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Posted to commits@ctakes.apache.org by cl...@apache.org on 2013/04/09 20:23:28 UTC
svn commit: r1466170 - in
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal: ae/
ae/feature/ eval/
Author: clin
Date: Tue Apr 9 18:23:27 2013
New Revision: 1466170
URL: http://svn.apache.org/r1466170
Log:
add several feature extractors to help docTimeRel classification:
For an event,
1. get the closest verb, and its pos
2. get the closest time expression
3. get the segment id.
4. get nearby verbs' pos pattern
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java (with props)
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java (with props)
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXExtractor.java (with props)
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseXExtractor.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java?rev=1466170&r1=1466169&r2=1466170&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotator.java Tue Apr 9 18:23:27 2013
@@ -21,7 +21,10 @@ package org.apache.ctakes.temporal.ae;
import java.io.File;
import java.util.List;
+import org.apache.ctakes.temporal.ae.feature.ClosestVerbExtractor;
import org.apache.ctakes.temporal.ae.feature.NearbyVerbTenseXExtractor;
+import org.apache.ctakes.temporal.ae.feature.SectionHeaderExtractor;
+import org.apache.ctakes.temporal.ae.feature.TimeXExtractor;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.uima.UimaContext;
@@ -73,6 +76,9 @@ public class DocTimeRelAnnotator extends
private CleartkExtractor contextExtractor;
private NearbyVerbTenseXExtractor verbTensePatternExtractor;
+ private SectionHeaderExtractor sectionIDExtractor;
+ private ClosestVerbExtractor closestVerbExtractor;
+ private TimeXExtractor timeXExtractor;
@Override
public void initialize(UimaContext context) throws ResourceInitializationException {
@@ -87,6 +93,9 @@ public class DocTimeRelAnnotator extends
new Covered(),
new Following(3));
this.verbTensePatternExtractor = new NearbyVerbTenseXExtractor();
+ this.sectionIDExtractor = new SectionHeaderExtractor();
+ this.closestVerbExtractor = new ClosestVerbExtractor();
+ this.timeXExtractor = new TimeXExtractor();
}
@Override
@@ -95,6 +104,9 @@ public class DocTimeRelAnnotator extends
if (eventMention.getEvent() != null) {
List<Feature> features = this.contextExtractor.extract(jCas, eventMention);
features.addAll(this.verbTensePatternExtractor.extract(jCas, eventMention));//add nearby verb POS pattern feature
+ features.addAll(this.sectionIDExtractor.extract(jCas, eventMention)); //add section heading
+ features.addAll(this.closestVerbExtractor.extract(jCas, eventMention)); //add closest verb
+ features.addAll(this.timeXExtractor.extract(jCas, eventMention)); //add the closest time expression types
if (this.isTraining()) {
String outcome = eventMention.getEvent().getProperties().getDocTimeRel();
this.dataWriter.write(new Instance<String>(outcome, features));
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java?rev=1466170&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java Tue Apr 9 18:23:27 2013
@@ -0,0 +1,88 @@
+/**
+ * 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.feature;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+//import java.util.logging.Logger;
+
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.classifier.Feature;
+import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
+import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.uimafit.util.JCasUtil;
+
+public class ClosestVerbExtractor implements SimpleFeatureExtractor {
+
+ private String name;
+
+// private Logger logger = Logger.getLogger(this.getClass().getName());
+
+ public ClosestVerbExtractor() {
+ super();
+ this.name = "ClosestVerb";
+
+ }
+
+ @Override
+ public List<Feature> extract(JCas view, Annotation annotation) throws CleartkExtractorException {
+ List<Feature> features = new ArrayList<Feature>();
+
+ //1 get covering sentence:
+ Map<EventMention, Collection<Sentence>> coveringMap =
+ JCasUtil.indexCovering(view, EventMention.class, Sentence.class);
+ EventMention targetTokenAnnotation = (EventMention)annotation;
