You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@ctakes.apache.org by tm...@apache.org on 2015/03/13 17:22:11 UTC
svn commit: r1666500 - in
/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features:
./ cluster/ salience/
Author: tmill
Date: Fri Mar 13 16:22:11 2015
New Revision: 1666500
URL: http://svn.apache.org/r1666500
Log:
New features and modified features ported from temporal.
Added:
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/CorefSyntaxFeatureExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/SectionFeatureExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/TemporalFeatureExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterAgreementFeaturesExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterPartOfSpeechFeaturesExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterStringFeaturesExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/ClinicalFeatureExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/GrammaticalRoleFeatureExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/MorphosyntacticFeatureExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/SemanticEnvironmentFeatureExtractor.java
Modified:
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/DistSemFeatureExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/DistanceFeatureExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/StringMatchingFeatureExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/TokenFeatureExtractor.java
ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java
Added: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/CorefSyntaxFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/CorefSyntaxFeatureExtractor.java?rev=1666500&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/CorefSyntaxFeatureExtractor.java (added)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/CorefSyntaxFeatureExtractor.java Fri Mar 13 16:22:11 2015
@@ -0,0 +1,32 @@
+package org.apache.ctakes.coreference.ae.features;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.dependency.parser.util.DependencyUtility;
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+
+public class CorefSyntaxFeatureExtractor implements RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
+
+ public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
+ IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+ List<Feature> feats = new ArrayList<>();
+
+ ConllDependencyNode head1 = DependencyUtility.getNominalHeadNode(jCas, arg1);
+ ConllDependencyNode head2 = DependencyUtility.getNominalHeadNode(jCas, arg2);
+
+ if(head1 != null){
+ feats.add(new Feature("Arg1Head", head1.getCoveredText().toLowerCase()));
+ }
+ if(head2 != null){
+ feats.add(new Feature("Arg2Head", head2.getCoveredText().toLowerCase()));
+ }
+ return feats;
+ }
+
+}
Modified: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/DistSemFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/DistSemFeatureExtractor.java?rev=1666500&r1=1666499&r2=1666500&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/DistSemFeatureExtractor.java (original)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/DistSemFeatureExtractor.java Fri Mar 13 16:22:11 2015
@@ -18,10 +18,10 @@ import org.apache.ctakes.utils.distsem.W
import org.apache.ctakes.utils.distsem.WordVectorReader;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
-public class DistSemFeatureExtractor implements RelationFeaturesExtractor {
+public class DistSemFeatureExtractor implements RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
// default value is 0.5 (rather than 0.0) because we don't want to assume OOV words are dissimilar
public static final double DEFAULT_SIM = 0.5;
Modified: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/DistanceFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/DistanceFeatureExtractor.java?rev=1666500&r1=1666499&r2=1666500&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/DistanceFeatureExtractor.java (original)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/DistanceFeatureExtractor.java Fri Mar 13 16:22:11 2015
@@ -10,15 +10,15 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.apache.uima.fit.util.JCasUtil;
-public class DistanceFeatureExtractor implements RelationFeaturesExtractor {
+public class DistanceFeatureExtractor implements RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
@Override
public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
- List<Feature> feats = new ArrayList<Feature>();
+ List<Feature> feats = new ArrayList<>();
feats.add(new Feature("TOK_DIST",
JCasUtil.selectCovered(jCas, BaseToken.class, arg1.getBegin(), arg2.getEnd()).size() / (double)CorefConst.TOKEN_DIST));
feats.add(new Feature("SENT_DIST",
Added: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/SectionFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/SectionFeatureExtractor.java?rev=1666500&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/SectionFeatureExtractor.java (added)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/SectionFeatureExtractor.java Fri Mar 13 16:22:11 2015
@@ -0,0 +1,56 @@
+package org.apache.ctakes.coreference.ae.features;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Paragraph;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+
+public class SectionFeatureExtractor implements RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
+
+ public List<Feature> extract(JCas jcas, IdentifiedAnnotation ante,
