It can wait if the current models work. Sent from my iPhone
> On Nov 10, 2014, at 12:18 PM, "Chen, Pei" <pei.c...@childrens.harvard.edu> > wrote: > > Chen, > Does this need to go into this upcoming release or can it wait till the next > one? > > Sent from my iPhone > >> On Nov 10, 2014, at 10:20 AM, "c...@apache.org" <c...@apache.org> wrote: >> >> Author: clin >> Date: Mon Nov 10 15:19:55 2014 >> New Revision: 1637884 >> >> URL: http://svn.apache.org/r1637884 >> Log: >> add annotators and update evaluation code for i2b2 data. >> add more system-generated events for candidate temporal relations. >> >> Added: >> >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java >> >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java >> Modified: >> >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java >> >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java >> >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java >> >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfI2B2TemporalRelations.java >> >> Added: >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java >> URL: >> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java?rev=1637884&view=auto >> ============================================================================== >> --- >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java >> (added) >> +++ >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java >> Mon Nov 10 15:19:55 2014 >> @@ -0,0 +1,280 @@ >> +/** >> + * Licensed to the Apache Software Foundation (ASF) under one >> + * or more contributor license agreements. See the NOTICE file >> + * distributed with this work for additional information >> + * regarding copyright ownership. The ASF licenses this file >> + * to you under the Apache License, Version 2.0 (the >> + * "License"); you may not use this file except in compliance >> + * with the License. You may obtain a copy of the License at >> + * >> + * http://www.apache.org/licenses/LICENSE-2.0 >> + * >> + * Unless required by applicable law or agreed to in writing, >> + * software distributed under the License is distributed on an >> + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY >> + * KIND, either express or implied. See the License for the >> + * specific language governing permissions and limitations >> + * under the License. >> + */ >> +package org.apache.ctakes.temporal.ae; >> + >> +import java.io.File; >> +import java.util.ArrayList; >> +import java.util.Arrays; >> +import java.util.Collection; >> +import java.util.List; >> +import java.util.Map; >> + >> +import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator; >> +import >> org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor; >> +import >> org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor; >> +//import >> org.apache.ctakes.relationextractor.ae.features.TokenFeaturesExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.CheckSpecialWordRelationExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.ConjunctionRelationFeaturesExtractor; >> +//import org.apache.ctakes.temporal.ae.feature.DependencyParseUtils; >> +import >> org.apache.ctakes.temporal.ae.feature.DependencyPathFeaturesExtractor; >> +import org.apache.ctakes.temporal.ae.feature.CoordinateFeaturesExtractor; >> +import org.apache.ctakes.temporal.ae.feature.DependingVerbsFeatureExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.EventInBetweenPropertyExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.EventOutsidePropertyExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.SpecialAnnotationRelationExtractor; >> +import org.apache.ctakes.temporal.ae.feature.TemporalPETFlatExtractor; >> +import org.apache.ctakes.temporal.ae.feature.TokenPropertyFeaturesExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.DeterminerRelationFeaturesExtractor; >> +import org.apache.ctakes.temporal.ae.feature.EventArgumentPropertyExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.EventTimeRelationFeatureExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.EventPositionRelationFeaturesExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.NumberOfEventsInTheSameSentenceExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.NearbyVerbTenseRelationExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.NumberOfEventTimeBetweenCandidatesExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.OverlappedHeadFeaturesExtractor; >> +import org.apache.ctakes.temporal.ae.feature.SRLRelationFeaturesExtractor; >> +import org.apache.ctakes.temporal.ae.feature.TimeXRelationFeaturesExtractor; >> +import org.apache.ctakes.temporal.ae.feature.SectionHeaderRelationExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.TemporalAttributeFeatureExtractor; >> +import org.apache.ctakes.temporal.ae.feature.UmlsFeatureExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPETExtractor; >> +import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation; >> +import org.apache.ctakes.typesystem.type.relation.RelationArgument; >> +import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation; >> +//import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode; >> +import