value = Integer.toString(annotation.getEnd()); } else if (property == CTAKESAnnotationProperty.CONDITIONAL) { value = Boolean.toString(annotation.getConditional()); } else if (property == CTAKESAnnotationProperty.CONFIDENCE) { value = Float.toString(annotation.getConfidence());
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 conditional = entityOrEventMention.getConditional(); // downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling if ( !conditional && coin.nextDouble() >= this.probabilityOfKeepingADefaultExample ) { return; } instance.setOutcome( "" + conditional ); } else { String label = this.classifier.classify( instance.getFeatures() ); boolean conditional = false; if ( label != null ) { conditional = Boolean.parseBoolean( label ); } entityOrEventMention.setConditional( conditional ); } }
@Override public void setClassLabel(IdentifiedAnnotation entityOrEventMention, Instance<String> instance) throws AnalysisEngineProcessException { if (this.isTraining()) { boolean conditional = entityOrEventMention.getConditional(); // downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling if (!conditional && coin.nextDouble() >= this.probabilityOfKeepingADefaultExample) { return; } instance.setOutcome(""+conditional); } else { String label = this.classifier.classify(instance.getFeatures()); boolean conditional = false; if (label!= null){ conditional = Boolean.parseBoolean(label); } entityOrEventMention.setConditional(conditional); } } public static FeatureSelection<String> createFeatureSelection(double threshold) {
value = Integer.toString(annotation.getEnd()); } else if (property == CTAKESAnnotationProperty.CONDITIONAL) { value = Boolean.toString(annotation.getConditional()); } else if (property == CTAKESAnnotationProperty.CONFIDENCE) { value = Float.toString(annotation.getConfidence());
@Override public void setClassLabel(IdentifiedAnnotation entityOrEventMention, Instance<String> instance) throws AnalysisEngineProcessException { if (this.isTraining()) { boolean conditional = entityOrEventMention.getConditional(); // downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling if (!conditional && coin.nextDouble() >= this.probabilityOfKeepingADefaultExample) { return; } instance.setOutcome(""+conditional); } else { String label = this.classifier.classify(instance.getFeatures()); boolean conditional = false; if (label!= null){ conditional = Boolean.parseBoolean(label); } entityOrEventMention.setConditional(conditional); } } public static FeatureSelection<String> createFeatureSelection(double threshold) {
value = Integer.toString(annotation.getEnd()); } else if (property == CTAKESAnnotationProperty.CONDITIONAL) { value = Boolean.toString(annotation.getConditional()); } else if (property == CTAKESAnnotationProperty.CONFIDENCE) { value = Float.toString(annotation.getConfidence());
+ " === Subject: " + entity.getSubject() + " === Generic? " + (entity.getGeneric() == CONST.NE_GENERIC_TRUE) + " === Conditional? " + (entity.getConditional() == CONST.NE_CONDITIONAL_TRUE) + " === History? " + (entity.getHistoryOf() == CONST.NE_HISTORY_OF_PRESENT) );
switch (s) { case CONDITIONAL: m.setConditional(mention.getConditional()); break; case GENERIC:
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(); }
switch (s) { case CONDITIONAL: m.setConditional(mention.getConditional()); break; case GENERIC:
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(); }