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)); > >