+ IdentifiedAnnotation ana) throws AnalysisEngineProcessException {
+ List<Feature> feats = new ArrayList<>();
+ boolean anteInHeader = false;
+ boolean anaInHeader = false;
+ int antePar = -1;
+ int anaPar = -1;
+
+ // Find section headers -- paragraphs
+ List<Paragraph> pars = new ArrayList<>(JCasUtil.select(jcas, Paragraph.class));
+ for(int i = 0; i < pars.size(); i++){
+ Paragraph par = pars.get(i);
+ if(par.getBegin() > ana.getEnd()){
+ break;
+ }
+ if(ante.getBegin() >= par.getBegin() && ante.getEnd() <= par.getEnd()){
+ antePar = i;
+ }
+ if(ana.getBegin() >= par.getBegin() && ana.getEnd() <= par.getEnd()){
+ anaPar = i;
+ }
+ List<Sentence> coveredSents = JCasUtil.selectCovered(jcas, Sentence.class, par);
+ if(coveredSents != null && coveredSents.size() == 1){
+ if(antePar == i){
+ anteInHeader = true;
+ }
+ if(anaPar == i){
+ anaInHeader = true;
+ }
+ }
+ }
+
+ feats.add(new Feature("AnteInHeader", anteInHeader));
+ feats.add(new Feature("AnaInHeader", anaInHeader));
+ if(anteInHeader && antePar+1 == anaPar){
+ feats.add(new Feature("AnteHeaderHeadsAna", true));
+ }
+ return feats;
+ }
+}
Modified: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/StringMatchingFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/StringMatchingFeatureExtractor.java?rev=1666500&r1=1666499&r2=1666500&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/StringMatchingFeatureExtractor.java (original)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/StringMatchingFeatureExtractor.java Fri Mar 13 16:22:11 2015
@@ -9,18 +9,21 @@ import org.apache.ctakes.relationextract
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
public class StringMatchingFeatureExtractor implements
- RelationFeaturesExtractor {
+ RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
@Override
public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
- List<Feature> feats = new ArrayList<Feature>();
+ List<Feature> feats = new ArrayList<>();
+
+ // don't extract sim features if one of the markables is a pronoun
+ if(isPronoun(arg1) || isPronoun(arg2)) return feats;
String s1 = arg1.getCoveredText();
String s2 = arg2.getCoveredText();
@@ -53,8 +56,8 @@ public class StringMatchingFeatureExtrac
public static boolean endMatch (String a, String b) {
int ia = a.lastIndexOf(" ");
int ib = b.lastIndexOf(" ");
- String aa = a.substring(ia==-1?(a.length()>5?a.length()-5:0):ia);
- String bb = b.substring(ib==-1?(b.length()>5?b.length()-5:0):ib);
+ String aa = a.substring(ia==-1?(a.length()>5?a.length()-5:0):ia+1);
+ String bb = b.substring(ib==-1?(b.length()>5?b.length()-5:0):ib+1);
return aa.equalsIgnoreCase(bb);
}
@@ -89,10 +92,28 @@ public class StringMatchingFeatureExtrac
}
public static Set<String> contentWords(Annotation a1){
- Set<String> words = new HashSet<String>();
+ Set<String> words = new HashSet<>();
for(BaseToken tok : JCasUtil.selectCovered(BaseToken.class, a1)){
words.add(tok.getCoveredText().toLowerCase());
}
return words;
}
+
+ public static boolean isPronoun(IdentifiedAnnotation a1){
+ List<BaseToken> tokens = JCasUtil.selectCovered(BaseToken.class, a1);
+
+ if(tokens.size() != 1){
+ return false;
+ }
+
+ BaseToken token = tokens.get(0);
+ if(token.getPartOfSpeech() == null){
+ return false;
+ }
+ if(token.getPartOfSpeech().startsWith("PRP")) return true;
+ if(token.getPartOfSpeech().equals("DT")) return true;
+
+
+ return false;
+ }
}
Added: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/TemporalFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/TemporalFeatureExtractor.java?rev=1666500&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/TemporalFeatureExtractor.java (added)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/TemporalFeatureExtractor.java Fri Mar 13 16:22:11 2015
@@ -0,0 +1,51 @@
+package org.apache.ctakes.coreference.ae.features;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.dependency.parser.util.DependencyUtility;
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+
+public class TemporalFeatureExtractor implements RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
+
+ public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
+ IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+ List<Feature> feats = new ArrayList<>();
+
+ String a1dtr = getDocTimeRelForArg(jCas, arg1);
+ feats.add(new Feature("Arg1DTR_" + a1dtr, true));
+ String a2dtr = getDocTimeRelForArg(jCas, arg2);
+ feats.add(new Feature("Arg2DTR_" + a2dtr, true));
+
+ if(a1dtr.equals(a2dtr) && !a1dtr.equals("NA")){
+ feats.add(new Feature("DTR_Match", true));
+ }
+
+ return feats;
+ }
+
+ private static String getDocTimeRelForArg(JCas jCas, IdentifiedAnnotation arg){
+ String dtr = "NA";
+
+ // find EventMentions and grab their event properties
+ ConllDependencyNode node = DependencyUtility.getNominalHeadNode(jCas, arg);
+ if(node != null){
+ List<EventMention> events = JCasUtil.selectCovered(jCas, EventMention.class, node);
+ for(EventMention event : events){
+ if(event.getClass().getSimpleName().equals("EventMention")){
+ if(event.getEvent() != null && event.getEvent().getProperties() != null && event.getEvent().getProperties().getDocTimeRel() != null){
+ dtr = event.getEvent().getProperties().getDocTimeRel();
+ }
+ }
+ }
+ }
+ return dtr;
+ }
+}
\ No newline at end of file
Modified: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/TokenFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/TokenFeatureExtractor.java?rev=1666500&r1=1666499&r2=1666500&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/TokenFeatureExtractor.java (original)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/TokenFeatureExtractor.java Fri Mar 13 16:22:11 2015
