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From stevenbeth...@apache.org
Subject svn commit: r1439730 - in /incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae: ./ baselines/
Date Tue, 29 Jan 2013 01:32:14 GMT
Author: stevenbethard
Date: Tue Jan 29 01:32:13 2013
New Revision: 1439730

URL: http://svn.apache.org/viewvc?rev=1439730&view=rev
Log:
Refactors RelationExtractorAnnotator and subclasses to reduce code duplication and make it
easier to extend.

Modified:
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1EntityMentionPairRelationExtractorAnnotator.java
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2DegreeOfRelationExtractorAnnotator.java
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2EntityMentionPairRelationExtractorAnnotator.java
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3DegreeOfRelationExtractorAnnotator.java
    incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3EntityMentionPairRelationExtractorAnnotator.java

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java?rev=1439730&r1=1439729&r2=1439730&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java
(original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/DegreeOfRelationExtractorAnnotator.java
Tue Jan 29 01:32:13 2013
@@ -19,21 +19,13 @@
 package org.apache.ctakes.relationextractor.ae;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 
-import org.apache.uima.jcas.JCas;
-import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.util.JCasUtil;
-
-import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.textsem.Modifier;
 import org.apache.ctakes.typesystem.type.textspan.Sentence;
-import org.cleartk.classifier.CleartkProcessingException;
-import org.cleartk.classifier.Feature;
+import org.apache.uima.jcas.JCas;
+import org.uimafit.util.JCasUtil;
 
 /**
  * Identifies Degree_Of relation between entities and modifiers
@@ -56,17 +48,4 @@ public class DegreeOfRelationExtractorAn
 		}
 		return pairs;
 	}
-
-	@Override
-	protected String getRelationCategory(
-			Map<List<Annotation>, BinaryTextRelation> relationLookup,
-			IdentifiedAnnotation arg1, IdentifiedAnnotation arg2) {
-		BinaryTextRelation relation = relationLookup.get(Arrays.asList(arg1, arg2));
-		return (relation != null) ? relation.getCategory() : NO_RELATION_CATEGORY;
-	}
-
-  @Override
-  public String classify(List<Feature> features) throws CleartkProcessingException
{
-    return this.classifier.classify(features);
-  }
 }

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java?rev=1439730&r1=1439729&r2=1439730&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java
(original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/EntityMentionPairRelationExtractorAnnotator.java
Tue Jan 29 01:32:13 2013
@@ -23,17 +23,14 @@ import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 
-import org.apache.uima.jcas.JCas;
-import org.apache.uima.jcas.tcas.Annotation;
-import org.uimafit.descriptor.ConfigurationParameter;
-import org.uimafit.util.JCasUtil;
-
 import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
 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.cleartk.classifier.CleartkProcessingException;
-import org.cleartk.classifier.Feature;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.uimafit.descriptor.ConfigurationParameter;
+import org.uimafit.util.JCasUtil;
 
 /**
  * Identifies and classifies relations between pairs of named entities
@@ -115,10 +112,4 @@ public class EntityMentionPairRelationEx
 		}
 		return category;
 	}
-
-  @Override
-  public String classify(List<Feature> features) throws CleartkProcessingException
{
-    return this.classifier.classify(features);
-  }
-
 }

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java?rev=1439730&r1=1439729&r2=1439730&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
(original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/RelationExtractorAnnotator.java
Tue Jan 29 01:32:13 2013
@@ -95,14 +95,9 @@ public abstract class RelationExtractorA
   /**
    * Selects the relevant mentions/annotations within a sentence for relation identification/extraction.
    */
-  public abstract List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(JCas
identifiedAnnotationView, Sentence sentence);
+  protected abstract List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(JCas
identifiedAnnotationView, Sentence sentence);
 