+ Collection<Sentence> sentList = coveringMap.get(targetTokenAnnotation);
+
+ Map<Integer, WordToken> verbDistMap = null;
+
+ //2 get all Verbs within the same sentence as target event lies
+ if (sentList != null && !sentList.isEmpty()){
+ for(Sentence sent : sentList) {
+ verbDistMap = new TreeMap<Integer, WordToken>();
+ for ( WordToken wt : JCasUtil.selectCovered(view, WordToken.class, sent)) {
+ if (wt != null){
+ String pos = wt.getPartOfSpeech();
+ if (pos.startsWith("VB")){
+ verbDistMap.put(Math.abs(wt.getBegin() - annotation.getBegin()), wt);
+ }
+ }
+ }
+ for (Map.Entry<Integer, WordToken> entry : verbDistMap.entrySet()) {
+ //Feature feature = new Feature(this.name, entry.getValue().getCoveredText());
+ // features.add(feature);
+ //logger.info("found nearby closest verb: "+ entry.getValue().getCoveredText() + " POS:" + entry.getValue().getPartOfSpeech());
+ Feature posfeature = new Feature(this.name, entry.getValue().getPartOfSpeech());
+ features.add(posfeature);
+ break;
+ }
+ }
+
+ }
+ return features;
+ }
+
+}
Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/ClosestVerbExtractor.java
------------------------------------------------------------------------------
svn:mime-type = text/plain
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseXExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseXExtractor.java?rev=1466170&r1=1466169&r2=1466170&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseXExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/NearbyVerbTenseXExtractor.java Tue Apr 9 18:23:27 2013
@@ -22,7 +22,7 @@ import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.Map;
-import java.util.logging.Logger;
+//import java.util.logging.Logger;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
@@ -38,7 +38,7 @@ public class NearbyVerbTenseXExtractor i
private String name;
- private Logger logger = Logger.getLogger(this.getClass().getName());
+ //private Logger logger = Logger.getLogger(this.getClass().getName());
public NearbyVerbTenseXExtractor() {
super();
@@ -70,7 +70,7 @@ public class NearbyVerbTenseXExtractor i
}
Feature feature = new Feature(this.name, verbTP);
features.add(feature);
- logger.info("found nearby verb's pos tag: "+ verbTP);
+ //logger.info("found nearby verb's pos tag: "+ verbTP);
}
}
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java?rev=1466170&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java Tue Apr 9 18:23:27 2013
@@ -0,0 +1,71 @@
+/**
+ * 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.feature;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+//import java.util.logging.Logger;
+
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textspan.Segment;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.classifier.Feature;
+import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
+import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.uimafit.util.JCasUtil;
+
+public class SectionHeaderExtractor implements SimpleFeatureExtractor {
+
+ private String name;
+
+// private Logger logger = Logger.getLogger(this.getClass().getName());
+
+ public SectionHeaderExtractor() {
+ super();
+ this.name = "SectionHeader";
+
+ }
+
+ @Override
+ public List<Feature> extract(JCas view, Annotation annotation) throws CleartkExtractorException {
+ List<Feature> features = new ArrayList<Feature>();
+
+ //1 get covering sentence:
+ Map<EventMention, Collection<Segment>> coveringMap =
+ JCasUtil.indexCovering(view, EventMention.class, Segment.class);
+ EventMention targetTokenAnnotation = (EventMention)annotation;
+ Collection<Segment> segList = coveringMap.get(targetTokenAnnotation);
+
+ //2 get Verb Tense
+ if (segList != null && !segList.isEmpty()){
+ for(Segment seg : segList) {
+ String segname = seg.getId();
+ Feature feature = new Feature(this.name, segname);
+ features.add(feature);
+// logger.info("found segment id: "+ segname);
+ }
+
+ }
+ return features;
+ }
+
+}
Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/SectionHeaderExtractor.java
------------------------------------------------------------------------------
svn:mime-type = text/plain
