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Posted to commits@ctakes.apache.org by dl...@apache.org on 2013/01/14 22:52:24 UTC
svn commit: r1433160 - in
/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor:
ae/baselines/ eval/
Author: dligach
Date: Mon Jan 14 21:52:23 2013
New Revision: 1433160
URL: http://svn.apache.org/viewvc?rev=1433160&view=rev
Log:
initial version of baseline1 for degree_of
Added:
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/Utils.java
Modified:
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/Baseline2EntityMentionPairRelationExtractorAnnotator.java
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline3EntityMentionPairRelationExtractorAnnotator.java
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java
Added: 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=1433160&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java (added)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Baseline1DegreeOfRelationExtractorAnnotator.java Mon Jan 14 21:52:23 2013
@@ -0,0 +1,78 @@
+/**
+ * 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.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.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.classifier.CleartkProcessingException;
+import org.cleartk.classifier.Feature;
+import org.uimafit.util.JCasUtil;
+
+/**
+ *
+ */
+public class Baseline1DegreeOfRelationExtractorAnnotator extends RelationExtractorAnnotator {
+
+ @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);
+
+ // 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(Utils.validateDegreeOfArgumentTypes(pair)) {
+ System.out.println(sentence.getCoveredText());
+ System.out.println("arg1: " + pair.getArg1().getCoveredText());
+ System.out.println("arg2: " + pair.getArg2().getCoveredText());
+ System.out.println();
+ result.add(pair);
+ }
+ }
+
+ 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=1433160&r1=1433159&r2=1433160&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 Mon Jan 14 21:52:23 2013
@@ -20,12 +20,10 @@ package org.apache.ctakes.relationextrac
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.HashSet;
import java.util.List;
import java.util.Map;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
-import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
@@ -87,7 +85,7 @@ public class Baseline1EntityMentionPairR
// there are two entities in this sentence
// are they of suitable types for location_of?
for(IdentifiedAnnotationPair pair : pairs) {
- if(validateArgumentTypes(pair)) {
+ if(Utils.validateLocationOfArgumentTypes(pair)) {
System.out.println(sentence.getCoveredText());
System.out.println("arg1: " + pair.getArg1().getCoveredText());
System.out.println("arg2: " + pair.getArg2().getCoveredText());
@@ -104,32 +102,7 @@ public class Baseline1EntityMentionPairR
// for all other cases, return no entity pairs
return new ArrayList<IdentifiedAnnotationPair>();
}
-
- /*
- * 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) {
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=1433160&r1=1433159&r2=1433160&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 Mon Jan 14 21:52:23 2013
@@ -108,7 +108,7 @@ public class Baseline2EntityMentionPairR
// 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)) {
+ if(Utils.validateLocationOfArgumentTypes(pair)) {
try {
int distance = getDistance(identifiedAnnotationView.getView(CAS.NAME_DEFAULT_SOFA), pair);
distanceLookup.put(pair, distance);
@@ -147,31 +147,6 @@ public class Baseline2EntityMentionPairR
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) {
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=1433160&r1=1433159&r2=1433160&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 Mon Jan 14 21:52:23 2013
@@ -20,12 +20,10 @@ package org.apache.ctakes.relationextrac
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.HashSet;
import java.util.List;
import java.util.Map;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
-import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
@@ -85,7 +83,7 @@ public class Baseline3EntityMentionPairR
// find pairs enclosed inside a noun phrase
List<IdentifiedAnnotationPair> result = new ArrayList<IdentifiedAnnotationPair>();
for(IdentifiedAnnotationPair pair : pairs) {
- if(validateArgumentTypes(pair)) {
+ if(Utils.validateLocationOfArgumentTypes(pair)) {
for(TreebankNode nounPhrase : getNounPhrases(identifiedAnnotationView, sentence)) {
if(isEnclosed(pair, nounPhrase)) {
IdentifiedAnnotation arg1 = pair.getArg1();
@@ -148,31 +146,6 @@ public class Baseline3EntityMentionPairR
return nounPhrases;
}
- /*
- * 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) {
Added: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java?rev=1433160&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java (added)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java Mon Jan 14 21:52:23 2013
@@ -0,0 +1,59 @@
+package org.apache.ctakes.relationextractor.ae.baselines;
+
+import java.util.Arrays;
+import java.util.HashSet;
+
+import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+
+public class Utils {
+
+ /**
+ * Are entity types of the arguments valid for location_of relation?