@@ -3,20 +3,24 @@ package org.apache.ctakes.coreference.ae
import java.util.ArrayList;
import java.util.List;
+import org.apache.ctakes.dependency.parser.util.DependencyUtility;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.syntax.NewlineToken;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.ml.Feature;
-public class TokenFeatureExtractor implements RelationFeaturesExtractor {
+public class TokenFeatureExtractor implements RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
@Override
public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
- List<Feature> feats = new ArrayList<Feature>();
+ List<Feature> feats = new ArrayList<>();
String s1 = arg1.getCoveredText().toLowerCase();
String s2 = arg2.getCoveredText().toLowerCase();
@@ -29,19 +33,53 @@ public class TokenFeatureExtractor imple
feats.add(new Feature("TOKEN_DEF1", isDefinite(s1)));
feats.add(new Feature("TOKEN_DEF2", isDefinite(s2)));
feats.add(new Feature("TOKEN_NUMAGREE",
- numberSingular(arg1) == numberSingular(arg2)));
-
+ numberSingular(jCas, arg1, s1) == numberSingular(jCas, arg2, s2)));
+
String gen1 = getGender(s1);
String gen2 = getGender(s2);
feats.add(new Feature("TOKEN_GEN1", gen1));
feats.add(new Feature("TOKEN_GEN2", gen2));
feats.add(new Feature("TOKEN_GENAGREE", gen1.equals(gen2)));
- String p1 = getPerson(s1);
- String p2 = getPerson(s2);
- feats.add(new Feature("TOKEN_PERSON1", p1));
- feats.add(new Feature("TOKEN_PERSON2", p2));
- feats.add(new Feature("TOKEN_PERSONAGREE", p1.equals(p2)));
+// String p1 = getPerson(s1);
+// String p2 = getPerson(s2);
+// feats.add(new Feature("TOKEN_PERSON1", p1));
+// feats.add(new Feature("TOKEN_PERSON2", p2));
+// feats.add(new Feature("TOKEN_PERSONAGREE", p1.equals(p2)));
+// feats.add(new Feature("TOKEN_PERSONPAIR", p1+"-"+p2));
+// feats.add(new Feature("IS_TITLE1", isTitle(s1)));
+// feats.add(new Feature("IS_TITLE2", isTitle(s2)));
+
+// feats.add(new Feature("IS_DOCTOR1", s1.startsWith("dr.")));
+// feats.add(new Feature("IS_DOCTOR2", s2.startsWith("dr.")));
+// feats.add(new Feature("BOTH_DOCTOR", s1.startsWith("dr.") && s2.startsWith("dr.")));
+
+// boolean a1IsHuman = false;
+// boolean a2IsHuman = false;
+
+ // if has some person (1st, 2nd, 3rd) or gender (masc., fem), is doctor
+// a1IsHuman |= (!p1.equals("NONE"));
+// a1IsHuman |= (!gen1.equals("NEUTER"));
+// a1IsHuman |= (isTitle(s1));
+//
+// a2IsHuman |= (!p2.equals("NONE"));
+// a2IsHuman |= (!gen2.equals("NEUTER"));
+// a2IsHuman |= (isTitle(s2));
+//
+// feats.add(new Feature("IS_HUMAN1", a1IsHuman));
+// feats.add(new Feature("IS_HUMAN2", a2IsHuman));
+// feats.add(new Feature("BOTH_HUMAN", a1IsHuman && a2IsHuman));
+// feats.add(new Feature("NEITHER_HUMAN", !a1IsHuman && !a2IsHuman));
+
+ // is it a section header?
+ List<BaseToken> nextToks = JCasUtil.selectFollowing(jCas, BaseToken.class, arg1, 1);
+ if(nextToks.size() > 0 && nextToks.get(0) instanceof NewlineToken){
+ feats.add(new Feature("IS_HEADER1", true));
+ }
+ nextToks = JCasUtil.selectFollowing(jCas, BaseToken.class, arg2, 1);
+ if(nextToks.size() > 0 && nextToks.get(0) instanceof NewlineToken){
+ feats.add(new Feature("IS_HEADER2", true));
+ }
return feats;
}
@@ -49,9 +87,10 @@ public class TokenFeatureExtractor imple
if (s.startsWith("this") ||
s.startsWith("that") ||
s.startsWith("these") ||
- s.startsWith("those"))
+ s.startsWith("those")){
return true;
- else return false;
+ }
+ return false;
}
public static boolean isDefinite (String s) {
@@ -60,34 +99,39 @@ public class TokenFeatureExtractor imple
// FYI - old code used treebanknode types and found head using head rules filled in by the parser
// not sure if there is an appreciable difference...
- public static boolean numberSingular(IdentifiedAnnotation arg){
- List<BaseToken> tokens = new ArrayList<BaseToken>(JCasUtil.selectCovered(BaseToken.class, arg));
- for (int i = tokens.size()-1; i >=0; i--){
- BaseToken t = tokens.get(i);
- String pos = t.getPartOfSpeech();
- if ("NN".equals(pos) || "NNP".equals(pos)){
- return true;
- }else if ("NNS".equals(pos) || "NNPS".equals(pos)){
- return false;
- }else if(t.getCoveredText().toLowerCase().equals("we")){
- return true;
- }
- }
+ public static boolean numberSingular(JCas jcas, Annotation arg, String s1){
+ ConllDependencyNode head = DependencyUtility.getNominalHeadNode(jcas, arg);
+// List<BaseToken> tokens = new ArrayList<>(JCasUtil.selectCovered(BaseToken.class, arg));
+// for (int i = tokens.size()-1; i >=0; i--){
+// BaseToken t = tokens.get(i);
+// String pos = t.getPartOfSpeech();
+ if(head != null && head.getPostag() != null){
+ String pos = head.getPostag();
+ if ("NN".equals(pos) || "NNP".equals(pos)){
+ return true;
+ }else if ("NNS".equals(pos) || "NNPS".equals(pos)){
+ return false;
+ }else if(s1.equals("we") || s1.equals("they")){
+ return false;
+ }
+ }
+// }
return true;
}
public static String getGender(String s1){
- if(s1.equals("he") || s1.equals("his") || s1.startsWith("mr.")) return "MALE";
+ if(s1.equals("he") || s1.equals("his") || s1.equals("him") || s1.startsWith("mr.")) return "MALE";
else if(s1.equals("she") || s1.equals("her") || s1.startsWith("mrs.") || s1.startsWith("ms.")) return "FEMALE";
else return "NEUTER";
}
public static String getPerson(String s1){
- if(s1.equals("i")) return "FIRST";
