svn commit: r1431112 - /incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/

[dl...@apache.org]

Author: dligach
Date: Wed Jan  9 21:56:43 2013
New Revision: 1431112

URL: http://svn.apache.org/viewvc?rev=1431112&view=rev
Log:
Initial commit of the second baseline (closest entities of correct type)

Added:
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline1EntityMentionPairRelationExtractorAnnotator.java
      - copied, changed from r1431015, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/BaselineEntityMentionPairRelationExtractorAnnotator.java
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline2EntityMentionPairRelationExtractorAnnotator.java
Removed:
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/BaselineEntityMentionPairRelationExtractorAnnotator.java

Copied: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline1EntityMentionPairRelationExtractorAnnotator.java (from r1431015, incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/BaselineEntityMentionPairRelationExtractorAnnotator.java)
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline1EntityMentionPairRelationExtractorAnnotator.java?p2=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline1EntityMentionPairRelationExtractorAnnotator.java&p1=incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/BaselineEntityMentionPairRelationExtractorAnnotator.java&r1=1431015&r2=1431112&rev=1431112&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/BaselineEntityMentionPairRelationExtractorAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline1EntityMentionPairRelationExtractorAnnotator.java Wed Jan  9 21:56:43 2013
@@ -38,7 +38,7 @@ import org.uimafit.util.JCasUtil;
  * Annotate location_of relation between two entities in sentences containing
  * exactly two entities (where the entities are of the correct types).
  */
-public class BaselineEntityMentionPairRelationExtractorAnnotator extends RelationExtractorAnnotator {
+public class Baseline1EntityMentionPairRelationExtractorAnnotator extends RelationExtractorAnnotator {
 	
 	public static final String PARAM_CLASSIFY_BOTH_DIRECTIONS = "ClassifyBothDirections";
 