   /*
-   * Make a prediction given a list of features.
-   */
-  public abstract String classify(List<Feature> features) throws CleartkProcessingException;
-  
-  /*
    * Implement the standard UIMA process method.
    */
   @Override
@@ -124,7 +119,13 @@ public abstract class RelationExtractorA
     Map<List<Annotation>, BinaryTextRelation> relationLookup;
     relationLookup = new HashMap<List<Annotation>, BinaryTextRelation>();
     if (this.isTraining()) {
-    	relationLookup = createRelationLookup(relationView);
+      relationLookup = new HashMap<List<Annotation>, BinaryTextRelation>();
+      for (BinaryTextRelation relation : JCasUtil.select(relationView, BinaryTextRelation.class))
{
+        Annotation arg1 = relation.getArg1().getArgument();
+        Annotation arg2 = relation.getArg2().getArgument();
+        // The key is a list of args so we can do bi-directional lookup
+        relationLookup.put(Arrays.asList(arg1, arg2), relation);
+      }
     }
 
     // walk through each sentence in the text
@@ -203,34 +204,33 @@ public abstract class RelationExtractorA
    * @return If this category should not be processed for training return <i>null</i>
    *         otherwise it returns the label sent to the datawriter
    */
-  protected abstract String getRelationCategory(Map<List<Annotation>, BinaryTextRelation>
relationLookup,
-		  IdentifiedAnnotation arg1, IdentifiedAnnotation arg2);
+  protected String getRelationCategory(Map<List<Annotation>, BinaryTextRelation>
relationLookup,
+		  IdentifiedAnnotation arg1, IdentifiedAnnotation arg2) {
+    BinaryTextRelation relation = relationLookup.get(Arrays.asList(arg1, arg2));
+    String category;
+    if (relation != null) {
+      category = relation.getCategory();
+    } else if (coin.nextDouble() <= this.probabilityOfKeepingANegativeExample) {
+      category = NO_RELATION_CATEGORY;
+    } else {
+      category = null;
+    }
+    return category;
+  }
 
   /**
-   * Creates a lookup map between lists of arguments and their relation
-   * This map does not key in simply on a HashableArgument because 
-   * @param relationView
-   * @return
+   * Predict an outcome given a set of features.
+   * By default, this simply delegates to the object's <code>classifier</code>.
+   * Subclasses may override this method to implement more complex classification procedures.

+   * 
+   * @param features The features to be classified.
+   * @return The predicted outcome (label) for the features.
    */
-  private static Map<List<Annotation>, BinaryTextRelation> createRelationLookup(
-		  JCas relationView) {
-	  Map<List<Annotation>, BinaryTextRelation> relationLookup;
-	  relationLookup = new HashMap<List<Annotation>, BinaryTextRelation>();
-	  for (BinaryTextRelation relation : JCasUtil.select(relationView, BinaryTextRelation.class))
{
-		  Annotation arg1, arg2;
-		  if (relation.getArg1().getRole().equals("Argument")) {
-			  arg1 = relation.getArg1().getArgument();
-			  arg2 = relation.getArg2().getArgument();
-		  } else {
-			  arg2 = relation.getArg1().getArgument();
-			  arg1 = relation.getArg2().getArgument();
-		  }
-		  // The key is a list of args so we can do bi-directional lookup
-		  relationLookup.put(Arrays.asList(arg1, arg2), relation);
-	  }
-	  return relationLookup;
+  protected String classify(List<Feature> features) throws CleartkProcessingException
{
+    return this.classifier.classify(features);
   }
 
+  
   public static class IdentifiedAnnotationPair {
 	  
 	 private final IdentifiedAnnotation arg1;

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java?rev=1439730&r1=1439729&r2=1439730&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java
(original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java
Tue Jan 29 01:32:13 2013
@@ -19,39 +19,29 @@
 package org.apache.ctakes.relationextractor.ae.baselines;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 
-import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
-import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
-import org.apache.ctakes.typesystem.type.textsem.EntityMention;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.Modifier;
+import org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator;
 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.CleartkProcessingException;
 import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
 
