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Posted to commits@ctakes.apache.org by cl...@apache.org on 2014/11/20 22:49:46 UTC
svn commit: r1640825 - in
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal: ae/
eval/
Author: clin
Date: Thu Nov 20 21:49:45 2014
New Revision: 1640825
URL: http://svn.apache.org/r1640825
Log:
check in the best i2b2 temporal result setting
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java
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
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfI2B2TemporalRelations.java
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java?rev=1640825&r1=1640824&r2=1640825&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAdmissionTimeAnnotator.java Thu Nov 20 21:49:45 2014
@@ -220,17 +220,17 @@ public class EventAdmissionTimeAnnotator
if(category!=null){
this.dataWriter.write(new Instance<>(category, features));
//add nearby system-generated events as additional instances
- Collection<EventMention> eventList = coveringMap.get(eventMention);
- for(EventMention covEvent : eventList){
- if(!covEvent.getClass().equals(EventMention.class)){
- List<Feature> covEvfeatures = extractFeatures(jCas,covEvent);
- this.dataWriter.write(new Instance<>(category, covEvfeatures));
- }
- }
- for(EventMention covedEvent : JCasUtil.selectCovered(jCas, EventMention.class, eventMention)){//select covered events
- List<Feature> covedEvfeatures = extractFeatures(jCas,covedEvent);
- this.dataWriter.write(new Instance<>(category, covedEvfeatures));
- }
+// Collection<EventMention> eventList = coveringMap.get(eventMention);
+// for(EventMention covEvent : eventList){
+// if(!covEvent.getClass().equals(EventMention.class)){
+// List<Feature> covEvfeatures = extractFeatures(jCas,covEvent);
+// this.dataWriter.write(new Instance<>(category, covEvfeatures));
+// }
+// }
+// for(EventMention covedEvent : JCasUtil.selectCovered(jCas, EventMention.class, eventMention)){//select covered events
+// List<Feature> covedEvfeatures = extractFeatures(jCas,covedEvent);
+// this.dataWriter.write(new Instance<>(category, covedEvfeatures));
+// }
}
} else {
String outcome = this.classifier.classify(features);
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java?rev=1640825&r1=1640824&r2=1640825&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventDischargeTimeAnnotator.java Thu Nov 20 21:49:45 2014
@@ -220,17 +220,17 @@ public class EventDischargeTimeAnnotator
if(category!=null){
this.dataWriter.write(new Instance<>(category, features));
//add nearby system-generated events as additional instances
- Collection<EventMention> eventList = coveringMap.get(eventMention);
- for(EventMention covEvent : eventList){
- if(!covEvent.getClass().equals(EventMention.class)){
- List<Feature> covEvfeatures = extractFeatures(jCas,covEvent);
- this.dataWriter.write(new Instance<>(category, covEvfeatures));
- }
- }
- for(EventMention covedEvent : JCasUtil.selectCovered(jCas, EventMention.class, eventMention)){//select covered events
- List<Feature> covedEvfeatures = extractFeatures(jCas,covedEvent);
- this.dataWriter.write(new Instance<>(category, covedEvfeatures));
- }
+// Collection<EventMention> eventList = coveringMap.get(eventMention);
+// for(EventMention covEvent : eventList){
+// if(!covEvent.getClass().equals(EventMention.class)){
+// List<Feature> covEvfeatures = extractFeatures(jCas,covEvent);
+// this.dataWriter.write(new Instance<>(category, covEvfeatures));
+// }
+// }
+// for(EventMention covedEvent : JCasUtil.selectCovered(jCas, EventMention.class, eventMention)){//select covered events
+// List<Feature> covedEvfeatures = extractFeatures(jCas,covedEvent);
+// this.dataWriter.write(new Instance<>(category, covedEvfeatures));
+// }
}
} else {
String outcome = this.classifier.classify(features);
Modified: 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=1640825&r1=1640824&r2=1640825&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventEventI2B2RelationAnnotator.java Thu Nov 20 21:49:45 2014
@@ -132,7 +132,7 @@ public class EventEventI2B2RelationAnnot
// , new TemporalPETExtractor()
, new EventArgumentPropertyExtractor()
, new NumberOfEventTimeBetweenCandidatesExtractor()
- , new SectionHeaderRelationExtractor()
+// , new SectionHeaderRelationExtractor()
