value = Integer.toString(annotation.getDiscoveryTechnique()); } else if (property == CTAKESAnnotationProperty.GENERIC) { value = Boolean.toString(annotation.getGeneric()); } else if (property == CTAKESAnnotationProperty.HISTORY_OF) { value = Integer.toString(annotation.getHistoryOf());
public static boolean isGeneric(IdentifiedAnnotation mention){ return mention.getGeneric() == CONST.NE_GENERIC_TRUE; }
public static boolean isGeneric(IdentifiedAnnotation mention){ return mention.getGeneric() == CONST.NE_GENERIC_TRUE; }
@Override public void process(JCas jCas) throws AnalysisEngineProcessException { for (IdentifiedAnnotation mention : JCasUtil.select(jCas, IdentifiedAnnotation.class)) { Boolean oldgeneric = mention.getGeneric(); mention.setGeneric( GenericAttributeClassifier.getGeneric(jCas, mention) ); // System.err.println("Word:"+mention.getCoveredText()+", overwrote generic "+oldgeneric+" with "+mention.getGeneric()); } } }
@Override public void process(JCas jCas) throws AnalysisEngineProcessException { for (IdentifiedAnnotation mention : JCasUtil.select(jCas, IdentifiedAnnotation.class)) { Boolean oldgeneric = mention.getGeneric(); mention.setGeneric( GenericAttributeClassifier.getGeneric(jCas, mention) ); // System.err.println("Word:"+mention.getCoveredText()+", overwrote generic "+oldgeneric+" with "+mention.getGeneric()); } } }
static private String getAssertion( final IdentifiedAnnotation annotation ) { final StringBuilder sb = new StringBuilder(); if ( annotation.getPolarity() == CONST.NE_POLARITY_NEGATION_PRESENT ) { sb.append( "AFFIRMED" ); } else { sb.append( "NEGATED" ); } if ( annotation.getUncertainty() == CONST.NE_UNCERTAINTY_PRESENT ) { sb.append( "UNCERTAIN" ); } if ( annotation.getGeneric() ) { sb.append( "GENERIC" ); } if ( annotation.getConditional() ) { sb.append( "CONDITIONAL" ); } return sb.toString(); }
private String getAttrValueString(IdentifiedAnnotation mention, Selector s) { switch (s) { case CONDITIONAL: return String.valueOf(mention.getConditional()); case GENERIC: return String.valueOf(mention.getGeneric()); case HISTORYOF: return String.valueOf(mention.getHistoryOf()); case POLARITY: return String.valueOf(mention.getPolarity()); case SUBJECT: return String.valueOf(mention.getSubject()); case UNCERTAINTY: return String.valueOf(mention.getUncertainty()); default: return "?"; } }
private String getAttrValueString(IdentifiedAnnotation mention, Selector s) { switch (s) { case CONDITIONAL: return String.valueOf(mention.getConditional()); case GENERIC: return String.valueOf(mention.getGeneric()); case HISTORYOF: return String.valueOf(mention.getHistoryOf()); case POLARITY: return String.valueOf(mention.getPolarity()); case SUBJECT: return String.valueOf(mention.getSubject()); case UNCERTAINTY: return String.valueOf(mention.getUncertainty()); default: return "?"; } }
private void printContext(String text, IdentifiedAnnotation mention, int radius) { int mentionBegin = mention.getBegin(); int mentionEnd = mention.getEnd(); StringBuilder sb = new StringBuilder(); int snipBegin; int snipEnd; snipBegin = (mentionBegin-radius<0)? 0 : mentionBegin-radius; snipEnd = (mentionEnd+radius>text.length()-1)? text.length()-1 : mentionEnd+radius; String[] tmp = mention.getClass().getName().split("\\."); String semGroup = tmp[tmp.length-1]; sb.append(text.substring(snipBegin, mentionBegin)); sb.append("[[["+mention.getCoveredText()+"]]]"); sb.append(text.substring(mentionEnd, snipEnd)); // sb.toString().replaceAll("\\n", "\\n| "); System.out.println("| "+ sb.toString().replaceAll("\\n", "\n| ")); System.out.println(": "+ semGroup + " : beg=" + mention.getBegin() + " : end=" + mention.getEnd() + " : c=" + mention.getConditional() + " : g=" + mention.getGeneric() + " : h=" + mention.getHistoryOf() + " : p=" + mention.getPolarity() + " : s=" + mention.getSubject() + " : u=" + mention.getUncertainty()); }
