org.apache.ctakes.relationextractor.ae

Class RelationExtractorAnnotator

java.lang.Object

org.apache.uima.analysis_component.AnalysisComponent_ImplBase

org.apache.uima.analysis_component.Annotator_ImplBase

org.apache.uima.analysis_component.JCasAnnotator_ImplBase

org.apache.uima.fit.component.JCasAnnotator_ImplBase

org.cleartk.ml.CleartkAnnotator<String>

org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent, org.apache.uima.fit.factory.initializable.Initializable

Direct Known Subclasses:

Baseline1EntityMentionPairRelationExtractorAnnotator, Baseline2DegreeOfRelationExtractorAnnotator, Baseline2EntityMentionPairRelationExtractorAnnotator, Baseline3DegreeOfRelationExtractorAnnotator, Baseline3EntityMentionPairRelationExtractorAnnotator, Baseline4EntityMentionPairRelationExtractorAnnotator, CausesBringsAboutRelationExtractorAnnotator, ConsecutiveSentencesEventEventRelationAnnotator, ConsecutiveSentencesEventTimeRelationAnnotator, DegreeOfRelationExtractorAnnotator, EventCoreferenceAnnotator, EventEventI2B2RelationAnnotator, EventEventRelationGoldContainerAnnotator, EventEventRelationSeedBasedAnnotator, EventTimeI2B2RelationAnnotator, EventTimeRelationAnnotator, F1BaselineEventTimeRelationAnnotator, LocationOfRelationExtractorAnnotator, ManagesTreatsRelationExtractorAnnotator, ManifestationOfRelationExtractorAnnotator, PrecisionBaselineEventTimeRelationAnnotator, RecallBaselineEventEventRelationAnnotator, RecallBaselineEventTimeRelationAnnotator, TimidBaselineEventTimeRelationAnnotator, TreeHeightBaseline

public abstract class RelationExtractorAnnotator
extends org.cleartk.ml.CleartkAnnotator<String>

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	RelationExtractorAnnotator.IdentifiedAnnotationPair

Field Summary

Fields

Modifier and Type	Field and Description
static Map<String,Integer>	category_frequency
protected Random	coin
static String	NO_RELATION_CATEGORY
static String	PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE
protected double	probabilityOfKeepingANegativeExample

Fields inherited from class org.cleartk.ml.CleartkAnnotator

classifier, dataWriter, PARAM_CLASSIFIER_FACTORY_CLASS_NAME, PARAM_DATA_WRITER_FACTORY_CLASS_NAME, PARAM_IS_TRAINING

Constructor Summary

Constructors

Constructor and Description
RelationExtractorAnnotator()

Method Summary

Modifier and Type	Method and Description
protected String	classify(List<org.cleartk.ml.Feature> features) Predict an outcome given a set of features.
static void	clearCategoryFrequency()
protected void	createRelation(org.apache.uima.jcas.JCas jCas, IdentifiedAnnotation arg1, IdentifiedAnnotation arg2, String predictedCategory) Create a UIMA relation type based on arguments and the relation label.
protected abstract Iterable<RelationExtractorAnnotator.IdentifiedAnnotationPair>	getCandidateRelationArgumentPairs(org.apache.uima.jcas.JCas identifiedAnnotationView, org.apache.uima.jcas.tcas.Annotation coveringAnnotation) Selects the relevant mentions/annotations within a covering annotation for relation identification/extraction.
protected abstract Class<? extends org.apache.uima.jcas.tcas.Annotation>	getCoveringClass()
protected List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>>	getFeatureExtractors() Defines the list of feature extractors used by the classifier.
protected String	getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup, IdentifiedAnnotation arg1, IdentifiedAnnotation arg2) Looks up the arguments in the specified lookup table and converts the relation into a label for classification
protected Class<? extends BinaryTextRelation>	getRelationClass()
void	initialize(org.apache.uima.UimaContext context)
void	process(org.apache.uima.jcas.JCas jCas)

Methods inherited from class org.cleartk.ml.CleartkAnnotator

collectionProcessComplete, isTraining

Methods inherited from class org.apache.uima.fit.component.JCasAnnotator_ImplBase

getLogger

Methods inherited from class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

getRequiredCasInterface, process

Methods inherited from class org.apache.uima.analysis_component.Annotator_ImplBase

getCasInstancesRequired, hasNext, next

Methods inherited from class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

batchProcessComplete, destroy, getContext, getResultSpecification, reconfigure, setResultSpecification

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

NO_RELATION_CATEGORY

public static final String NO_RELATION_CATEGORY

See Also:

Constant Field Values

PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE

public static final String PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE

See Also:

Constant Field Values

category_frequency

public static Map<String,Integer> category_frequency

probabilityOfKeepingANegativeExample

protected double probabilityOfKeepingANegativeExample

coin

protected Random coin

Constructor Detail

RelationExtractorAnnotator

public RelationExtractorAnnotator()

Method Detail

getFeatureExtractors

protected List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>> getFeatureExtractors()

Defines the list of feature extractors used by the classifier. Subclasses may override this method to provide a different set of feature extractors.

Returns:

The list of feature extractors to use.

getRelationClass

protected Class<? extends BinaryTextRelation> getRelationClass()

getCoveringClass

protected abstract Class<? extends org.apache.uima.jcas.tcas.Annotation> getCoveringClass()

getCandidateRelationArgumentPairs

protected abstract Iterable<RelationExtractorAnnotator.IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(org.apache.uima.jcas.JCas identifiedAnnotationView,
                                                                                                                   org.apache.uima.jcas.tcas.Annotation coveringAnnotation)

Selects the relevant mentions/annotations within a covering annotation for relation identification/extraction.

initialize

public void initialize(org.apache.uima.UimaContext context)
                throws org.apache.uima.resource.ResourceInitializationException

Specified by:

initialize in interface org.apache.uima.analysis_component.AnalysisComponent

Specified by:

initialize in interface org.apache.uima.fit.factory.initializable.Initializable

Overrides:

initialize in class org.cleartk.ml.CleartkAnnotator<String>

Throws:

org.apache.uima.resource.ResourceInitializationException

process

public void process(org.apache.uima.jcas.JCas jCas)
             throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Specified by:

process in class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

getRelationCategory

protected String getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
                                     IdentifiedAnnotation arg1,
                                     IdentifiedAnnotation arg2)

Looks up the arguments in the specified lookup table and converts the relation into a label for classification

Returns:

If this category should not be processed for training return null otherwise it returns the label sent to the datawriter

classify

protected String classify(List<org.cleartk.ml.Feature> features)
                   throws org.cleartk.ml.CleartkProcessingException

Predict an outcome given a set of features. By default, this simply delegates to the object's classifier. Subclasses may override this method to implement more complex classification procedures.

Parameters:

features - The features to be classified.

Returns:

The predicted outcome (label) for the features.

Throws:

org.cleartk.ml.CleartkProcessingException

createRelation

protected void createRelation(org.apache.uima.jcas.JCas jCas,
                              IdentifiedAnnotation arg1,
                              IdentifiedAnnotation arg2,
                              String predictedCategory)

Create a UIMA relation type based on arguments and the relation label. This allows subclasses to create/define their own types: e.g. coreference can create CoreferenceRelation instead of BinaryTextRelation

Parameters:

jCas - - JCas object, needed to create new UIMA types

arg1 - - First argument to relation

arg2 - - Second argument to relation

predictedCategory - - Name of relation

clearCategoryFrequency

public static void clearCategoryFrequency()