, new NearbyVerbTenseRelationExtractor()
, new CheckSpecialWordRelationExtractor()
, new UmlsFeatureExtractor()
@@ -146,10 +146,10 @@ public class EventEventI2B2RelationAnnot
, new ConjunctionRelationFeaturesExtractor()
// , new DeterminerRelationFeaturesExtractor()
, new EventTimeRelationFeatureExtractor()
- , new TokenPropertyFeaturesExtractor()
- , new DependingVerbsFeatureExtractor()
- , new SpecialAnnotationRelationExtractor() //not helpful
- , new TemporalPETFlatExtractor()
+// , new TokenPropertyFeaturesExtractor()
+// , new DependingVerbsFeatureExtractor()
+// , new SpecialAnnotationRelationExtractor() //not helpful
+// , new TemporalPETFlatExtractor()
// , new EventInBetweenPropertyExtractor()
// , new EventOutsidePropertyExtractor()
);
@@ -186,28 +186,28 @@ public class EventEventI2B2RelationAnnot
EventMention eventA = events.get(j);
if(j-i==1 || j-i==eventNum-1||ifDependent(jCas, eventA, eventB)){
- 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));
- }
- }
+// 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));
}
}
Modified: 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=1640825&r1=1640824&r2=1640825&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventTimeI2B2RelationAnnotator.java Thu Nov 20 21:49:45 2014
@@ -142,8 +142,8 @@ public class EventTimeI2B2RelationAnnota
, new ConjunctionRelationFeaturesExtractor()
// , new EventPositionRelationFeaturesExtractor() //tried, but not helpful
, new TimeXRelationFeaturesExtractor()
- , new TemporalPETFlatExtractor()
- , new TimeXPropertyRelationFeaturesExtractor()
+// , new TemporalPETFlatExtractor()
+// , new TimeXPropertyRelationFeaturesExtractor()
// , new TimeWordTypeRelationExtractor() //tried, but not helpful
// , new EventIndexOfSameSentenceRelationFeaturesExtractor() //tried, but not helpful
);
@@ -172,14 +172,14 @@ public class EventTimeI2B2RelationAnnota
// 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));
- }
+// 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));
- }
+// 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)) {
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=1640825&r1=1640824&r2=1640825&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 Thu Nov 20 21:49:45 2014
@@ -304,15 +304,16 @@ EvaluationOfTemporalRelations_ImplBase{
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(AddEEPotentialRelations.class));
aggregateBuilder.add(EventTimeI2B2RelationAnnotator.createDataWriterDescription(
- // LibSvmStringOutcomeDataWriter.class,
- LibLinearStringOutcomeDataWriter.class,
+ LibSvmStringOutcomeDataWriter.class,
+// LibLinearStringOutcomeDataWriter.class,
// TKSVMlightStringOutcomeDataWriter.class,
// TKLIBSVMStringOutcomeDataWriter.class,
// SVMlightStringOutcomeDataWriter.class,
new File(directory,EVENT_TIME),
params.probabilityOfKeepingANegativeExample));
aggregateBuilder.add(EventEventI2B2RelationAnnotator.createDataWriterDescription(
- LibLinearStringOutcomeDataWriter.class,//TKSVMlightStringOutcomeDataWriter.class,//
+ LibSvmStringOutcomeDataWriter.class,
+// LibLinearStringOutcomeDataWriter.class,//TKSVMlightStringOutcomeDataWriter.class,//
// LIBLINEARStringOutcomeDataWriter.class,
new File(directory,EVENT_EVENT),
params.probabilityOfKeepingANegativeExample));
@@ -360,8 +361,8 @@ EvaluationOfTemporalRelations_ImplBase{
}
// HideOutput hider = new HideOutput();
- JarClassifierBuilder.trainAndPackage(new File(directory,EVENT_TIME), "-c", "0.0002", "-w2","0.5","-w3","5","-w4","8");//"-h","0","-c", "1000");//optArray);//"-c", "0.05");//
- JarClassifierBuilder.trainAndPackage(new File(directory,EVENT_EVENT), "-c", "0.0002","-w2","0.5","-w3","4","-w4","3");
+ JarClassifierBuilder.trainAndPackage(new File(directory,EVENT_TIME), "-h","0","-c", "1000", "-w2","0.5","-w3","5","-w4","8");//"-h","0","-c", "1000");//optArray);//"-c", "0.05");//
+ JarClassifierBuilder.trainAndPackage(new File(directory,EVENT_EVENT), "-h","0","-c", "1000","-w2","0.5","-w3","4","-w4","3");
JarClassifierBuilder.trainAndPackage(new File(directory,EVENT_DISCHARGE), "-h","0","-c", "1000");//,"-w2","23","-w3","24");
JarClassifierBuilder.trainAndPackage(new File(directory,EVENT_ADMISSION), "-h","0","-c", "1000");//,"-w2","22","-w3","5");
// JarClassifierBuilder.trainAndPackage(new File(directory,TIME_ADMISSION), "-h","0","-c", "1000");