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Posted to commits@ctakes.apache.org by cl...@apache.org on 2014/12/15 21:39:57 UTC
svn commit: r1645742 -
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java
Author: clin
Date: Mon Dec 15 20:39:57 2014
New Revision: 1645742
URL: http://svn.apache.org/r1645742
Log:
Add a feature extractor to extract token features for any covering UMLS entities.
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java (with props)
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java?rev=1645742&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java Mon Dec 15 20:39:57 2014
@@ -0,0 +1,194 @@
+/**
+ * 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 org.apache.ctakes.constituency.parser.util.AnnotationTreeUtils;
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractor;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.Bag;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.Covered;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.FirstCovered;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.Following;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.LastCovered;
+import org.cleartk.ml.feature.extractor.CleartkExtractor.Preceding;
+import org.cleartk.ml.feature.extractor.CombinedExtractor1;
+import org.cleartk.ml.feature.extractor.CoveredTextExtractor;
+import org.cleartk.ml.feature.extractor.DistanceExtractor;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
+import org.cleartk.ml.feature.extractor.NamingExtractor1;
+import org.cleartk.util.ViewUriUtil;
+
+import com.google.common.collect.Multimap;
+
+/**
+ * for every UMLS entities covering the annotation, extracted related token features
+ * @author CH151862
+ *
+ */
+public class MultiTokenFeaturesExtractor implements RelationFeaturesExtractor {
+
+ private FeatureExtractor1 coveredText = new CoveredTextExtractor();
+
+ /**
+ * First word of the mention, last word of the mention, all words of the mention as a bag, the
+ * preceding 3 words, the following 3 words
+ */
+ private FeatureExtractor1 tokenContext = new CleartkExtractor(
+ BaseToken.class,
+ coveredText,
+ new FirstCovered(1),
+ new LastCovered(1),
+ new Bag(new Covered()),
+ new Preceding(3),
+ new Following(3));
+
+ /**
+ * All extractors for mention 1, with features named to distinguish them from mention 2
+ */
+ private FeatureExtractor1 mention1FeaturesExtractor = new NamingExtractor1(
+ "mention1",
+ new CombinedExtractor1(coveredText, tokenContext));
+
+ /**
+ * All extractors for mention 2, with features named to distinguish them from mention 1
+ */
+ private FeatureExtractor1 mention2FeaturesExtractor = new NamingExtractor1(
+ "mention2",
+ new CombinedExtractor1(coveredText, tokenContext));
+
+ /**
+ * First word, last word, and all words between the mentions
+ */
+ private CleartkExtractor tokensBetween = new CleartkExtractor(
+ BaseToken.class,
+ new NamingExtractor1("BetweenMentions", coveredText),
+ new FirstCovered(1),
+ new LastCovered(1),
+ new Bag(new Covered()));
+
+ private String cachedDocID = null;
+ private Map<EventMention, Collection<EventMention>> coveringMap;
+
+ /**
+ * Number of words between the mentions
+ */
+ private DistanceExtractor nTokensBetween = new DistanceExtractor(null, BaseToken.class);
+
+ @Override
+ public List<Feature> extract(JCas jCas, IdentifiedAnnotation mention1, IdentifiedAnnotation mention2)
+ throws AnalysisEngineProcessException {
+
+ String docId=null;
+ try{
+ docId = ViewUriUtil.getURI(jCas).toString();// get docID
+ }catch(Exception e){
+ docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+ }
+ if(!docId.equals(cachedDocID)){
+ // rebuild event-event map
+ cachedDocID = docId;
+ coveringMap = JCasUtil.indexCovering(jCas, EventMention.class, EventMention.class);
+ }
+
+ List<Feature> features = new ArrayList<>();
+ Annotation arg1 = mention1;
+ Annotation arg2 = mention2;
+
+ List<Annotation> arg1s = new ArrayList<>();
+ if(arg1 instanceof EventMention){
+ for (EventMention event1 : coveringMap.get(arg1)){
+ Annotation tempAnn = getExpandedEvent(jCas, event1);
+ if(tempAnn == null) tempAnn = event1;
+ arg1s.add(tempAnn);
+ }
+ arg1 = getExpandedEvent(jCas, mention1);
+ if(arg1 == null) arg1 = mention1;
+ }
+ arg1s.add(arg1);
+
+ List<Annotation> arg2s = new ArrayList<>();
+ if(arg2 instanceof EventMention){
+ for (EventMention event2 : coveringMap.get(arg2)){
+ Annotation tempAnn = getExpandedEvent(jCas, event2);
+ if(tempAnn == null) tempAnn = event2;
+ arg2s.add(tempAnn);
+ }
+ arg2 = getExpandedEvent(jCas, mention2);
+ if(arg2 == null) arg2 = mention2;
+ }
+ arg2s.add(arg2);
+
+ for (Annotation ann1 : arg1s){
+ features.addAll(this.mention1FeaturesExtractor.extract(jCas, ann1));
+ for (Annotation ann2: arg2s){
+ features.addAll(this.tokensBetween.extractBetween(jCas, ann1, ann2));
+ features.addAll(this.nTokensBetween.extract(jCas, ann1, ann2));
+ }
+ }
+ for (Annotation ann2: arg2s){
+ features.addAll(this.mention2FeaturesExtractor.extract(jCas, ann2));
+ }
+
+ return features;
+ }
+
+ private static TreebankNode getExpandedEvent(JCas jCas, IdentifiedAnnotation mention){
+ // since events are single words, we are at a terminal node:
+ List<TerminalTreebankNode> terms = JCasUtil.selectCovered(TerminalTreebankNode.class, mention);
+ if(terms == null || terms.size() == 0){
+ return null;
+ }
+
+ TreebankNode coveringNode = AnnotationTreeUtils.annotationNode(jCas, mention);
+ if(coveringNode == null) return terms.get(0);
+
+ String pos =terms.get(0).getNodeType();
+ // do not expand Verbs
+ if(pos.startsWith("V")) return coveringNode;
+
+ if(pos.startsWith("N")){
+ // get first NP node:
+ while(coveringNode != null && !coveringNode.getNodeType().equals("NP")){
+ coveringNode = coveringNode.getParent();
+ }
+ }else if(pos.startsWith("J")){
+ while(coveringNode != null && !coveringNode.getNodeType().equals("ADJP")){
+ coveringNode = coveringNode.getParent();
+ }
+ }
+ if(coveringNode == null) coveringNode = terms.get(0);
+ return coveringNode;
+ }
+}
Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/feature/MultiTokenFeaturesExtractor.java
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