 /**
  * Annotated degree_of relation in sentences containing a single entity mention
  * of a valid degree_of type and a single modifier.
  */
-public class Baseline1DegreeOfRelationExtractorAnnotator extends RelationExtractorAnnotator
{
+public class Baseline1DegreeOfRelationExtractorAnnotator extends DegreeOfRelationExtractorAnnotator
{
 
 	@Override
 	public List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(
 			JCas identifiedAnnotationView, Sentence sentence) {
-		
-		List<EntityMention> entities = JCasUtil.selectCovered(identifiedAnnotationView, EntityMention.class,
sentence);
-		List<Modifier> modifiers = JCasUtil.selectCovered(identifiedAnnotationView, Modifier.class,
sentence);
+	  List<IdentifiedAnnotationPair> pairs = super.getCandidateRelationArgumentPairs(identifiedAnnotationView,
sentence);
 		
 		// look for sentences with one entity and one modifier
     List<IdentifiedAnnotationPair> result = new ArrayList<IdentifiedAnnotationPair>();
-		if((entities.size() == 1) && (modifiers.size() == 1)) {
-		  IdentifiedAnnotationPair pair = new IdentifiedAnnotationPair(entities.get(0), modifiers.get(0));
+		if (pairs.size() == 1) {
+		  IdentifiedAnnotationPair pair = pairs.get(0);
 		  if(Utils.validateDegreeOfArgumentTypes(pair)) {
 		    System.out.println(sentence.getCoveredText());
 		    System.out.println("arg1: " + pair.getArg1().getCoveredText());
@@ -64,14 +54,6 @@ public class Baseline1DegreeOfRelationEx
 		return result;
 	}
 
-	@Override
-	protected String getRelationCategory(
-			Map<List<Annotation>, BinaryTextRelation> relationLookup,
-			IdentifiedAnnotation arg1, IdentifiedAnnotation arg2) {
-		BinaryTextRelation relation = relationLookup.get(Arrays.asList(arg1, arg2));
-		return (relation != null) ? relation.getCategory() : NO_RELATION_CATEGORY;
-	}
-
   @Override
   public String classify(List<Feature> features) throws CleartkProcessingException
{
     return "degree_of";

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1EntityMentionPairRelationExtractorAnnotator.java?rev=1439730&r1=1439729&r2=1439730&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1EntityMentionPairRelationExtractorAnnotator.java
(original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1EntityMentionPairRelationExtractorAnnotator.java
Tue Jan 29 01:32:13 2013
@@ -19,40 +19,23 @@
 package org.apache.ctakes.relationextractor.ae.baselines;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 
 import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
-import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
 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.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.collect.Lists;
+
 /**
  * Annotate location_of relation between two entities in sentences containing
  * exactly two entities (where the entities are of the correct types).
- * This implementation assumes classifyBothDirections is set to true (i.e.
- * each pair of entities is considered twice).
  */
 public class Baseline1EntityMentionPairRelationExtractorAnnotator 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) {
@@ -63,37 +46,21 @@ public class Baseline1EntityMentionPairR
 				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));
-			}
-		}
-
 		// look for sentence with two entities
-		// because each pair of entities is cosidered twice, pairs.size() should be 2.
-		if(pairs.size() == 2) {
+		if (args.size() == 2) {
+		  EntityMention arg1 = args.get(0);
+		  EntityMention arg2 = args.get(1);
 		  // there are two entities in this sentence
 		  // are they of suitable types for location_of?
-		  for(IdentifiedAnnotationPair pair : pairs) {
-		    if(Utils.validateLocationOfArgumentTypes(pair)) {
+		  for (IdentifiedAnnotationPair pair : Lists.newArrayList(
+		      new IdentifiedAnnotationPair(arg1, arg2),
+		      new IdentifiedAnnotationPair(arg2, arg1))) {
+		    if (Utils.validateLocationOfArgumentTypes(pair)) {
 	        System.out.println(sentence.getCoveredText());
 	        System.out.println("arg1: " + pair.getArg1().getCoveredText());
 	        System.out.println("arg2: " + pair.getArg2().getCoveredText());
 	        System.out.println();
-	        
-		      List<IdentifiedAnnotationPair> result = new ArrayList<IdentifiedAnnotationPair>();
-		      result.add(pair);
-		      return result;
+		      return Lists.newArrayList(pair);
 		    }
 		  }
 		}
@@ -102,45 +69,8 @@ public class Baseline1EntityMentionPairR
 		// for all other cases, return no entity pairs
 		return new ArrayList<IdentifiedAnnotationPair>();
 	}
-		
-	@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
+	@Override
   public String classify(List<Feature> features) {
     return "location_of";
   }