private void printContext(String text, IdentifiedAnnotation mention, int radius) { int mentionBegin = mention.getBegin(); int mentionEnd = mention.getEnd(); StringBuilder sb = new StringBuilder(); int snipBegin; int snipEnd; snipBegin = (mentionBegin-radius<0)? 0 : mentionBegin-radius; snipEnd = (mentionEnd+radius>text.length()-1)? text.length()-1 : mentionEnd+radius; String[] tmp = mention.getClass().getName().split("\\."); String semGroup = tmp[tmp.length-1]; sb.append(text.substring(snipBegin, mentionBegin)); sb.append("[[["+mention.getCoveredText()+"]]]"); sb.append(text.substring(mentionEnd, snipEnd)); // sb.toString().replaceAll("\\n", "\\n| "); System.out.println("| "+ sb.toString().replaceAll("\\n", "\n| ")); System.out.println(": "+ semGroup + " : beg=" + mention.getBegin() + " : end=" + mention.getEnd() + " : c=" + mention.getConditional() + " : g=" + mention.getGeneric() + " : h=" + mention.getHistoryOf() + " : p=" + mention.getPolarity() + " : s=" + mention.getSubject() + " : u=" + mention.getUncertainty()); }
/** * @param annotation - * @return a line of text with doctimerel, modality, aspect and permanence ; if available */ static private String getAnnotationProperties( final IdentifiedAnnotation annotation ) { final StringBuilder sb = new StringBuilder(); if ( annotation.getPolarity() < 0 ) { sb.append( " negated" ); } if ( annotation.getUncertainty() == 1 ) { sb.append( " uncertain" ); } if ( annotation.getGeneric() ) { sb.append( " generic" ); } if ( annotation.getConditional() ) { sb.append( " conditional" ); } if ( annotation.getHistoryOf() == 1 ) { sb.append( " in history" ); } if ( annotation.getSubject() != null && !annotation.getSubject().isEmpty() ) { sb.append( " for " ).append( annotation.getSubject() ); } return sb.toString(); }
/** * @param annotation - * @return a line of text with doctimerel, modality, aspect and permanence ; if available */ static private String getAnnotationProperties( final IdentifiedAnnotation annotation ) { final StringBuilder sb = new StringBuilder(); if ( annotation.getPolarity() < 0 ) { sb.append( " negated" ); } if ( annotation.getUncertainty() == 1 ) { sb.append( " uncertain" ); } if ( annotation.getGeneric() ) { sb.append( " generic" ); } if ( annotation.getConditional() ) { sb.append( " conditional" ); } if ( annotation.getHistoryOf() == 1 ) { sb.append( " in history" ); } if ( annotation.getSubject() != null && !annotation.getSubject().isEmpty() ) { sb.append( " for " ).append( annotation.getSubject() ); } return sb.toString(); }
@Override public void setClassLabel( IdentifiedAnnotation entityOrEventMention, Instance<String> instance ) throws AnalysisEngineProcessException { if ( this.isTraining() ) { boolean generic = entityOrEventMention.getGeneric(); // downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling if ( !generic && coin.nextDouble() >= this.probabilityOfKeepingADefaultExample ) { return; } instance.setOutcome( "" + generic ); } else { String label = this.classifier.classify( instance.getFeatures() ); entityOrEventMention.setGeneric( Boolean.parseBoolean( label ) ); } }
@Override public void setClassLabel(IdentifiedAnnotation entityOrEventMention, Instance<String> instance) throws AnalysisEngineProcessException { if (this.isTraining()) { boolean generic = entityOrEventMention.getGeneric(); // downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling if (!generic && coin.nextDouble() >= this.probabilityOfKeepingADefaultExample) { return; } instance.setOutcome(""+generic); } else { String label = this.classifier.classify(instance.getFeatures()); entityOrEventMention.setGeneric(Boolean.parseBoolean(label)); } } public static FeatureSelection<String> createFeatureSelection(double threshold) {