+ if(s1.equals("i") || s1.equals("my")) return "FIRST";
else if(s1.equals("he") || s1.equals("she") || s1.equals("his") || s1.equals("her") || s1.equals("hers")){
return "THIRD";
}else if(s1.equals("you") || s1.equals("your")) return "SECOND";
- else if(s1.equals("we")) return "FIRST_PLURAL";
+ else if(s1.equals("we") || s1.equals("our")) return "FIRST_PLURAL";
+ else if(s1.equals("they") || s1.equals("their")) return "THIRD_PLURAL";
else return "NONE";
}
@@ -95,4 +139,8 @@ public class TokenFeatureExtractor imple
if(s1.equals("i")) return true;
return false;
}
+
+ public static boolean isTitle(String s1){
+ return s1.startsWith("dr.") || s1.startsWith("mr.") || s1.startsWith("mrs.") || s1.startsWith("ms.");
+ }
}
Modified: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java?rev=1666500&r1=1666499&r2=1666500&view=diff
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java (original)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/UMLSFeatureExtractor.java Fri Mar 13 16:22:11 2015
@@ -1,43 +1,131 @@
package org.apache.ctakes.coreference.ae.features;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashSet;
import java.util.List;
+import java.util.Map;
+import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
import org.apache.ctakes.dependency.parser.util.DependencyUtility;
import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textsem.Markable;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
-import org.cleartk.classifier.Feature;
-import org.uimafit.util.JCasUtil;
+import org.cleartk.ml.Feature;
+import org.cleartk.util.ViewUriUtil;
-public class UMLSFeatureExtractor implements RelationFeaturesExtractor {
+public class UMLSFeatureExtractor implements RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation> {
+ String docId = null;
+ Map<ConllDependencyNode,Collection<IdentifiedAnnotation>> coveringMap = null;
+
@Override
public List<Feature> extract(JCas jCas, IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
- List<Feature> feats = new ArrayList<Feature>();
+ List<Feature> feats = new ArrayList<>();
+
+ if(docId == null || !getDocId(jCas).equals(docId)){
+ docId = getDocId(jCas);
+ coveringMap = JCasUtil.indexCovering(jCas, ConllDependencyNode.class, IdentifiedAnnotation.class);
+ }
+
if(arg1 instanceof Markable && arg2 instanceof Markable){
+// feats.add(new Feature("AntecedentSalience", arg1.getConfidence()));
+// feats.add(new Feature("AnaphorSalience", arg2.getConfidence()));
+
// get the head of each markable
ConllDependencyNode head1 = DependencyUtility.getNominalHeadNode(jCas, arg1);
ConllDependencyNode head2 = DependencyUtility.getNominalHeadNode(jCas, arg2);
+ List<IdentifiedAnnotation> rmList = new ArrayList<>();
if(head1 != null && head2 != null){
- List<IdentifiedAnnotation> ents1 = JCasUtil.selectCovering(jCas, IdentifiedAnnotation.class, head1.getBegin(), head1.getEnd());
- List<IdentifiedAnnotation> ents2 = JCasUtil.selectCovering(jCas, IdentifiedAnnotation.class, head2.getBegin(), head2.getEnd());
-
+ List<IdentifiedAnnotation> ents1 = new ArrayList<>(coveringMap.get(head1)); //JCasUtil.selectCovering(jCas, IdentifiedAnnotation.class, head1.getBegin(), head1.getEnd());'
+ for(IdentifiedAnnotation ann : ents1){
+ if(!(ann instanceof EntityMention || ann instanceof EventMention)){
+ rmList.add(ann);
+ }
+ }
+ for(IdentifiedAnnotation toRm : rmList){
+ ents1.remove(toRm);
+ }
+ rmList.clear();
+ List<IdentifiedAnnotation> ents2 = new ArrayList<>(coveringMap.get(head2)); //JCasUtil.selectCovering(jCas, IdentifiedAnnotation.class, head2.getBegin(), head2.getEnd());
+ for(IdentifiedAnnotation ann : ents2){
+ if(!(ann instanceof EntityMention || ann instanceof EventMention)){
+ rmList.add(ann);
+ }
+ }
+ for(IdentifiedAnnotation toRm : rmList){
+ ents2.remove(toRm);
+ }
+
+ if(ents1.size() == 0 && ents2.size() > 0){
+ feats.add(new Feature("Arg1NoCui_Arg2Cui", true));
+ }else if(ents1.size() > 0 && ents2.size() == 0){
+ feats.add(new Feature("Arg1Cui_Arg2NoCui", true));
+ }else if(ents1.size() == 0 && ents2.size() == 0){
+ feats.add(new Feature("Arg1Arg2NoCui", true));
+ }else{
+ feats.add(new Feature("Arg1Arg2BothCui", true));
+ }
+
+ if((ents1.size() == 0 & ents2.size() > 0) ||
+ (ents1.size() > 0 && ents2.size() == 0)){
+ feats.add(new Feature("Arg1OrArg2NoCui", true));
+ }
+
for(IdentifiedAnnotation ent1 : ents1){
+ HashSet<String> a1Tuis = new HashSet<>();
+ String a1SemType = ent1.getClass().getSimpleName();
+ feats.add(new Feature("Arg1SemType" + a1SemType, true));
+ FSArray cons1 = ent1.getOntologyConceptArr();
+ if(cons1 != null){
+ for(int i = 0; i < cons1.size(); i++){
+ if(cons1.get(i) instanceof UmlsConcept){
+ a1Tuis.add(((UmlsConcept)cons1.get(i)).getTui());
+ }
+ }
+ }
for(IdentifiedAnnotation ent2 : ents2){
+ HashSet<String> a2Tuis = new HashSet<>();
+ String a2SemType = ent2.getClass().getSimpleName();
+ feats.add(new Feature("Arg2SemType" + a2SemType, true));
if(alias(ent1, ent2)){
feats.add(new Feature("UMLS_ALIAS", true));
break;
}
+ feats.add(new Feature("Arg1Arg2SemType" + a1SemType + "_" + a2SemType, true));
+
+ FSArray cons2 = ent2.getOntologyConceptArr();
+ if(cons2 != null){
+ for(int i = 0; i < cons2.size(); i++){
+ if(cons2.get(i) instanceof UmlsConcept){
+ a2Tuis.add(((UmlsConcept)cons2.get(i)).getTui());
+ }
+ }
+ }
+ for(String tui1 : a1Tuis){
+ feats.add(new Feature("Arg1Tui_" + tui1, true));
+ for(String tui2 : a2Tuis){
+ feats.add(new Feature("Arg1Tui_" + tui1 + "_Arg2Tui_ " + tui2, true));
