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Posted to commits@ctakes.apache.org by dl...@apache.org on 2013/01/14 15:12:43 UTC
svn commit: r1432925 - in
/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor:
ae/Baseline3EntityMentionPairRelationExtractorAnnotator.java
eval/RelationExtractorEvaluation.java
Author: dligach
Date: Mon Jan 14 14:12:43 2013
New Revision: 1432925
URL: http://svn.apache.org/viewvc?rev=1432925&view=rev
Log:
Initial version of baseline 3
Added:
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline3EntityMentionPairRelationExtractorAnnotator.java
Modified:
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/Baseline3EntityMentionPairRelationExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline3EntityMentionPairRelationExtractorAnnotator.java?rev=1432925&view=auto
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline3EntityMentionPairRelationExtractorAnnotator.java (added)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/Baseline3EntityMentionPairRelationExtractorAnnotator.java Mon Jan 14 14:12:43 2013
@@ -0,0 +1,196 @@
+/**
+ * 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.HashSet;
+import java.util.List;
+import java.util.Map;
+
+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.cas.CAS;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.cas.FeatureStructure;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.cas.FSArray;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.classifier.Feature;
+import org.uimafit.descriptor.ConfigurationParameter;
+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).
+ * This implementation assumes classifyBothDirections is set to true (i.e.
+ * each pair of entities is considered twice).
+ */
+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) {
+
+ // 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));
+ }
+ }
+
+ List<EntityMention> anatomicalSites = new ArrayList<EntityMention>();
+ for(EntityMention entityMention : args) {
+ if(entityMention.getTypeID() == 6) {
+ anatomicalSites.add(entityMention);
+ }
+ }
+
+ if(anatomicalSites.size() == 0) {
+ return new ArrayList<IdentifiedAnnotationPair>();
+ }
+
+ for(EntityMention anatomicalSite : anatomicalSites) {
+ try {
+ List<TreebankNode> treebankNodes = JCasUtil.selectCovering(
+ identifiedAnnotationView.getView(CAS.NAME_DEFAULT_SOFA),
+ TreebankNode.class,
+ anatomicalSite.getBegin(),
+ anatomicalSite.getEnd());
+ for(TreebankNode treebankNode : treebankNodes) {
+ if(treebankNode.getNodeType().equals("NP")) {
+ FSArray fsArray = treebankNode.getChildren();
+ if(fsArray == null) {
+ System.out.println("NULL");
+ } else {
+ for(FeatureStructure featureStructure : fsArray.toArray()) {
+ TreebankNode childNode = (TreebankNode) featureStructure;
+ System.out.println(sentence.getCoveredText());
+ System.out.println("anatomical site: " + anatomicalSite.getCoveredText());
+ System.out.println("child node: " + childNode.getCoveredText());
+ System.out.println();
+ }
+ }
+ }
+ }
+ } catch (CASException e) {
+ e.printStackTrace();
+ }
+ }
+
+ // 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) {
+
+ 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";
+ }
+}
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=1432925&r1=1432924&r2=1432925&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 14:12:43 2013
@@ -28,6 +28,15 @@ import java.util.List;
import java.util.Map;
import java.util.Set;
+import org.apache.ctakes.relationextractor.ae.Baseline3EntityMentionPairRelationExtractorAnnotator;
+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;
import org.apache.uima.UIMAFramework;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
@@ -72,15 +81,6 @@ 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 +138,7 @@ public class RelationExtractorEvaluation
// parameter settings currently optimized for SHARP data
private static final ParameterSettings BEST_DEGREE_OF_PARAMETERS = new ParameterSettings(false, 0.5f, "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();
@@ -163,7 +163,7 @@ public class RelationExtractorEvaluation
boolean isDegreeOf = relationCategory.equals("degree_of");
Class<? extends RelationExtractorAnnotator> annotatorClass = isDegreeOf
? DegreeOfRelationExtractorAnnotator.class
- : EntityMentionPairRelationExtractorAnnotator.class;
+ : Baseline3EntityMentionPairRelationExtractorAnnotator.class;
// determine the type of classifier to be trained
Class<? extends DataWriter<String>> dataWriterClass = LIBSVMStringOutcomeDataWriter.class;