org.apache.ctakes.typesystem.type.textsem.EventMention; >> +import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation; >> +import org.apache.ctakes.typesystem.type.textspan.Sentence; >> +import org.apache.uima.analysis_engine.AnalysisEngineDescription; >> +import org.apache.uima.jcas.JCas; >> +import org.apache.uima.jcas.tcas.Annotation; >> +import org.apache.uima.resource.ResourceInitializationException; >> +import org.cleartk.ml.CleartkAnnotator; >> +import org.cleartk.ml.DataWriter; >> +import org.cleartk.ml.jar.DefaultDataWriterFactory; >> +import org.cleartk.ml.jar.DirectoryDataWriterFactory; >> +import org.cleartk.ml.jar.GenericJarClassifierFactory; >> +import org.apache.uima.fit.factory.AnalysisEngineFactory; >> +import org.apache.uima.fit.util.JCasUtil; >> + >> +import com.google.common.collect.Lists; >> + >> +public class EventEventI2B2RelationAnnotator extends >> RelationExtractorAnnotator { >> + >> + public static AnalysisEngineDescription createDataWriterDescription( >> + Class<? extends DataWriter<String>> dataWriterClass, >> + File outputDirectory, >> + double probabilityOfKeepingANegativeExample) throws >> ResourceInitializationException { >> + return AnalysisEngineFactory.createEngineDescription( >> + EventEventI2B2RelationAnnotator.class, >> + CleartkAnnotator.PARAM_IS_TRAINING, >> + true, >> + DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME, >> + dataWriterClass, >> + DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY, >> + outputDirectory, >> + >> RelationExtractorAnnotator.PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE, >> + // not sure why this has to be cast; something funny going >> on in uimaFIT maybe? >> + (float) probabilityOfKeepingANegativeExample); >> + } >> + >> + public static AnalysisEngineDescription >> createAnnotatorDescription(String modelPath) >> + throws ResourceInitializationException { >> + return AnalysisEngineFactory.createEngineDescription( >> + EventEventI2B2RelationAnnotator.class, >> + CleartkAnnotator.PARAM_IS_TRAINING, >> + false, >> + GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH, >> + modelPath); >> + } >> + >> + /** >> + * @deprecated use String path instead of File. >> + * ClearTK will automatically Resolve the String to an InputStream. >> + * This will allow resources to be read within from a jar as well as >> File. >> + */ >> + @SuppressWarnings("dep-ann") >> + public static AnalysisEngineDescription createAnnotatorDescription(File >> modelDirectory) >> + throws ResourceInitializationException { >> + return AnalysisEngineFactory.createEngineDescription( >> + EventEventI2B2RelationAnnotator.class, >> + CleartkAnnotator.PARAM_IS_TRAINING, >> + false, >> + GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH, >> + new File(modelDirectory, "model.jar")); >> + } >> + >> + @Override >> + protected List<RelationFeaturesExtractor> getFeatureExtractors() { >> + return Lists.newArrayList( >> + // new TokenFeaturesExtractor() >> + new UnexpandedTokenFeaturesExtractor() //use unexpanded >> version for i2b2 data >> + , new PartOfSpeechFeaturesExtractor() >> + // , new TemporalPETExtractor() >> + , new EventArgumentPropertyExtractor() >> + , new NumberOfEventTimeBetweenCandidatesExtractor() >> + , new SectionHeaderRelationExtractor() >> + , new NearbyVerbTenseRelationExtractor() >> + , new CheckSpecialWordRelationExtractor() >> + , new UmlsFeatureExtractor() >> + , new DependencyPathFeaturesExtractor() >> + , new CoordinateFeaturesExtractor() >> + , new OverlappedHeadFeaturesExtractor() >> + , new SRLRelationFeaturesExtractor() >> + , new NumberOfEventsInTheSameSentenceExtractor() >> + , new EventPositionRelationFeaturesExtractor() //not helpful >> + , new TimeXRelationFeaturesExtractor() //not helpful >> + , new ConjunctionRelationFeaturesExtractor() >> + , new DeterminerRelationFeaturesExtractor() >> + , new EventTimeRelationFeatureExtractor() >> + , new TokenPropertyFeaturesExtractor() >> + , new DependingVerbsFeatureExtractor() >> + , new SpecialAnnotationRelationExtractor() //not helpful >> + , new TemporalPETFlatExtractor() >> + // , new EventInBetweenPropertyExtractor() >> + // , new EventOutsidePropertyExtractor() >> + ); >> + } >> + >> + @Override >> + protected Class<? extends Annotation> getCoveringClass() { >> + return Sentence.class; >> + } >> + >> + @Override >> + protected List<IdentifiedAnnotationPair> >> getCandidateRelationArgumentPairs( >> + JCas jCas, Annotation sentence) { >> + >> + Map<EventMention, Collection<EventMention>> coveringMap = >> + JCasUtil.indexCovering(jCas, EventMention.class, >> EventMention.class); >> + >> + List<IdentifiedAnnotationPair> pairs = Lists.newArrayList(); >> + List<EventMention> events = new >> ArrayList<>(JCasUtil.selectCovered(jCas, EventMention.class, sentence)); >> + //filter events: >> + List<EventMention> realEvents = Lists.newArrayList(); >> + for( EventMention event : events){ >> + if(event.getClass().equals(EventMention.class)){ >> + realEvents.add(event); >> + } >> + } >> + events = realEvents; >> + >> + int eventNum = events.size(); >> + >> + for (int i = 0; i < eventNum-1; i++){ >> + for(int j = i+1; j < eventNum; j++){ >> + EventMention eventA = events.get(j); >> + EventMention eventB = events.get(i); >> + >> + if(this.isTraining()){ >> + //pairing covering system events: >> + for (EventMention event1 : coveringMap.get(eventA)){ >> + for(EventMention event2 : coveringMap.get(eventB)){ >> + pairs.add(new IdentifiedAnnotationPair(event1, >> event2)); >> + } >> + pairs.add(new IdentifiedAnnotationPair(event1, >> eventB)); >> + } >> + for(EventMention event2 : coveringMap.get(eventB)){ >> + pairs.add(new IdentifiedAnnotationPair(eventA, >> event2)); >> + } >> + //pairing covered system events: >> + for(EventMention event1 : JCasUtil.selectCovered(jCas, >> EventMention.class, eventA)){ >> + for(EventMention event2 : >> JCasUtil.selectCovered(jCas, EventMention.class, eventB)){ >> + pairs.add(new IdentifiedAnnotationPair(event1, >> event2)); >> + } >> + pairs.add(new IdentifiedAnnotationPair(event1, >> eventB)); >> + } >> + for(EventMention event2 : JCasUtil.selectCovered(jCas, >> EventMention.class, eventB)){ >> + pairs.add(new IdentifiedAnnotationPair(eventA, >> event2)); >> + } >> + } >> + pairs.add(new IdentifiedAnnotationPair(eventA, eventB)); >> + >> + } >> + } >> + >> + >> + // if(eventNum >= 2){ >> + // for ( int i = 0; i< eventNum -1 ; i ++){ >> + // EventMention evI = events.get(i); >> + // for(int j = i+1; j< eventNum; j++){ >> + // EventMention evJ = events.get(j); >> + // if(j-i==1 || j-i==eventNum-1){//if two events >> are consecutive, or major events >> + // pairs.add(new >> IdentifiedAnnotationPair(evJ, evI)); >> + // }else if(ifDependent(jCas, evI, evJ)){//if >> the event pairs are dependent// eventNum < 7 && >> + // pairs.add(new >> IdentifiedAnnotationPair(evJ, evI)); >> + // }else{// if the >> + // continue; >> + // } >> + // } >> + // } >> + // } >> + >> + return pairs; >> + } >> + >> + @Override >> + protected void createRelation(JCas jCas, IdentifiedAnnotation arg1, >> + IdentifiedAnnotation arg2, String predictedCategory) { >> + RelationArgument relArg1 = new RelationArgument(jCas); >> + relArg1.setArgument(arg1); >> + relArg1.setRole("Arg1"); >> + relArg1.addToIndexes(); >> + RelationArgument relArg2 = new RelationArgument(jCas); >> + relArg2.setArgument(arg2); >> + relArg2.setRole("Arg2"); >> + relArg2.addToIndexes(); >> + TemporalTextRelation relation = new TemporalTextRelation(jCas); >> + relation.setArg1(relArg1); >> + relation.setArg2(relArg2); >> + relation.setCategory(predictedCategory); >> + relation.addToIndexes(); >> + } >> + >> + @Override >> + protected String getRelationCategory( >> + Map<List<Annotation>, BinaryTextRelation> relationLookup, >> + IdentifiedAnnotation arg1, >> + IdentifiedAnnotation arg2) { >> + BinaryTextRelation relation = >> relationLookup.get(Arrays.asList(arg1, arg2)); >> + String category = null; >> + if (relation != null && relation instanceof TemporalTextRelation) { >> + category = relation.getCategory(); >> + } else { >> + relation = relationLookup.get(Arrays.asList(arg2, arg1)); >> + if (relation != null && relation instanceof >> TemporalTextRelation) { >> + if(relation.getCategory().equals("OVERLAP")){ >> + category = relation.getCategory(); >> + // }else if >> (relation.getCategory().equals("BEFORE")){ >> + // category = "AFTER"; >> + // }else if >> (relation.getCategory().equals("AFTER")){ >> + // category = "BEFORE"; >> + // } >> + }else{ >> + category = relation.getCategory() + "-1"; >> + } >> + } >> + } >> + if (category == null && coin.nextDouble() <= >> this.probabilityOfKeepingANegativeExample) { >> + category = NO_RELATION_CATEGORY; >> + } >> + return category; >> + } >> +} >> >> Modified: >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java >> URL: >> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java?rev=1637884&r1=1637883&r2=1637884&view=diff >> ============================================================================== >> --- >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java >> (original) >> +++ >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotator.java >> Mon Nov 10 15:19:55 2014 >> @@ -198,15 +198,25 @@ public class EventEventRelationAnnotator >> } >> if(eventAValid && eventBValid){ >> if(this.isTraining()){ >> + //pairing covering system events: >> for (EventMention event1 : coveringMap.get(eventA)){ >> for(EventMention event2 : coveringMap.get(eventB)){ >> pairs.add(new IdentifiedAnnotationPair(event1, >> event2)); >> } >> + pairs.add(new IdentifiedAnnotationPair(event1, >> eventB)); >> } >> + for(EventMention event2 : coveringMap.get(eventB)){ >> + pairs.add(new IdentifiedAnnotationPair(eventA, >> event2)); >> + } >> + //pairing covered system events: >> for(EventMention event1 : JCasUtil.selectCovered(jCas, >> EventMention.class, eventA)){ >> for(EventMention event2 : >> JCasUtil.selectCovered(jCas, EventMention.class, eventB)){ >> pairs.add(new IdentifiedAnnotationPair(event1, >> event2)); >> } >> + pairs.add(new IdentifiedAnnotationPair(event1, >> eventB)); >> + } >> + for(EventMention event2 : >> JCasUtil.selectCovered(jCas, EventMention.class, eventB)){ >> + pairs.add(new