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2DegreeOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2DegreeOfRelationExtractorAnnotator.java?rev=1439730&r1=1439729&r2=1439730&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2DegreeOfRelationExtractorAnnotator.java
(original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2DegreeOfRelationExtractorAnnotator.java
Tue Jan 29 01:32:13 2013
@@ -19,22 +19,17 @@
 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.List;
-import java.util.Map;
 
 import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
-import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
 import org.apache.ctakes.typesystem.type.textsem.EntityMention;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
 import org.apache.ctakes.typesystem.type.textsem.Modifier;
 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.CleartkProcessingException;
 import org.cleartk.classifier.Feature;
 import org.uimafit.util.JCasUtil;
@@ -105,16 +100,6 @@ public class Baseline2DegreeOfRelationEx
     
     return result;
 	}
-	
-	
-
-	@Override
-	protected String getRelationCategory(
-			Map<List<Annotation>, BinaryTextRelation> relationLookup,
-			IdentifiedAnnotation arg1, IdentifiedAnnotation arg2) {
-		BinaryTextRelation relation = relationLookup.get(Arrays.asList(arg1, arg2));
-		return (relation != null) ? relation.getCategory() : NO_RELATION_CATEGORY;
-	}
 
   @Override
   public String classify(List<Feature> features) throws CleartkProcessingException
{

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2EntityMentionPairRelationExtractorAnnotator.java?rev=1439730&r1=1439729&r2=1439730&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2EntityMentionPairRelationExtractorAnnotator.java
(original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline2EntityMentionPairRelationExtractorAnnotator.java
Tue Jan 29 01:32:13 2013
@@ -24,19 +24,14 @@ import java.util.Collections;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
 
 import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
-import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
 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;
@@ -46,21 +41,9 @@ import com.google.common.collect.Orderin
 /**
  * Annotate location_of relation between two entities in sentences with multiple anatomical
sites
  * and a single legitimate location_of arg2. Use the pair of arguments that are the closest
to each other.
- * This implementation assumes classifyBothDirections = true.
  */
 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) {
@@ -71,16 +54,11 @@ public class Baseline2EntityMentionPairR
 				EntityMention.class,
 				sentence);
 
-		// Create pairings (this will change depending on the classification direction)
+		// Create pairings
 		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()))
{
+		for (EntityMention arg1 : args) {
+			for (EntityMention arg2 : args) {
+				if (arg1.getBegin() == arg2.getBegin() && arg1.getEnd() == arg2.getEnd()) {
 				  continue;
 				}
 				pairs.add(new IdentifiedAnnotationPair(arg1, arg2));
@@ -136,43 +114,6 @@ public class Baseline2EntityMentionPairR
     
     return result;
 	}
-	
-	@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) {

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3DegreeOfRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3DegreeOfRelationExtractorAnnotator.java?rev=1439730&r1=1439729&r2=1439730&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3DegreeOfRelationExtractorAnnotator.java
(original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3DegreeOfRelationExtractorAnnotator.java
Tue Jan 29 01:32:13 2013
@@ -19,42 +19,24 @@
 package org.apache.ctakes.relationextractor.ae.baselines;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 
-import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
-import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator;
 import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
-import org.apache.ctakes.typesystem.type.textsem.EntityMention;
 import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.Modifier;
 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.CleartkProcessingException;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
 