+ * 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)
+ */
+ public static boolean validateLocationOfArgumentTypes(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;
+ }
+
+ /**
+ * Are entity types of the arguments valid for degree_of relation?
+ * The following are the valid combinations:
+ *
+ * degree-of(disorder/2, modifier)
+ * degree-of(sign/symptom/3, modifier)
+ */
+ public static boolean validateDegreeOfArgumentTypes(IdentifiedAnnotationPair pair) {
+
+ // allowable arg1 types
+ HashSet<Integer> okArg1Types = new HashSet<Integer>(Arrays.asList(2, 3));
+
+ IdentifiedAnnotation arg1 = pair.getArg1(); // Argument (should be either disease/disorder or sign/symptom
+ IdentifiedAnnotation arg2 = pair.getArg2(); // Related_to (should be a modifier)
+ int type1 = arg1.getTypeID();
+ int type2 = arg2.getTypeID();
+
+ if(okArg1Types.contains(type1)) {
+ return true; // assume arg2 is a moddifier
+ }
+
+ return false;
+ }
+}
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java?rev=1433160&r1=1433159&r2=1433160&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java Mon Jan 14 21:52:23 2013
@@ -28,6 +28,14 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
+import org.apache.ctakes.relationextractor.ae.EntityMentionPairRelationExtractorAnnotator;
+import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
+import org.apache.ctakes.relationextractor.ae.baselines.Baseline1DegreeOfRelationExtractorAnnotator;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.relation.RelationArgument;
+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.uima.UIMAFramework;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
@@ -72,15 +80,6 @@ import com.google.common.collect.Maps;
import com.google.common.collect.Ordering;
import com.google.common.collect.Sets;
-import org.apache.ctakes.relationextractor.ae.DegreeOfRelationExtractorAnnotator;
-import org.apache.ctakes.relationextractor.ae.EntityMentionPairRelationExtractorAnnotator;
-import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
-import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
-import org.apache.ctakes.typesystem.type.relation.RelationArgument;
-import org.apache.ctakes.typesystem.type.textsem.EntityMention;
-import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.Modifier;
-
public class RelationExtractorEvaluation extends Evaluation_ImplBase<File, AnnotationStatistics<String>> {
public static class Options extends Options_ImplBase {
@@ -138,7 +137,7 @@ public class RelationExtractorEvaluation
// parameter settings currently optimized for SHARP data
private static final ParameterSettings BEST_DEGREE_OF_PARAMETERS = new ParameterSettings(false, 1.0f, "radial basis function", 10.0, 0.0010);
- private static final ParameterSettings BEST_NON_DEGREE_OF_PARAMETERS = new ParameterSettings(false, 1.0f, "radial basis function", 10.0, 0.01);
+ private static final ParameterSettings BEST_NON_DEGREE_OF_PARAMETERS = new ParameterSettings(true, 1.0f, "radial basis function", 10.0, 0.01);
public static void main(String[] args) throws Exception {
Options options = new Options();
@@ -162,7 +161,7 @@ public class RelationExtractorEvaluation
// determine class for the classifier annotator
boolean isDegreeOf = relationCategory.equals("degree_of");
Class<? extends RelationExtractorAnnotator> annotatorClass = isDegreeOf
- ? DegreeOfRelationExtractorAnnotator.class
+ ? Baseline1DegreeOfRelationExtractorAnnotator.class
: EntityMentionPairRelationExtractorAnnotator.class;
// determine the type of classifier to be trained