+ if(tui1.equals(tui2)){
+ feats.add(new Feature("Arg1Arg2TuiMatch", true));
+ }
+ }
+ }
+ for(String tui2 : a2Tuis){
+ feats.add(new Feature("Arg2Tui_" + tui2, true));
+ }
}
}
}
@@ -45,11 +133,27 @@ public class UMLSFeatureExtractor implem
return feats;
}
- public static boolean alias(IdentifiedAnnotation a1, IdentifiedAnnotation a2){
+ private static String getDocId(JCas jcas) throws AnalysisEngineProcessException {
+ String docId = null;
+
+ docId = DocumentIDAnnotationUtil.getDocumentID(jcas);
+ if(docId != null) return docId;
+
+ try{
+ if(jcas.getView(ViewUriUtil.URI) != null){
+ docId = ViewUriUtil.getURI(jcas).toString();
+ }
+ }catch(Exception e){
+ // don't need to do anything -- just return null
+ }
+ return docId;
+ }
+
+ public static boolean alias(IdentifiedAnnotation a1, IdentifiedAnnotation a2){
if(a1 != null && a2 != null){
FSArray fsa = a1.getOntologyConceptArr();
if(fsa != null){
- HashSet<String> cuis = new HashSet<String>();
+ HashSet<String> cuis = new HashSet<>();
for(int i = 0; i < fsa.size(); i++){
if(fsa.get(i) instanceof UmlsConcept){
cuis.add(((UmlsConcept)fsa.get(i)).getCui());
Added: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterAgreementFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterAgreementFeaturesExtractor.java?rev=1666500&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterAgreementFeaturesExtractor.java (added)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterAgreementFeaturesExtractor.java Fri Mar 13 16:22:11 2015
@@ -0,0 +1,73 @@
+package org.apache.ctakes.coreference.ae.features.cluster;
+
+import static org.apache.ctakes.coreference.ae.features.TokenFeatureExtractor.getGender;
+import static org.apache.ctakes.coreference.ae.features.TokenFeatureExtractor.isDefinite;
+import static org.apache.ctakes.coreference.ae.features.TokenFeatureExtractor.isDemonstrative;
+import static org.apache.ctakes.coreference.ae.features.TokenFeatureExtractor.numberSingular;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.core.util.ListIterable;
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+
+public class MentionClusterAgreementFeaturesExtractor implements RelationFeaturesExtractor<CollectionTextRelation,IdentifiedAnnotation> {
+
+ public List<Feature> extract(JCas jCas, CollectionTextRelation cluster,
+ IdentifiedAnnotation mention) throws AnalysisEngineProcessException {
+ List<Feature> features = new ArrayList<>();
+
+ String s = mention.getCoveredText().toLowerCase();
+ boolean isDem = isDemonstrative(s);
+ boolean isDef = isDefinite(s);
+ features.add(new Feature("MC_MENTION_DEM", isDem));
+ features.add(new Feature("MC_MENTION_DEF", isDef));
+
+ String gender = getGender(s);
+ features.add(new Feature("MC_MENTION_GENDER", gender));
+
+ boolean singular = numberSingular(jCas, mention, s);
+ features.add(new Feature("MC_MENTION_NUMBER", singular));
+
+ boolean matchDem = false;
+ boolean matchDef = false;
+ boolean matchGender = false;
+ boolean matchNumber = false;
+
+ for(IdentifiedAnnotation member : new ListIterable<IdentifiedAnnotation>(cluster.getMembers())){
+ if(member == null){
+ System.err.println("Something that shouldn't happen has happened");
+ continue;
+ }else if(mention.getBegin() < member.getEnd()){
+ // during training this might happen -- see a member of a cluster that
+ // is actually subsequent to the candidate mention
+ continue;
+ }
+ String m = member.getCoveredText().toLowerCase();
+ if(!matchDem && isDemonstrative(m) == isDem){
+ matchDem = true;
+ }
+ if(!matchDef && isDefinite(m) == isDef){
+ matchDef = true;
+ }
+ if(!matchGender && getGender(m).equals(gender)){
+ matchGender = true;
+ }
+ if(!matchNumber && numberSingular(jCas, member, m) == singular){
+ matchNumber = true;
+ }
+ }
+
+ features.add(new Feature("MC_AGREE_DEM", matchDem));
+ features.add(new Feature("MC_AGREE_DEF", matchDef));
+ features.add(new Feature("MC_AGREE_GEN", matchGender));
+ features.add(new Feature("MC_AGREE_NUM", matchNumber));
+
+ return features;
+ }
+}
Added: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterPartOfSpeechFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterPartOfSpeechFeaturesExtractor.java?rev=1666500&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterPartOfSpeechFeaturesExtractor.java (added)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterPartOfSpeechFeaturesExtractor.java Fri Mar 13 16:22:11 2015
@@ -0,0 +1,22 @@
+package org.apache.ctakes.coreference.ae.features.cluster;
+
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+
+public class MentionClusterPartOfSpeechFeaturesExtractor implements
+ RelationFeaturesExtractor<CollectionTextRelation,IdentifiedAnnotation> {
+
+ public List<Feature> extract(JCas jCas, CollectionTextRelation arg1,
+ IdentifiedAnnotation arg2) throws AnalysisEngineProcessException {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+
+}
Added: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterStringFeaturesExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterStringFeaturesExtractor.java?rev=1666500&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterStringFeaturesExtractor.java (added)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/cluster/MentionClusterStringFeaturesExtractor.java Fri Mar 13 16:22:11 2015
@@ -0,0 +1,56 @@
+package org.apache.ctakes.coreference.ae.features.cluster;
+
+import static org.apache.ctakes.coreference.ae.features.StringMatchingFeatureExtractor.*;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.ctakes.core.util.ListIterable;