 /**
- * Annotate location_of relation between two entities whenever 
+ * Annotate degree_of relation between two entities whenever 
  * they are enclosed within the same noun phrse.
  */
-public class Baseline3DegreeOfRelationExtractorAnnotator extends RelationExtractorAnnotator
{
+public class Baseline3DegreeOfRelationExtractorAnnotator extends DegreeOfRelationExtractorAnnotator
{
 
 	@Override
 	public List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(
 			JCas identifiedAnnotationView, Sentence sentence) {
-		
-		List<EntityMention> entities = JCasUtil.selectCovered(identifiedAnnotationView, EntityMention.class,
sentence);
-		List<Modifier> modifiers = JCasUtil.selectCovered(identifiedAnnotationView, Modifier.class,
sentence);
-		
-		List<IdentifiedAnnotationPair> pairs = new ArrayList<IdentifiedAnnotationPair>();
-		for (EntityMention entity : entities) {
-			for (Modifier modifier : modifiers) {
-				pairs.add(new IdentifiedAnnotationPair(entity, modifier));
-			}
-		}
+		List<IdentifiedAnnotationPair> pairs = super.getCandidateRelationArgumentPairs(identifiedAnnotationView,
sentence);
 		
     // find pairs enclosed inside a noun phrase
     List<IdentifiedAnnotationPair> result = new ArrayList<IdentifiedAnnotationPair>();
@@ -77,17 +59,4 @@ public class Baseline3DegreeOfRelationEx
     
     return result;
 	}
-
-	@Override
-	protected String getRelationCategory(
-			Map<List<Annotation>, BinaryTextRelation> relationLookup,
-			IdentifiedAnnotation arg1, IdentifiedAnnotation arg2) {
-		BinaryTextRelation relation = relationLookup.get(Arrays.asList(arg1, arg2));
-		return (relation != null) ? relation.getCategory() : NO_RELATION_CATEGORY;
-	}
-
-  @Override
-  public String classify(List<Feature> features) throws CleartkProcessingException
{
-    return this.classifier.classify(features);
-  }
 }

Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3EntityMentionPairRelationExtractorAnnotator.java?rev=1439730&r1=1439729&r2=1439730&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3EntityMentionPairRelationExtractorAnnotator.java
(original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3EntityMentionPairRelationExtractorAnnotator.java
Tue Jan 29 01:32:13 2013
@@ -19,20 +19,15 @@
 package org.apache.ctakes.relationextractor.ae.baselines;
 
 import java.util.ArrayList;
-import java.util.Arrays;
 import java.util.List;
-import java.util.Map;
 
 import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
-import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
 import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
 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.jcas.JCas;
-import org.apache.uima.jcas.tcas.Annotation;
 import org.cleartk.classifier.Feature;
-import org.uimafit.descriptor.ConfigurationParameter;
 import org.uimafit.util.JCasUtil;
 
 /**
@@ -41,17 +36,6 @@ import org.uimafit.util.JCasUtil;
  */
 public class Baseline3EntityMentionPairRelationExtractorAnnotator 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) {
@@ -62,21 +46,16 @@ public class Baseline3EntityMentionPairR
 				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));
-			}
-		}
+		// Create pairings
+    List<IdentifiedAnnotationPair> pairs = new ArrayList<IdentifiedAnnotationPair>();
+    for (EntityMention arg1 : args) {
+      for (EntityMention arg2 : args) {
+        if (arg1.getBegin() == arg2.getBegin() && arg1.getEnd() == arg2.getEnd())
{
+          continue;
+        }
+        pairs.add(new IdentifiedAnnotationPair(arg1, arg2));
+      }
+    }
 
 		// find pairs enclosed inside a noun phrase
 		List<IdentifiedAnnotationPair> result = new ArrayList<IdentifiedAnnotationPair>();
@@ -100,43 +79,6 @@ public class Baseline3EntityMentionPairR
 		return result;
 	}
 		
-	@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";



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