Added: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline2EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline2EntityMentionPairRelationExtractorAnnotator.java?rev=1431112&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline2EntityMentionPairRelationExtractorAnnotator.java (added)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline2EntityMentionPairRelationExtractorAnnotator.java Wed Jan  9 21:56:43 2013
@@ -0,0 +1,210 @@
+/**
+ * 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;
+
+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 org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.classifier.Feature;
+import org.uimafit.descriptor.ConfigurationParameter;
+import org.uimafit.util.JCasUtil;
+
+import com.google.common.base.Function;
+import com.google.common.base.Functions;
+import com.google.common.collect.Ordering;
+
+/**
+ * Annotate location_of relation between two entities in sentences containing
+ * exactly two entities (where the entities are of the correct types).
+ */
+public class Baseline2EntityMentionPairRelationExtractorAnnotator extends RelationExtractorAnnotator {
+	
+	public static final String PARAM_CLASSIFY_BOTH_DIRECTIONS = "ClassifyBothDirections";
+
+	@ConfigurationParameter(
+			name = PARAM_CLASSIFY_BOTH_DIRECTIONS,
+			mandatory = false,
+			description = "run the classifier in both directions, that is, classify each pair of events "
+					+ "{X,Y} once in the order X-to-Y and once in the order Y-to-X (default: classify each "
+					+ "pair of events {X, Y} once, giving the label 'R' if a relation exists with the order "
+					+ "X-to-Y, and 'R-1' if a relation exists with the order Y-to-X)")
+	protected boolean classifyBothDirections = false;
+
+	@Override
+	public List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(
+			JCas identifiedAnnotationView, Sentence sentence) {
+
+		// collect all possible relation arguments from the sentence
+		List<EntityMention> args = JCasUtil.selectCovered(
+				identifiedAnnotationView,
+				EntityMention.class,
+				sentence);
+
+		// Create pairings (this will change depending on the classification direction)
+		List<IdentifiedAnnotationPair> pairs = new ArrayList<IdentifiedAnnotationPair>();
+		
+		for (int i = 0; i < args.size(); ++i) {
+			EntityMention arg1 = args.get(i);
+			int jStart = this.classifyBothDirections ? 0 : i + 1;
+			for (int j = jStart; j < args.size(); ++j) {
+        EntityMention arg2 = args.get(j);
+			  // skip identical entity mentions and mentions with identical spans
+				if (i == j || (arg1.getBegin() == arg2.getBegin() && arg1.getEnd() == arg2.getEnd())) {
+				  continue;
+				}
+				pairs.add(new IdentifiedAnnotationPair(arg1, arg2));
+			}
+		}
+
+		// need sentences with a single legitimate arg2 and multiple anatomical sties
+		int legitimateArg1Count = 0;
+		int legitimateArg2Count = 0;
+		for(IdentifiedAnnotationPair pair : pairs) {
+		  if(pair.getArg1().getTypeID() == 6) {
+		    legitimateArg1Count++;
+		  }
+		  HashSet<Integer> okArg2Types = new HashSet<Integer>(Arrays.asList(2, 3, 5));
+		  if(okArg2Types.contains(pair.getArg2().getTypeID())) {
+		    legitimateArg2Count++;
+		  }
+		}
+		if(! (legitimateArg1Count > 1 && legitimateArg2Count == 1)) {
+		  return new ArrayList<IdentifiedAnnotationPair>();
+		}
+		
+		// compute distance between entities for the pairs where entity types are correct
+		HashMap<IdentifiedAnnotationPair, Integer> distanceLookup = new HashMap<IdentifiedAnnotationPair, Integer>();
+		for(IdentifiedAnnotationPair pair : pairs) {
+		  if(validateArgumentTypes(pair)) {
+		    try {
+          int distance = getDistance(identifiedAnnotationView.getView(CAS.NAME_DEFAULT_SOFA), pair);
+          distanceLookup.put(pair, distance);
+        } catch (CASException e) {
+          e.printStackTrace();
+        }
+		  } 
+		}
+		
+		if(distanceLookup.isEmpty()) {
+		  return new ArrayList<IdentifiedAnnotationPair>(); // no pairs with suitable argument types
+		}
+		
+		// find the pair where the distance between entities is the smallest and return it
+    List<IdentifiedAnnotationPair> rankedPairs = new ArrayList<IdentifiedAnnotationPair>(distanceLookup.keySet());
+    Function<IdentifiedAnnotationPair, Integer> getValue = Functions.forMap(distanceLookup);
+    Collections.sort(rankedPairs, Ordering.natural().onResultOf(getValue));
+
+    List<IdentifiedAnnotationPair> result = new ArrayList<IdentifiedAnnotationPair>();
+    result.add(rankedPairs.get(0));
+
+    System.out.println(sentence.getCoveredText());
+    System.out.println("arg1: " + result.get(0).getArg1().getCoveredText());
+    System.out.println("arg2: " + result.get(0).getArg2().getCoveredText());
+    System.out.println();
+    
+    return result;
+	}
+	
+	private static int getDistance(JCas jCas, IdentifiedAnnotationPair pair)  {
+	  
+	  List<BaseToken> baseTokens = JCasUtil.selectBetween(jCas, BaseToken.class, pair.getArg1(), pair.getArg2());
+	  return baseTokens.size();
+	}
+	
+	/*
+	 * Are entity types of the arguments valid for location_of? 
+	 * The following combinations are allowed:
+	 * 
+	 * location-of(anatomical site/6, disorder/2)
+   * location-of(anatomical site/6, sign/symptom/3)
+   * location-of(anatomical site/6, procedure/5)
+	 */
+	private static boolean validateArgumentTypes(IdentifiedAnnotationPair pair) {
+	  
+    // allowable arg2 types for location_of
+	  HashSet<Integer> okArg2Types = new HashSet<Integer>(Arrays.asList(2, 3, 5));
+    
+	  IdentifiedAnnotation arg1 = pair.getArg1(); // Argument (should be anatomical site)
+	  IdentifiedAnnotation arg2 = pair.getArg2(); // Related_to (should be either disorder, sign/symptom, or procedure)
+	  int type1 = arg1.getTypeID();
+	  int type2 = arg2.getTypeID();
+	  
+	  if(type1 == 6 && okArg2Types.contains(type2)) {
+	    return true;
+	  }
+	  
+	  return false;
+	}
+	
+	@Override
+	protected String getRelationCategory(Map<List<Annotation>, BinaryTextRelation> relationLookup,
+			IdentifiedAnnotation arg1, IdentifiedAnnotation arg2) {
+
+		BinaryTextRelation relation = relationLookup.get(Arrays.asList(arg1, arg2));
+		String category;
+		if (this.classifyBothDirections) {
+			// if classifying both directions, we'll see {X, Y} once when X is first and
+			// once when Y is first, so just do the single direction lookup here
+			if (relation != null) {
+				category = relation.getCategory();
+			} else if (coin.nextDouble() <= this.probabilityOfKeepingANegativeExample) {
+			  category = NO_RELATION_CATEGORY;
+			} else {
+			  category = null;
+			}
+		} else {
+			// if classifying in a single direction, we'll see {X, Y} only once,
+			// so do lookups in both directions, and change the category name for
+			// the relations in the reverse order
+			if (relation != null) {
+			  category = relation.getCategory();
+			} else {
+				relation = relationLookup.get(Arrays.asList(arg2, arg1));
+				if (relation != null) {
+					// Change category name to show reverse order
+				  category = relation.getCategory() + "-1";
+				} else if (coin.nextDouble() <= this.probabilityOfKeepingANegativeExample) {
+				  category = NO_RELATION_CATEGORY;
+				} else {
+				  category = null;
+				}
+			}
+		}
+		return category;
+	}
+
+  @Override
+  public String classify(List<Feature> features) {
+    return "location_of";
+  }
+}