+import org.apache.ctakes.relationextractor.ae.features.RelationFeaturesExtractor;
+import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.utils.struct.CounterMap;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+
+public class MentionClusterStringFeaturesExtractor implements
+ RelationFeaturesExtractor<CollectionTextRelation, IdentifiedAnnotation> {
+
+ public List<Feature> extract(JCas jCas, CollectionTextRelation cluster,
+ IdentifiedAnnotation mention) throws AnalysisEngineProcessException {
+ List<Feature> feats = new ArrayList<>();
+ CounterMap<String> featCounts = new CounterMap<>();
+
+ String m = mention.getCoveredText();
+ Set<String> mentionWords = contentWords(mention);
+
+ for(IdentifiedAnnotation member : new ListIterable<IdentifiedAnnotation>(cluster.getMembers())){
+ if(member == null){
+ System.err.println("Something that shouldn't happen has happened");
+ continue;
+ }else if(mention.getBegin() < member.getEnd()){
+ // during training this might happen -- see a member of a cluster that
+ // is actually subsequent to the candidate mention
+ continue;
+ }
+
+ String s = member.getCoveredText();
+ Set<String> memberWords = contentWords(member);
+
+ if(m.equalsIgnoreCase(s)) featCounts.add("MC_STRING_EXACT");
+ if(startMatch(m,s)) featCounts.add("MC_STRING_START");
+ if(endMatch(m,s)) featCounts.add("MC_STRING_END");
+ if(soonMatch(m,s)) featCounts.add("MC_STRING_SOON");
+ if(wordOverlap(mentionWords, memberWords)) featCounts.add("MC_OVERLAP");
+ if(wordSubstring(mentionWords, memberWords)) featCounts.add("MC_SUB");
+ }
+
+ for(String featKey : featCounts.keySet()){
+ feats.add(new Feature(featKey, featCounts.get(featKey)));
+ }
+ return feats;
+ }
+
+}
Added: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/ClinicalFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/ClinicalFeatureExtractor.java?rev=1666500&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/ClinicalFeatureExtractor.java (added)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/ClinicalFeatureExtractor.java Fri Mar 13 16:22:11 2015
@@ -0,0 +1,69 @@
+package org.apache.ctakes.coreference.ae.features.salience;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.dependency.parser.util.DependencyUtility;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.Markable;
+import org.apache.ctakes.typesystem.type.textspan.Paragraph;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
+
+public class ClinicalFeatureExtractor implements FeatureExtractor1<Markable> {
+
+ @Override
+ public List<Feature> extract(JCas jcas, Markable markable){
+ List<Feature> feats = new ArrayList<>();
+
+ List<Paragraph> coveringPars = JCasUtil.selectCovering(jcas, Paragraph.class, markable);
+ List<Sentence> coveringSents = JCasUtil.selectCovering(jcas, Sentence.class, markable);
+ Sentence coveringSent = DependencyUtility.getSentence(jcas, markable);
+
+ if(coveringPars.size() == 1 && coveringSents.size() == 1){
+ List<Sentence> parSents = JCasUtil.selectCovered(Sentence.class, coveringPars.get(0));
+ if(parSents.size() == 1){
+ // covering paragraph for this markable is exactly one sentence long --
+ // AKA it is a header
+ feats.add(new Feature("ClinIsHeader", true));
+ }else{
+ int sentPos = 0;
+ for(int i = 0; i < parSents.size(); i++){
+ if(parSents.get(i) == coveringSent){
+ sentPos = i;
+ break;
+ }
+ }
+ if(sentPos < parSents.size() / 3){
+ feats.add(new Feature("ClinSentPosBegin", true));
+ }else if(sentPos > (2*parSents.size() / 3)){
+ feats.add(new Feature("ClinSentPosEnd", true));
+ }else{
+ feats.add(new Feature("ClinSentPosMiddle", true));
+ }
+ }
+ }
+
+
+
+ List<EventMention> events = JCasUtil.selectCovered(EventMention.class, markable);
+ EventMention longestEvent = null;
+ for(EventMention event : events){
+ if(event.getTypeID() > 0){
+ if(longestEvent == null || (event.getEnd()-event.getBegin()) > (longestEvent.getEnd()-longestEvent.getBegin())){
+ longestEvent = event;
+ }
+ }
+ }
+ if(longestEvent != null){
+ feats.add(new Feature("ClinSemType" + longestEvent.getClass().getSimpleName(), true));
+ }
+
+
+
+ return feats;
+ }
+}
Added: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/GrammaticalRoleFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/GrammaticalRoleFeatureExtractor.java?rev=1666500&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/GrammaticalRoleFeatureExtractor.java (added)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/GrammaticalRoleFeatureExtractor.java Fri Mar 13 16:22:11 2015
@@ -0,0 +1,70 @@
+package org.apache.ctakes.coreference.ae.features.salience;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.dependency.parser.util.DependencyUtility;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.Markable;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
+
+/*
+ * Citations:
+ * Recasens, de Marneffe, Potts: The Life and Death of Discourse Entities: Identifying Singleton Mentions
+ * NAACL-HLT 2013 short paper, 627-633.
+ *
+ * This class implements features in Table 3. Since there is highly ambiguous descriptions
+ * of the features (e.g., Sentence Position=End as well as Sentence Position=Last,
+ * I looked at the source code for the system to determine precisely how the features
+ * were defined.
+ * First, last means literally first or last token in sentence.
+ * Begin, middle, and end mean which third of the sentence is it in.