IdentifiedAnnotationPair(eventA, >> event2)); >> } >> } >> pairs.add(new IdentifiedAnnotationPair(eventA, eventB)); >> >> Added: >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java >> URL: >> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java?rev=1637884&view=auto >> ============================================================================== >> --- >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java >> (added) >> +++ >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java >> Mon Nov 10 15:19:55 2014 >> @@ -0,0 +1,253 @@ >> +/** >> + * Licensed to the Apache Software Foundation (ASF) under one >> + * or more contributor license agreements. See the NOTICE file >> + * distributed with this work for additional information >> + * regarding copyright ownership. The ASF licenses this file >> + * to you under the Apache License, Version 2.0 (the >> + * "License"); you may not use this file except in compliance >> + * with the License. You may obtain a copy of the License at >> + * >> + * http://www.apache.org/licenses/LICENSE-2.0 >> + * >> + * Unless required by applicable law or agreed to in writing, >> + * software distributed under the License is distributed on an >> + * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY >> + * KIND, either express or implied. See the License for the >> + * specific language governing permissions and limitations >> + * under the License. >> + */ >> +package org.apache.ctakes.temporal.ae; >> + >> +import java.io.File; >> +import java.util.Arrays; >> +import java.util.Collection; >> +import java.util.List; >> +import java.util.Map; >> + >> +import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator; >> +import >> org.apache.ctakes.relationextractor.ae.features.PartOfSpeechFeaturesExtractor; >> +import >> org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.CheckSpecialWordRelationExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.ConjunctionRelationFeaturesExtractor; >> +import org.apache.ctakes.temporal.ae.feature.DependencyFeatureExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.DependencyPathFeaturesExtractor; >> +import org.apache.ctakes.temporal.ae.feature.EventArgumentPropertyExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.EventIndexOfSameSentenceRelationFeaturesExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.EventPositionRelationFeaturesExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.EventTimeRelationFeatureExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.NearbyVerbTenseRelationExtractor; >> +import org.apache.ctakes.temporal.ae.feature.NearestFlagFeatureExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.NumberOfEventTimeBetweenCandidatesExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.OverlappedHeadFeaturesExtractor; >> +//import org.apache.ctakes.temporal.ae.feature.SRLRelationFeaturesExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.SectionHeaderRelationExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.TemporalAttributeFeatureExtractor; >> +import org.apache.ctakes.temporal.ae.feature.TemporalPETFlatExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.TimeWordTypeRelationExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.TimeXPropertyRelationFeaturesExtractor; >> +import org.apache.ctakes.temporal.ae.feature.TimeXRelationFeaturesExtractor; >> +import >> org.apache.ctakes.temporal.ae.feature.UnexpandedTokenFeaturesExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.TemporalAttributeFeatureExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.treekernel.EventTimeFlatTreeFeatureExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.treekernel.EventVerbRelationTreeExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPETExtractor; >> +//import >> org.apache.ctakes.temporal.ae.feature.treekernel.TemporalPathExtractor; >> +import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation; >> +import org.apache.ctakes.typesystem.type.relation.RelationArgument; >> +import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation; >> +import org.apache.ctakes.typesystem.type.textsem.EventMention; >> +import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation; >> +import org.apache.ctakes.typesystem.type.textsem.TimeMention; >> +import org.apache.ctakes.typesystem.type.textspan.Sentence; >> +import org.apache.uima.analysis_engine.AnalysisEngineDescription; >> +import org.apache.uima.jcas.JCas; >> +import org.apache.uima.jcas.tcas.Annotation; >> +import org.apache.uima.resource.ResourceInitializationException; >> +import org.cleartk.ml.CleartkAnnotator; >> +import org.cleartk.ml.DataWriter; >> +import org.cleartk.ml.jar.DefaultDataWriterFactory; >> +import org.cleartk.ml.jar.DirectoryDataWriterFactory; >> +import org.cleartk.ml.jar.GenericJarClassifierFactory; >> +import org.apache.uima.fit.factory.AnalysisEngineFactory; >> +import org.apache.uima.fit.util.JCasUtil; >> + >> +import com.google.common.collect.Lists; >> + >> +public class EventTimeI2B2RelationAnnotator extends >> RelationExtractorAnnotator { >> + >> + public static AnalysisEngineDescription createDataWriterDescription( >> + Class<? extends