SlotSpecification
 
store(Writer) - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
 
store(Writer) - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation
 
store(Writer) - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
Stores this FeatureDictionary to the given Writer.

T

TEST_SEPARATOR - Static variable in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation
 
toString() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation.SetEvaluation
 
toString() - Method in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation
 
toString() - Method in class de.unibi.techfak.scie.classifiers.data.CoreDataPoint
 
toString() - Method in class de.unibi.techfak.scie.classifiers.data.CoreSlotCombinationDataPoint
 
toString() - Method in class de.unibi.techfak.scie.classifiers.data.FeatureDictionary
 
toString() - Method in class de.unibi.techfak.scie.classifiers.data.LabeledDataPoint
 
toString() - Method in class de.unibi.techfak.scie.classifiers.data.RelationDataPoint
 
toString() - Method in class de.unibi.techfak.scie.classifiers.Tuple
 
train(ArrayList<LabeledDataPoint>) - Method in interface de.unibi.techfak.scie.classifiers.Classifier
Adjust the classifier parameters according to the given training data.
train(ArrayList<LabeledDataPoint>) - Method in class de.unibi.techfak.scie.classifiers.LibLinearClassifier
Adjust the classifier parameters according to the given training data.
TRAIN_SEPARATOR - Static variable in class de.unibi.techfak.scie.classifiers.ClassifierEvaluation
 
TrainingDataReader - Interface in de.unibi.techfak.scie.classifiers.data
This is an interface for objects that are able to construct LabeledDataPoints from manually annotated training data files.
TrainingUtils - Class in de.unibi.techfak.scie.classifiers
This is a wrapper class for some classifier training functionality.
TrainingUtils() - Constructor for class de.unibi.techfak.scie.classifiers.TrainingUtils
 
TrainingUtils.ParameterSweep<C extends Classifier> - Interface in de.unibi.techfak.scie.classifiers
This is an interface to define a parameter sweep on some classifier.
Tuple<A,B> - Class in de.unibi.techfak.scie.classifiers
 
Tuple() - Constructor for class de.unibi.techfak.scie.classifiers.Tuple
 
Tuple(A, B) - Constructor for class de.unibi.techfak.scie.classifiers.Tuple
 

W

writeParamters(Writer, Writer) - Method in interface de.unibi.techfak.scie.classifiers.Classifier
Write the current parameters and features of the classifier to the given Writer.
writeParamters(Writer, Writer) - Method in class de.unibi.techfak.scie.classifiers.LibLinearClassifier
Write the current parameters and features of the classifier to the given Writer.
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