+ */
+public class GrammaticalRoleFeatureExtractor implements FeatureExtractor1<Markable> {
+
+ public List<Feature> extract(JCas jcas, Markable markable)
+ throws CleartkExtractorException {
+ List<Feature> feats = new ArrayList<>();
+
+ ConllDependencyNode head = DependencyUtility.getNominalHeadNode(jcas, markable);
+ if(head == null){
+ return feats;
+ }
+ Sentence sent = DependencyUtility.getSentence(jcas, markable);
+ List<ConllDependencyNode> sentNodes = DependencyUtility.getDependencyNodes(jcas, sent);
+// List<ConllDependencyNode> covering = DependencyUtility.getProgeny(head, sentNodes);
+ int numNodes = sentNodes.size()-1; // remove root whole sentence node
+
+ feats.add(new Feature("GrammaticalRoleSentencePositionFirst", head.getId() == 1));
+ feats.add(new Feature("GrammaticalRoleSentencePositionLast", head.getId() == numNodes));
+ if(head.getId() < (numNodes / 3)){
+ feats.add(new Feature("GrammaticalRoleSentencePositionBegin", true));
+ }else if(head.getId() > 2*(numNodes/3)){
+ feats.add(new Feature("GrammaticalRoleSentencePositionEnd", true));
+ }else{
+ feats.add(new Feature("GrammaticalRoleSentencePositionMiddle", true));
+ }
+
+ String deprel = head.getDeprel();
+ if(deprel.equals("nsubj")){
+ feats.add(new Feature("GrammaticalRoleRelSubj", true));
+ }else if(deprel.equals("dobj") || deprel.equals("iobj")){
+ feats.add(new Feature("GrammaticalRoleRelVerbArg", true));
+ }else if(deprel.equals("nn")){
+ feats.add(new Feature("GrammaticalRoleRelNounArg", true));
+ }else if(deprel.equals("root")){
+ feats.add(new Feature("GrammaticalRoleRelRoot", true));
+ }else if(deprel.equals("conj")){
+ feats.add(new Feature("GrammaticalRoleRelConj", true));
+ }else{
+ feats.add(new Feature("GrammaticalRoleRelOther", true));
+ }
+
+ return feats;
+ }
+
+}
Added: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/MorphosyntacticFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/MorphosyntacticFeatureExtractor.java?rev=1666500&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/MorphosyntacticFeatureExtractor.java (added)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/MorphosyntacticFeatureExtractor.java Fri Mar 13 16:22:11 2015
@@ -0,0 +1,78 @@
+package org.apache.ctakes.coreference.ae.features.salience;
+
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.dependency.parser.util.DependencyUtility;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.Markable;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
+
+/*
+ * Citations:
+ * Recasens, de Marneffe, Potts: The Life and Death of Discourse Entities: Identifying Singleton Mentions
+ * NAACL-HLT 2013 short paper, 627-633.
+ *
+ * BBN corpus description (for the 18 named entity types)
+ * https://catalog.ldc.upenn.edu/docs/LDC2013T19/OntoNotes-Release-5.0.pdf
+ *
+ * This feature extractor is intended to implement the features in Table 2, described
+ * in the subsection of 3 called "Internal morphosyntax of the mention."
+ * Left off the table are the 18 NE types from CoNLL. Most of these are not relevant
+ * to our task, especially since we resolve person mentions with simple rules.
+ */
+public class MorphosyntacticFeatureExtractor implements FeatureExtractor1<Markable> {
+
+ public List<Feature> extract(JCas jcas, Markable markable)
+ throws CleartkExtractorException {
+ List<Feature> feats = new ArrayList<>();
+
+ ConllDependencyNode head = DependencyUtility.getNominalHeadNode(jcas, markable);
+ if(head == null){
+ return feats;
+ }
+ List<ConllDependencyNode> covering = DependencyUtility.getProgeny(head, DependencyUtility.getDependencyNodes(jcas, DependencyUtility.getSentence(jcas, markable)));
+
+ if(head.getId() != 0 && (head.getPostag().startsWith("PRP") ||
+ (head.getPostag().equals("DT") && !head.getDeprel().equals("det")))){
+ // 2 conditions -- head is a pronoun POS tag (he, she, it) like PRP or PRP$
+ // or head is a determiner (This, that) that does not have a determiner dependency relation
+ // -- usually marked as nsubj or dobj when used as pronoun (This was..., discussed this with...)
+ // but would be "det" when used as in "this discussion"
+ feats.add(new Feature("MorphoIsPronoun", true));
+ }else{
+ feats.add(new Feature("MorphoIsPronoun", false));
+ }
+
+ feats.add(new Feature("MorphoIsProper", head.getPostag().equals("NNP")));
+
+ // skip animacy and person features for now -- planning to not do person mentions
+
+ // replace singular/other with plural/other
+ feats.add(new Feature("MorphoPlural", head.getPostag().equals("NNS")));
+
+ boolean indefinite = false;
+ boolean containsNum = false;
+ for(ConllDependencyNode node : covering){
+ if(node.getPostag().equals("DT") &&
+ (node.getLemma().equals("a") || node.getLemma().equals("an"))){
+ indefinite = true;
+ }
+
+ if(node.getPostag().equals("CD")){
+ containsNum = true;
+ }
+ }
+
+ feats.add(new Feature("MorphoIndefinite", indefinite));
+ feats.add(new Feature("MorphoNumeric", containsNum)); // lump together many NE types from OntoNotes (date, time, ordinal, percent, quantity)
+ feats.add(new Feature("MorphoNumModifiers", covering.size()-1));
+
+ return feats;
+ }
+
+
+}
Added: ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/SemanticEnvironmentFeatureExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/SemanticEnvironmentFeatureExtractor.java?rev=1666500&view=auto
==============================================================================
--- ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/SemanticEnvironmentFeatureExtractor.java (added)
+++ ctakes/sandbox/ctakes-coref-cleartk/src/main/java/org/apache/ctakes/coreference/ae/features/salience/SemanticEnvironmentFeatureExtractor.java Fri Mar 13 16:22:11 2015
@@ -0,0 +1,136 @@
+package org.apache.ctakes.coreference.ae.features.salience;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.ctakes.dependency.parser.util.DependencyUtility;
+import org.apache.ctakes.typesystem.type.constants.CONST;
+import org.apache.ctakes.typesystem.type.syntax.ConllDependencyNode;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.Markable;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.feature.extractor.CleartkExtractorException;
+import org.cleartk.ml.feature.extractor.FeatureExtractor1;
+
+import com.google.common.collect.Sets;
+
+import static org.apache.ctakes.dependency.parser.util.DependencyUtility.*;
+
+public class SemanticEnvironmentFeatureExtractor implements
+ FeatureExtractor1<Markable> {
+
+ // this is a subset of the attitude verbs listed in White et al:
+ // Discovering classes of attitude verbs using subcategorization frame distributsion
+ // NELS 2012.
