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Subject: svn commit: r1487513 -
 /ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/BaselineEntityMentionPairRelationExtractorAnnotator.java
Date: Wed, 29 May 2013 15:20:58 -0000
To: commits@ctakes.apache.org
From: dligach@apache.org
Message-Id: <20130529152058.61A732388847@eris.apache.org>

Author: dligach
Date: Wed May 29 15:20:58 2013
New Revision: 1487513

URL: http://svn.apache.org/r1487513
Log:
Baseline requested by reviewer 2 (second set of revisions)

Added:
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/BaselineEntityMentionPairRelationExtractorAnnotator.java

Added: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/BaselineEntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/BaselineEntityMentionPairRelationExtractorAnnotator.java?rev=1487513&view=auto
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/BaselineEntityMentionPairRelationExtractorAnnotator.java (added)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/BaselineEntityMentionPairRelationExtractorAnnotator.java Wed May 29 15:20:58 2013
@@ -0,0 +1,162 @@
+/**
+ * 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.relationextractor.ae.baselines;
+
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+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.uimafit.util.JCasUtil;
+
+import com.google.common.base.Function;
+import com.google.common.base.Functions;
+import com.google.common.collect.Ordering;
+
+/**
+ * This baseline links each anatomical site with the closest entity of a type  
+ * that's suitable for location_of, as long as there is no intervening anatomical site. 
+ */
+public class BaselineEntityMentionPairRelationExtractorAnnotator extends RelationExtractorAnnotator {
+	
+	@Override
+	public Class<? extends Annotation> getCoveringClass(){
+		return Sentence.class;
+	}
+	
+	@Override
+	public List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(
+			JCas identifiedAnnotationView, Annotation sentence) {
+
+		List<EntityMention> entityMentions = JCasUtil.selectCovered(
+				identifiedAnnotationView,
+				EntityMention.class,
+				sentence);
+		
+		List<EntityMention> anatomicalSites = getAnatomicalSites(entityMentions);
+		List<EntityMention> entitiesSuitableForLocationOf = getEntitiesSuitableForLocationOf(entityMentions);
+		
+		if((anatomicalSites.size() < 1) || (entitiesSuitableForLocationOf.size() < 1)) {
+		  return new ArrayList<IdentifiedAnnotationPair>();
+		}
+		
+		List<IdentifiedAnnotationPair> result = new ArrayList<IdentifiedAnnotationPair>();
+		Set<EntityMention> alreadyLinked = new HashSet<EntityMention>();
+		
+		for(EntityMention anatomicalSite : anatomicalSites) {
+		  EntityMention nearestEntity = getNearestEntity(identifiedAnnotationView, anatomicalSite, entitiesSuitableForLocationOf);
+		  
+		  // don't link if there's an another anatomical site between this one and its nearest entity
+		  if(checkForAnatomicalSiteBetween(identifiedAnnotationView, anatomicalSite, nearestEntity)) {
+		    continue;
+		  }
+		  
+		  // make sure this entity isn't already linked to an anatomical site
+		  if(! alreadyLinked.contains(nearestEntity)) {
+		    result.add(new IdentifiedAnnotationPair(anatomicalSite, nearestEntity));
+		    alreadyLinked.add(nearestEntity);
+		  }
+		}
+		
+    return result;
+	}
+
+	/*
+	 * Return entity mentions that are anatomical types (i.e. typeId is 6)
+	 */
+	private static List<EntityMention> getAnatomicalSites(List<EntityMention> entityMentions) {
+	  
+	  List<EntityMention> anatomicalSites = new ArrayList<EntityMention>();
+	  
+	  for(EntityMention entityMention : entityMentions) {
+	    if(entityMention.getTypeID() == 6) {
+	      anatomicalSites.add(entityMention);
+	    }
+	  }
+	  
+	  return anatomicalSites;
+	}
+	
+  /*
+   * Return entity mentions that qualityf to be the arg2 of location_of relation (i.e. 2, 3, or 5)
+   */
+  private List<EntityMention> getEntitiesSuitableForLocationOf(List<EntityMention> entityMentions) {
+    
+    HashSet<Integer> okArg2Types = new HashSet<Integer>(Arrays.asList(2, 3, 5));
+    List<EntityMention> suitableEntities = new ArrayList<EntityMention>();
+    
+    for(EntityMention entityMention : entityMentions) {
+      if(okArg2Types.contains(entityMention.getTypeID())) {
+        suitableEntities.add(entityMention);
+      }
+    }
+    
+    return suitableEntities;
+  }
+	
+  /*
+   * Find the entity nearest to the anatomical site
+   */
+	private static EntityMention getNearestEntity(JCas jCas, EntityMention anatomicalSite, List<EntityMention> entityMentions) {
+
+	  // token distance from anatomical site to other entity mentions
+	  Map<EntityMention, Integer> distanceToEntities = new HashMap<EntityMention, Integer>();
+
+	  for(EntityMention entityMention : entityMentions) {
+	    List<BaseToken> baseTokens = JCasUtil.selectBetween(jCas, BaseToken.class, anatomicalSite, entityMention);
+	    distanceToEntities.put(entityMention, baseTokens.size());
+	  }
+	  
+    List<EntityMention> sortedEntityMentions = new ArrayList<EntityMention>(distanceToEntities.keySet());
+    Function<EntityMention, Integer> getValue = Functions.forMap(distanceToEntities);
+    Collections.sort(sortedEntityMentions, Ordering.natural().onResultOf(getValue));
+    
+    return sortedEntityMentions.get(0);
+	}
+  
+  /*
+   * Return true if there's an anatomical site entity mention between two entities.
+   */
+  private static boolean checkForAnatomicalSiteBetween(JCas jCas, EntityMention entity1, EntityMention entity2) {
+    
+    for(EntityMention entityMention : JCasUtil.selectBetween(jCas, EntityMention.class, entity1, entity2)) {
+      if(entityMention.getTypeID() == 6) {
+        return true;
+      }
+    }
+    
+    return false;
+  }
+  
+  @Override
+  public String classify(List<Feature> features) {
+    return "location_of";
+  }
+}