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXExtractor.java?rev=1466170&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXExtractor.java Tue Apr 9 18:23:27 2013
@@ -0,0 +1,87 @@
+/**
+ * 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.feature;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+//import java.util.logging.Logger;
+
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.classifier.Feature;
+import org.cleartk.classifier.feature.extractor.CleartkExtractorException;
+import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
+import org.uimafit.util.JCasUtil;
+
+public class TimeXExtractor implements SimpleFeatureExtractor {
+
+ private String name;
+
+// private Logger logger = Logger.getLogger(this.getClass().getName());
+
+ public TimeXExtractor() {
+ super();
+ this.name = "TimeXFeature";
+
+ }
+
+ @Override
+ public List<Feature> extract(JCas view, Annotation annotation) throws CleartkExtractorException {
+ List<Feature> features = new ArrayList<Feature>();
+
+ //1 get covering sentence:
+ Map<EventMention, Collection<Sentence>> coveringMap =
+ JCasUtil.indexCovering(view, EventMention.class, Sentence.class);
+ EventMention targetTokenAnnotation = (EventMention)annotation;
+ Collection<Sentence> sentList = coveringMap.get(targetTokenAnnotation);
+
+ //2 get TimeX
+ Map<Integer, TimeMention> timeDistMap = null;
+
+ if (sentList != null && !sentList.isEmpty()){
+ timeDistMap = new TreeMap<Integer, TimeMention>();
+
+ for(Sentence sent : sentList) {
+ for (TimeMention time : JCasUtil.selectCovered(view, TimeMention.class, sent)) {
+ timeDistMap.put(Math.abs(time.getBegin() - annotation.getBegin()), time);
+ }
+ }
+
+ //get the closest Time Expression feature
+ for (Map.Entry<Integer, TimeMention> entry : timeDistMap.entrySet()) {
+ Feature feature = new Feature(this.name, entry.getValue().getCoveredText());
+ features.add(feature);
+// logger.info("add time feature: "+ entry.getValue().getCoveredText() + entry.getValue().getTimeClass());
+ Feature indicator = new Feature("TimeXNearby", this.name);
+ features.add(indicator);
+ break;
+ }
+ }
+
+
+ return features;
+ }
+
+}
Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/TimeXExtractor.java
------------------------------------------------------------------------------
svn:mime-type = text/plain
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java?rev=1466170&r1=1466169&r2=1466170&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventProperties.java Tue Apr 9 18:23:27 2013
@@ -33,6 +33,7 @@ import java.util.logging.Logger;
import org.apache.ctakes.temporal.ae.DocTimeRelAnnotator;
import org.apache.ctakes.typesystem.type.refsem.EventProperties;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.Feature;
@@ -40,6 +41,7 @@ import org.apache.uima.collection.Collec
import org.apache.uima.jcas.JCas;
import org.cleartk.classifier.jar.JarClassifierBuilder;
import org.cleartk.classifier.libsvm.LIBSVMStringOutcomeDataWriter;
+//import org.cleartk.classifier.liblinear.LIBLINEARStringOutcomeDataWriter;
import org.cleartk.eval.AnnotationStatistics;
import org.uimafit.component.JCasAnnotator_ImplBase;
import org.uimafit.factory.AggregateBuilder;
@@ -97,11 +99,12 @@ public class EvaluationOfEventProperties
protected void train(CollectionReader collectionReader, File directory) throws Exception {
AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class));
+ aggregateBuilder.add(CopyFromGold.getDescription(TimeMention.class));
aggregateBuilder.add(DocTimeRelAnnotator.createDataWriterDescription(
- LIBSVMStringOutcomeDataWriter.class,
+ LIBSVMStringOutcomeDataWriter.class,
directory));
SimplePipeline.runPipeline(collectionReader, aggregateBuilder.createAggregate());
- JarClassifierBuilder.trainAndPackage(directory, "-c", "1000");
+ JarClassifierBuilder.trainAndPackage(directory, "-c", "10000");
}
@Override
@@ -110,6 +113,7 @@ public class EvaluationOfEventProperties
File directory) throws Exception {
AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class));
+ aggregateBuilder.add(CopyFromGold.getDescription(TimeMention.class));
aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ClearEventProperties.class));
aggregateBuilder.add(DocTimeRelAnnotator.createAnnotatorDescription(directory));