+ private static Set<String> propVerbs =
+ Sets.newHashSet("allow", "believe", "bother", "demand", "deny", "doubt", "expect", "feel", "forbid", "guess", "hate", "hear", "hope", "imagine", "need", "promise", "realize", "remember", "said", "say", "see", "suppose", "tell", "think", "understand", "want", "worry");
+
+ public List<Feature> extract(JCas jcas, Markable markable)
+ throws CleartkExtractorException {
+ List<Feature> feats = new ArrayList<>();
+
+ ConllDependencyNode head = DependencyUtility.getNominalHeadNode(jcas, markable);
+ if(head == null){
+ return feats;
+ }
+ Sentence sent = DependencyUtility.getSentence(jcas, markable);
+ List<ConllDependencyNode> sentNodes = DependencyUtility.getDependencyNodes(jcas, sent);
+ List<ConllDependencyNode> covering = DependencyUtility.getProgeny(head, sentNodes);
+
+ List<EventMention> events = JCasUtil.selectCovered(jcas, EventMention.class, markable);
+ EventMention markableEvent = null;
+ for(EventMention event : events){
+ ConllDependencyNode eventHead = getNominalHeadNode(jcas, event);
+ if(eventHead == head){
+ if(markableEvent == null || (event.getEnd()-event.getBegin()) > (markableEvent.getEnd()-markableEvent.getBegin())){
+ markableEvent = event;
+ }
+ }
+ }
+
+ boolean neg = false;
+ if(markableEvent != null){
+ neg = markableEvent.getPolarity() == CONST.NE_POLARITY_NEGATION_PRESENT;
+ feats.add(new Feature("SemEnvNegation", neg));
+ }
+
+ boolean modal = presenceOfModality(head, sentNodes);
+ feats.add(new Feature("SemEnvModality", modal));
+
+ boolean underPropVerb = presenceOfAttitude(jcas, head);
+ feats.add(new Feature("SemEnvAttitude", underPropVerb));
+
+
+ // modal * pronoun, neg * pronoun
+ if(head.getPostag().startsWith("PRP") || (head.getPostag().equals("DT") && !head.getDeprel().equals("det"))){
+ feats.add(new Feature("SemEnvProTrueModal"+modal, true));
+ feats.add(new Feature("SemEnvProTrueNeg"+neg, true));
+ feats.add(new Feature("SemEnvProTrueAtt"+underPropVerb, true));
+ }else{
+ feats.add(new Feature("SemEnvProFalseModal"+modal, true));
+ feats.add(new Feature("SemEnvProFalseNeg"+neg, true));
+ feats.add(new Feature("SemEnvProFalseAtt"+underPropVerb, true));
+ }
+
+ // modal * Proper noun
+ if(head.getPostag().equals("NNP")){
+ feats.add(new Feature("SemEnvProperTrueModal"+modal, true));
+ feats.add(new Feature("SemEnvProperTrueNeg"+neg, true));
+ feats.add(new Feature("SemEnvProperTrueAtt"+underPropVerb, true));
+ }else{
+ feats.add(new Feature("SemEnvProperFalseModal"+modal,true));
+ feats.add(new Feature("SemEnvProperFalseNeg"+neg, true));
+ feats.add(new Feature("SemEnvProperFalseAtt"+underPropVerb, true));
+ }
+
+ boolean indefinite = false;
+ for(ConllDependencyNode node : covering){
+ if(node.getId() != 0 && (node.getPostag().equals("DT") &&
+ (node.getLemma().equals("a") || node.getLemma().equals("an")))){
+ indefinite = true;
+ }
+ }
+ feats.add(new Feature("Neg"+neg+"Indef"+indefinite, true));
+
+ feats.add(new Feature("Neg"+neg+"Mods"+(covering.size()-1), true));
+
+ return feats;
+ }
+
+ private static final boolean presenceOfModality(ConllDependencyNode head, List<ConllDependencyNode> sentNodes) {
+ boolean modal = false;
+ ConllDependencyNode vb = null;
+
+ if(head.getHead() != null){
+ vb = head.getHead();
+ while(vb.getHead() != null && !vb.getPostag().startsWith("VB")){
+ vb = vb.getHead();
+ }
+
+ for(ConllDependencyNode node : sentNodes){
+ if(node.getHead() == vb && node.getPostag().equals("MD")){
+ modal = true;
+ break;
+ }
+ }
+ }
+ return modal;
+ }
+
+ private static final boolean presenceOfAttitude(JCas jcas, ConllDependencyNode head){
+ boolean att = false;
+
+ for(ConllDependencyNode cur : getPathToTop(jcas, head)){
+ if(propVerbs.contains(cur.getLemma())){
+ att = true;
+ break;
+ }
+ }
+
+ return att;
+ }
+}