DataWriter<String>> dataWriterClass, >> + File outputDirectory, >> + double probabilityOfKeepingANegativeExample) throws >> ResourceInitializationException { >> + return AnalysisEngineFactory.createEngineDescription( >> + EventTimeI2B2RelationAnnotator.class, >> + CleartkAnnotator.PARAM_IS_TRAINING, >> + true, >> + DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME, >> + dataWriterClass, >> + DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY, >> + outputDirectory, >> + >> RelationExtractorAnnotator.PARAM_PROBABILITY_OF_KEEPING_A_NEGATIVE_EXAMPLE, >> + // not sure why this has to be cast; something funny going >> on in uimaFIT maybe? >> + (float) probabilityOfKeepingANegativeExample); >> + } >> + >> + public static AnalysisEngineDescription createEngineDescription(String >> modelPath) >> + throws ResourceInitializationException { >> + return AnalysisEngineFactory.createEngineDescription( >> + EventTimeI2B2RelationAnnotator.class, >> + CleartkAnnotator.PARAM_IS_TRAINING, >> + false, >> + GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH, >> + modelPath); >> + } >> + /** >> + * @deprecated use String path instead of File. >> + * ClearTK will automatically Resolve the String to an InputStream. >> + * This will allow resources to be read within from a jar as well as >> File. >> + */ >> + @Deprecated >> + public static AnalysisEngineDescription createEngineDescription(File >> modelDirectory) >> + throws ResourceInitializationException { >> + return AnalysisEngineFactory.createEngineDescription( >> + EventTimeI2B2RelationAnnotator.class, >> + CleartkAnnotator.PARAM_IS_TRAINING, >> + false, >> + GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH, >> + new File(modelDirectory, "model.jar")); >> + } >> + >> + @Override >> + protected List<RelationFeaturesExtractor> getFeatureExtractors() { >> + return Lists.newArrayList( >> +// new TokenFeaturesExtractor() >> + new UnexpandedTokenFeaturesExtractor() //use unexpanded >> version for i2b2 data >> + , new PartOfSpeechFeaturesExtractor() >> + , new TemporalAttributeFeatureExtractor() >> + // , new EventTimeFlatTreeFeatureExtractor() >> + // , new TemporalPETExtractor() >> + //, new TemporalPathExtractor() >> + // , new EventVerbRelationTreeExtractor() >> + , new NumberOfEventTimeBetweenCandidatesExtractor() >> + // , new SectionHeaderRelationExtractor() >> + , new NearbyVerbTenseRelationExtractor() >> + , new CheckSpecialWordRelationExtractor() >> + , new NearestFlagFeatureExtractor() >> + , new DependencyPathFeaturesExtractor() >> + , new DependencyFeatureExtractor() >> + // , new SRLRelationFeaturesExtractor()// >> tried, but not helpful >> + , new EventArgumentPropertyExtractor() >> + , new OverlappedHeadFeaturesExtractor() >> + // , new EventTimeRelationFeatureExtractor() >> + , new ConjunctionRelationFeaturesExtractor() >> + // , new >> EventPositionRelationFeaturesExtractor() //tried, but not helpful >> + , new TimeXRelationFeaturesExtractor() >> + , new TemporalPETFlatExtractor() >> + , new TimeXPropertyRelationFeaturesExtractor() >> + // , new TimeWordTypeRelationExtractor() >> //tried, but not helpful >> + // , new >> EventIndexOfSameSentenceRelationFeaturesExtractor() //tried, but not helpful >> + ); >> + } >> + >> + @Override >> + protected Class<? extends Annotation> getCoveringClass() { >> + return Sentence.class; >> + } >> + >> + @Override >> + public List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs( >> + JCas jCas, >> + Annotation sentence) { >> + Map<EventMention, Collection<EventMention>> coveringMap = >> + JCasUtil.indexCovering(jCas, EventMention.class, >> EventMention.class); >> + >> + List<IdentifiedAnnotationPair> pairs = Lists.newArrayList(); >> + for (EventMention event : JCasUtil.selectCovered(jCas, >> EventMention.class, sentence)) { >> + boolean eventValid = false; >> + if (event.getClass().equals(EventMention.class)) {//event is a >> gold event >> + eventValid = true; >> + } >> + >> + if(eventValid){ >> + // ignore subclasses like Procedure and Disease/Disorder >> + if(this.isTraining()){//if training mode, train on both >> gold event and span-overlapping system events >> + for (TimeMention time : JCasUtil.selectCovered(jCas, >> TimeMention.class, sentence)) { >> + Collection<EventMention> eventList = >> coveringMap.get(event); >> + for(EventMention covEvent : eventList){ >> + pairs.add(new >> IdentifiedAnnotationPair(covEvent, time)); >> + } >> + pairs.add(new IdentifiedAnnotationPair(event, >> time)); >> + for(EventMention covedEvent : >> JCasUtil.selectCovered(jCas, EventMention.class, event)){//select covered >> events >> + pairs.add(new >> IdentifiedAnnotationPair(covedEvent, time)); >> + } >> + } >> + }else{//if testing mode, only test on system generated >> events >> + for (TimeMention time : JCasUtil.selectCovered(jCas, >> TimeMention.class, sentence)) { >> + pairs.add(new IdentifiedAnnotationPair(event, >> time)); >> + } >> + } >> + } >> + } >> + >> + return pairs; >> + } >> + >> + @Override >> + protected void createRelation(JCas jCas, IdentifiedAnnotation arg1, >> + IdentifiedAnnotation arg2, String