@Override public void setClassLabel(IdentifiedAnnotation entityOrEventMention, Instance<String> instance) throws AnalysisEngineProcessException { if (this.isTraining()) { boolean generic = entityOrEventMention.getGeneric(); // downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling if (!generic && coin.nextDouble() >= this.probabilityOfKeepingADefaultExample) { return; } instance.setOutcome(""+generic); } else { String label = this.classifier.classify(instance.getFeatures()); entityOrEventMention.setGeneric(Boolean.parseBoolean(label)); } } public static FeatureSelection<String> createFeatureSelection(double threshold) {
private Entity( final IdentifiedAnnotation annotation ) { _begin = annotation.getBegin(); _end = annotation.getEnd(); _coveredText = annotation.getCoveredText(); _polarity = annotation.getPolarity(); _uncertainty = annotation.getUncertainty(); _conditional = annotation.getConditional(); _generic = annotation.getGeneric(); _subject = annotation.getSubject(); _historyOf = annotation.getHistoryOf(); }
break; case GENERIC: m.setGeneric(mention.getGeneric()); break; case HISTORYOF:
private Entity( final IdentifiedAnnotation annotation ) { _begin = annotation.getBegin(); _end = annotation.getEnd(); _coveredText = annotation.getCoveredText(); _polarity = annotation.getPolarity(); _uncertainty = annotation.getUncertainty(); _conditional = annotation.getConditional(); _generic = annotation.getGeneric(); _subject = annotation.getSubject(); _historyOf = annotation.getHistoryOf(); }
/** * * @param goldAnnotation * @param jcas */ private static void copyAnnotation(Annotation goldAnnotation, JCas jcas) { Annotation newAnno; if (goldAnnotation instanceof IdentifiedAnnotation) { IdentifiedAnnotation ia = new IdentifiedAnnotation(jcas); ia.setConditional(((IdentifiedAnnotation) goldAnnotation).getConditional()); ia.setConfidence(((IdentifiedAnnotation) goldAnnotation).getConfidence()); ia.setDiscoveryTechnique(((IdentifiedAnnotation)goldAnnotation).getDiscoveryTechnique()); ia.setGeneric(((IdentifiedAnnotation) goldAnnotation).getGeneric()); ia.setHistoryOf(((IdentifiedAnnotation) goldAnnotation).getHistoryOf()); ia.setPolarity(((IdentifiedAnnotation) goldAnnotation).getPolarity()); ia.setSegmentID(((IdentifiedAnnotation) goldAnnotation).getSegmentID()); ia.setSentenceID(((IdentifiedAnnotation) goldAnnotation).getSentenceID()); ia.setSubject(((IdentifiedAnnotation) goldAnnotation).getSubject()); ia.setTypeID(((IdentifiedAnnotation) goldAnnotation).getTypeID()); ia.setUncertainty(((IdentifiedAnnotation) goldAnnotation).getUncertainty()); newAnno = ia; } else { throw new RuntimeException("Unexpected class of object " + goldAnnotation.getClass()); } newAnno.setBegin(goldAnnotation.getBegin()); newAnno.setEnd(goldAnnotation.getEnd()); newAnno.addToIndexes(); }
/** * * @param goldAnnotation * @param jcas */ private static void copyAnnotation(Annotation goldAnnotation, JCas jcas) { Annotation newAnno; if (goldAnnotation instanceof IdentifiedAnnotation) { IdentifiedAnnotation ia = new IdentifiedAnnotation(jcas); ia.setConditional(((IdentifiedAnnotation) goldAnnotation).getConditional()); ia.setConfidence(((IdentifiedAnnotation) goldAnnotation).getConfidence()); ia.setDiscoveryTechnique(((IdentifiedAnnotation)goldAnnotation).getDiscoveryTechnique()); ia.setGeneric(((IdentifiedAnnotation) goldAnnotation).getGeneric()); ia.setHistoryOf(((IdentifiedAnnotation) goldAnnotation).getHistoryOf()); ia.setPolarity(((IdentifiedAnnotation) goldAnnotation).getPolarity()); ia.setSegmentID(((IdentifiedAnnotation) goldAnnotation).getSegmentID()); ia.setSentenceID(((IdentifiedAnnotation) goldAnnotation).getSentenceID()); ia.setSubject(((IdentifiedAnnotation) goldAnnotation).getSubject()); ia.setTypeID(((IdentifiedAnnotation) goldAnnotation).getTypeID()); ia.setUncertainty(((IdentifiedAnnotation) goldAnnotation).getUncertainty()); newAnno = ia; } else { throw new RuntimeException("Unexpected class of object " + goldAnnotation.getClass()); } newAnno.setBegin(goldAnnotation.getBegin()); newAnno.setEnd(goldAnnotation.getEnd()); newAnno.addToIndexes(); }