predictedCategory) { >> + RelationArgument relArg1 = new RelationArgument(jCas); >> + relArg1.setArgument(arg1); >> + relArg1.setRole("Arg1"); >> + relArg1.addToIndexes(); >> + RelationArgument relArg2 = new RelationArgument(jCas); >> + relArg2.setArgument(arg2); >> + relArg2.setRole("Arg2"); >> + relArg2.addToIndexes(); >> + TemporalTextRelation relation = new TemporalTextRelation(jCas); >> + relation.setArg1(relArg1); >> + relation.setArg2(relArg2); >> + relation.setCategory(predictedCategory); >> + relation.addToIndexes(); >> + } >> + >> + >> + @Override >> + protected String getRelationCategory( >> + Map<List<Annotation>, BinaryTextRelation> relationLookup, >> + IdentifiedAnnotation arg1, >> + IdentifiedAnnotation arg2) { >> + BinaryTextRelation relation = >> relationLookup.get(Arrays.asList(arg1, arg2)); >> + String category = null; >> + if (relation != null) { >> + category = relation.getCategory(); >> + } else { >> + relation = relationLookup.get(Arrays.asList(arg2, arg1)); >> + if (relation != null) { >> + if(relation.getCategory().equals("OVERLAP")){ >> + category = relation.getCategory(); >> + // }else if >> (relation.getCategory().equals("BEFORE")){ >> + // category = "AFTER"; >> + // }else if >> (relation.getCategory().equals("AFTER")){ >> + // category = "BEFORE"; >> + // } >> + }else{ >> + category = relation.getCategory() + "-1"; >> + } >> + } >> + } >> + >> + if(category!=null){ >> + if(!((EventMention)arg1).getClass().equals(EventMention.class)){ >> + System.out.println("find system-event relations: "+ >> arg1.getCoveredText() + " -"+category+"- " + arg2.getCoveredText()); >> + }else{ >> + System.out.println("find gold-event relations: "+ >> arg1.getCoveredText() + " -"+category+"- " + arg2.getCoveredText()); >> + } >> + } >> + >> + if (category == null && coin.nextDouble() <= >> this.probabilityOfKeepingANegativeExample) { >> + category = NO_RELATION_CATEGORY; >> + } >> + >> + return category; >> + } >> +} >> >> Modified: >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java >> URL: >> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java?rev=1637884&r1=1637883&r2=1637884&view=diff >> ============================================================================== >> --- >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java >> (original) >> +++ >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java >> Mon Nov 10 15:19:55 2014 >> @@ -329,7 +329,7 @@ EvaluationOfTemporalRelations_ImplBase{ >> } >> >> // HideOutput hider = new HideOutput(); >> - JarClassifierBuilder.trainAndPackage(new >> File(directory,"event-event"),"-c", >> optArray[1]);//"-w1","0.09","-w2","4","-w3","9","-w5","2","-w6","16","-w7","10","-w8","6", >> "-w9","45","-w10","30","-c", optArray[1]);//"-c", "0.05");//optArray); >> + JarClassifierBuilder.trainAndPackage(new >> File(directory,"event-event"),"-w1","0.08","-w3","3","-w4","17","-w5","20","-w6","16","-w7","10","-w8","6", >> "-w9","45","-w10","30","-c", optArray[1]);//"-c", "0.05");//optArray); >> // JarClassifierBuilder.trainAndPackage(new >> File(directory,"event-event"), "-h","0","-c", "1000"); >> // hider.restoreOutput(); >> // hider.close(); >> @@ -529,6 +529,20 @@ EvaluationOfTemporalRelations_ImplBase{ >> for(EventMention covEventB : coveringMap.get(event2)){ >> createRelation(relationView, covEventA, covEventB, >> relation.getCategory()); >> } >> + createRelation(relationView, covEventA, event2, >> relation.getCategory()); >> + } >> + for(EventMention covEventB : coveringMap.get(event2)){ >> + createRelation(relationView, event1, covEventB, >> relation.getCategory()); >> + } >> + //get covered system events: >> + for(EventMention covedEventA : >> JCasUtil.selectCovered(jCas, EventMention.class, event1)){//select covered >> events >> + for(EventMention covedEventB : >> JCasUtil.selectCovered(jCas, EventMention.class, event2)){ >> + createRelation(relationView, covedEventA, >> covedEventB, relation.getCategory()); >> + } >> + createRelation(relationView, covedEventA, event2, >> relation.getCategory()); >> + } >> + for(EventMention covedEventB : >> JCasUtil.selectCovered(jCas, EventMention.class, event2)){ >> + createRelation(relationView, event1, covedEventB, >> relation.getCategory()); >> } >> } >> } >> >> Modified: >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java >> URL: >> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java?rev=1637884&r1=1637883&r2=1637884&view=diff >> ============================================================================== >> --- >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java >> (original) >> +++ >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java >> Mon Nov 10 15:19:55 2014 >> @@ -34,6 +34,7 @@ import java.util.List; >> import java.util.Map; >> import java.util.Set; >> >> +import >> org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair; >> import >> org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments; >> import org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator; >> import org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator; >> @@ -693,6 +694,9 @@ EvaluationOfTemporalRelations_ImplBase{ >> createRelation(relationView, covEvent, arg2, >> relation.getCategory()); >> } >> } >> + for(EventMention covedEvent : >> JCasUtil.selectCovered(jCas, EventMention.class, event)){//select covered >> events >> + createRelation(relationView, covedEvent, arg2, >> relation.getCategory()); >> + } >> }else if(arg2 instanceof EventMention && arg1 instanceof >> TimeMention){ >> event = (EventMention) arg2; >> Collection<EventMention> eventList = >> coveringMap.get(event); >> @@ -701,6 +705,9 @@ EvaluationOfTemporalRelations_ImplBase{ >> createRelation(relationView, arg1, covEvent, >> relation.getCategory()); >> } >> } >> + for(EventMention covedEvent : >> JCasUtil.selectCovered(jCas, EventMention.class, event)){//select covered >> events >> + createRelation(relationView, arg1, covedEvent, >> relation.getCategory()); >> + } >> } >> } >> >> >> Modified: >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfI2B2TemporalRelations.java >> URL: >> http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfI2B2TemporalRelations.java?rev=1637884&r1=1637883&r2=1637884&view=diff >> ============================================================================== >> --- >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfI2B2TemporalRelations.java >> (original) >> +++ >> ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfI2B2TemporalRelations.java >> Mon Nov 10 15:19:55 2014 >> @@ -38,14 +38,15 @@ import org.apache.ctakes.core.ae.CDASegm >> import >> org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments; >> import >> org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventEventRelationAnnotator; >> import >> org.apache.ctakes.temporal.ae.ConsecutiveSentencesEventTimeRelationAnnotator; >> -import org.apache.ctakes.temporal.ae.EventTimeSelfRelationAnnotator; >> import org.apache.ctakes.temporal.ae.TemporalRelationRuleAnnotator; >> import org.apache.ctakes.temporal.ae.DocTimeRelAnnotator; >> import org.apache.ctakes.temporal.ae.EventAdmissionTimeAnnotator; >> import org.apache.ctakes.temporal.ae.EventDischargeTimeAnnotator; >> -import org.apache.ctakes.temporal.ae.EventEventRelationAnnotator; >> -import org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator; >> +import org.apache.ctakes.temporal.ae.EventEventI2B2RelationAnnotator; >> +import org.apache.ctakes.temporal.ae.EventTimeI2B2RelationAnnotator; >> import >> org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventTimeRelationAnnotator; >> +import >> org.apache.ctakes.temporal.eval.EvaluationOfEventEventThymeRelations.AddEEPotentialRelations; >> +import >> org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.AddPotentialRelations; >> import >> org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings; >> import >> org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveNonContainsRelations.RemoveGoldAttributes; >> import org.apache.ctakes.temporal.utils.AnnotationIdCollection; >> @@ -66,7 +67,6 @@ import org.apache.uima.fit.component.JCa >> import org.apache.uima.fit.descriptor.ConfigurationParameter; >> import org.apache.uima.fit.factory.AggregateBuilder; >> import org.apache.uima.fit.factory.AnalysisEngineFactory; >> -import org.apache.uima.fit.pipeline.JCasIterator; >> import org.apache.uima.fit.pipeline.SimplePipeline; >> import org.apache.uima.fit.util.JCasUtil; >> import org.apache.uima.jcas.JCas; >> @@ -75,7 +75,7 @@ import org.apache.uima.resource.Resource >> import org.apache.uima.util.FileUtils; >> import org.cleartk.eval.AnnotationStatistics; >> import org.cleartk.ml.jar.JarClassifierBuilder; >> -//import org.cleartk.ml.libsvm.LibSvmStringOutcomeDataWriter; >> +import org.cleartk.ml.libsvm.LibSvmStringOutcomeDataWriter; >> import org.cleartk.ml.liblinear.LibLinearStringOutcomeDataWriter; >> //import org.cleartk.classifier.tksvmlight.TKSVMlightStringOutcomeDataWriter; >> import org.cleartk.ml.tksvmlight.model.CompositeKernel.ComboOperator; >> @@ -292,13 +292,18 @@ EvaluationOfTemporalRelations_ImplBase{ >> // CAS.NAME_DEFAULT_SOFA, >> // GOLD_VIEW_NAME); >> // >> aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveNonContainsRelations.class)); >> - >> aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(AddFlippedOverlap.class));//add >> flipped overlap instances to training data >> +// >> aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(AddFlippedOverlap.class));//add >> flipped overlap instances to training data >> >> // >> aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveEventEventRelations.class)); >> //test rules: >> // >> aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(TemporalRelationRuleAnnotator.class)); >> + >> + //add unlabeled nearby system events as potential event-time links: >> + >> aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(AddPotentialRelations.class)); >> + //add unlabeled nearby system events as potential event-event >> links: >> + >> aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(AddEEPotentialRelations.class)); >> >> - >> aggregateBuilder.add(EventTimeSelfRelationAnnotator.createDataWriterDescription( >> + >> aggregateBuilder.add(EventTimeI2B2RelationAnnotator.createDataWriterDescription( >> // LibSvmStringOutcomeDataWriter.class, >> LibLinearStringOutcomeDataWriter.class, >> // TKSVMlightStringOutcomeDataWriter.class, >> @@ -306,27 +311,27 @@ EvaluationOfTemporalRelations_ImplBase{ >> // SVMlightStringOutcomeDataWriter.class, >> new File(directory,EVENT_TIME), >> params.probabilityOfKeepingANegativeExample)); >> - >> aggregateBuilder.add(EventEventRelationAnnotator.createDataWriterDescription( >> + >> aggregateBuilder.add(EventEventI2B2RelationAnnotator.createDataWriterDescription( >> >> LibLinearStringOutcomeDataWriter.class,//TKSVMlightStringOutcomeDataWriter.class,// >> // LIBLINEARStringOutcomeDataWriter.class, >> new File(directory,EVENT_EVENT), >> params.probabilityOfKeepingANegativeExample)); >> >> aggregateBuilder.add(EventDischargeTimeAnnotator.createDataWriterDescription( >> - // LibSvmStringOutcomeDataWriter.class, >> - LibLinearStringOutcomeDataWriter.class, >> + LibSvmStringOutcomeDataWriter.class, >> +// LibLinearStringOutcomeDataWriter.class, >> new File(directory,EVENT_DISCHARGE))); >> >> aggregateBuilder.add(EventAdmissionTimeAnnotator.createDataWriterDescription( >> - // LibSvmStringOutcomeDataWriter.class, >> - LibLinearStringOutcomeDataWriter.class, >> + LibSvmStringOutcomeDataWriter.class, >> +// LibLinearStringOutcomeDataWriter.class, >> new File(directory,EVENT_ADMISSION))); >> >> aggregateBuilder.add(ConsecutiveSentencesEventEventRelationAnnotator.createDataWriterDescription( >> - // LibSvmStringOutcomeDataWriter.class, >> - LibLinearStringOutcomeDataWriter.class, >> + LibSvmStringOutcomeDataWriter.class, >> +// LibLinearStringOutcomeDataWriter.class, >> new File(directory,TEMP_CROSSSENT), >> params.probabilityOfKeepingANegativeExample)); >> >> aggregateBuilder.add(ConsecutiveSentencesEventTimeRelationAnnotator.createDataWriterDescription( >> - // LibSvmStringOutcomeDataWriter.class, >> - LibLinearStringOutcomeDataWriter.class, >> + LibSvmStringOutcomeDataWriter.class, >> +// LibLinearStringOutcomeDataWriter.class, >> new File(directory,TEMPET_CROSSSENT), >> params.probabilityOfKeepingANegativeExample)); >> SimplePipeline.runPipeline(collectionReader, >> aggregateBuilder.createAggregate()); >> @@ -355,14 +360,14 @@ EvaluationOfTemporalRelations_ImplBase{ >> } >> >> // HideOutput hider = new HideOutput(); >> - JarClassifierBuilder.trainAndPackage(new >> File(directory,EVENT_TIME), "-c", "0.001");//"-h","0","-c", >> "1000");//optArray);//"-c", "0.05");// >> - JarClassifierBuilder.trainAndPackage(new >> File(directory,EVENT_EVENT), "-c", "0.001"); >> - JarClassifierBuilder.trainAndPackage(new >> File(directory,EVENT_DISCHARGE), "-c", "0.001"); >> - JarClassifierBuilder.trainAndPackage(new >> File(directory,EVENT_ADMISSION), "-c", "0.001"); >> + JarClassifierBuilder.trainAndPackage(new >> File(directory,EVENT_TIME), "-c", "0.0002", >> "-w2","0.2","-w3","7","-w4","7","-w5","13");//"-h","0","-c", >> "1000");//optArray);//"-c", "0.05");// >> + JarClassifierBuilder.trainAndPackage(new >> File(directory,EVENT_EVENT), "-c", >> "0.0002","-w1","0.07","-w2","14","-w3","5","-w4","10","-w6","20"); >> + JarClassifierBuilder.trainAndPackage(new >> File(directory,EVENT_DISCHARGE), "-h","0","-c", "1000"); >> + JarClassifierBuilder.trainAndPackage(new >> File(directory,EVENT_ADMISSION), "-h","0","-c", "1000"); >> // JarClassifierBuilder.trainAndPackage(new >> File(directory,TIME_ADMISSION), "-h","0","-c", "1000"); >> // JarClassifierBuilder.trainAndPackage(new >> File(directory,TIME_DISCHARGE), "-h","0","-c", "1000"); >> - JarClassifierBuilder.trainAndPackage(new >> File(directory,TEMP_CROSSSENT), "-c", "0.001"); >> - JarClassifierBuilder.trainAndPackage(new >> File(directory,TEMPET_CROSSSENT), "-c", "0.001"); >> + JarClassifierBuilder.trainAndPackage(new >> File(directory,TEMP_CROSSSENT), "-h","0","-c", "1000"); >> + JarClassifierBuilder.trainAndPackage(new >> File(directory,TEMPET_CROSSSENT), "-h","0","-c", "1000"); >> // hider.restoreOutput(); >> // hider.close(); >> } >> @@ -419,8 +424,8 @@ EvaluationOfTemporalRelations_ImplBase{ >> // >> aggregateBuilder.add(TimexDischargeTimeAnnotator.createAnnotatorDescription(new >> File(directory,TIME_DISCHARGE))); >> >> aggregateBuilder.add(this.baseline ? >> RecallBaselineEventTimeRelationAnnotator.createAnnotatorDescription(directory) >> : >> - EventTimeSelfRelationAnnotator.createEngineDescription(new >> File(directory,EVENT_TIME))); >> - >> aggregateBuilder.add(EventEventRelationAnnotator.createAnnotatorDescription(new >> File(directory,EVENT_EVENT))); >> + EventTimeI2B2RelationAnnotator.createEngineDescription(new >> File(directory,EVENT_TIME))); >> + >> aggregateBuilder.add(EventEventI2B2RelationAnnotator.createAnnotatorDescription(new >> File(directory,EVENT_EVENT))); >> >> aggregateBuilder.add(ConsecutiveSentencesEventEventRelationAnnotator.createAnnotatorDescription(new >> File(directory,TEMP_CROSSSENT))); >> >> aggregateBuilder.add(ConsecutiveSentencesEventTimeRelationAnnotator.createAnnotatorDescription(new >> File(directory,TEMPET_CROSSSENT))); >> >> aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(TemporalRelationRuleAnnotator.class)); >> >>
