def countAgeMatches(self, aAgeTemplates, errorOut): """ count the number of age value matches in a set of annotated age templates """ annotatedAgeValues = { 'min': set([]), 'max': set([]), 'mean': set([]), 'median': set([]) } for template in aAgeTemplates: for type, avList in template.trueValues.items(): for av in avList: # print '@@@ ADDING AGE VALUE:', type, av.value # if len(annotatedAgeValues[type]) > 0: # print '-- Redundant value' annotatedAgeValues[type].add(av) self.nTrueAgeValues = 0 annotatedValueFound = {} for avSet in annotatedAgeValues.values(): for av in avSet: annotatedValueFound[av] = False self.nTrueAgeValues += 1 # count the number of detected values that match annotated ones stats = IRstats() for type, av in self.ageValues.items(): # print '@@@ Checking:', type, av.value if av.source != 'trial_registry': foundAgeValue = False for annotatedValue in annotatedAgeValues[type]: if av.value == annotatedValue.value: stats.incTP() errorOut.write(' +TP: %s = %d\n' % (type, av.value)) # print ' +TP: %s = %d' % (type,av.value) annotatedValueFound[annotatedValue] = True av.evaluation.markCorrect() foundAgeValue = True if foundAgeValue == False: stats.incFP() errorOut.write(' -FP: %s = %d\n' % (type, av.value)) # print ' -FP: %s = %d' % (type, av.value) av.evaluation.markIncorrect() # else: # print '@@@@ AGE VALUE SOURCE IS TRIAL REGISTRY' # count the ones that we missed for av, found in annotatedValueFound.items(): if found == False: stats.incFN() errorOut.write(' -FN: %s = %d\n' % (av.type, av.value)) # print ' -FN: %s = %d' % (av.type, av.value) return stats
def computeTupleMentionError(self, recomputeAnnotatedMentions, errorWeights={}): """ compute the number of FP, FN, Duplicate mentions in the sentence """ totalFP = 0 totalFN = 0 totalDuplicates = 0 stats = {} aList = {} if len(errorWeights) == 0: errorWeights['group'] = {'fp':1, 'fn':1, 'dup':1} errorWeights['outcome'] = {'fp':1, 'fn':1, 'dup':1} errorWeights['eventrate'] = {'fp':1, 'fn':1, 'dup':1} errorWeights['on'] = {'fp':1, 'fn':1, 'dup':1} errorWeights['gs'] = {'fp':1, 'fn':1, 'dup':1} mentions = {} mentions['group'] = (self.groupLabeling.entities['group'], self.groupLabeling.finder) mentions['outcome'] = (self.outcomeLabeling.entities['outcome'], self.outcomeLabeling.finder) mentions['eventrate'] = (self.eventrateLabeling.entities['eventrate'], self.eventrateLabeling.finder) mentions['on'] = (self.numberLabeling.entities['on'], self.numberLabeling.finder) mentions['gs'] = (self.numberLabeling.entities['gs'], self.numberLabeling.finder) for mType, (dList, finder) in mentions.items(): aList[mType] = self.sentence.getAnnotatedMentions(mType, recomputeMentions=recomputeAnnotatedMentions) stats[mType] = IRstats() finder.compareMentionLists(dList, aList[mType], mType, stats[mType]) totalFP += stats[mType].fp * errorWeights[mType]['fp'] totalFN += stats[mType].fn * errorWeights[mType]['fn'] totalDuplicates += stats[mType].duplicates * errorWeights[mType]['dup'] # mType = 'eventrate' # print 'True:', [m.text for m in aList[mType]] # print 'Detected:',[m.text for m in mentions[mType][0]] totalError = totalFP + totalDuplicates + totalFN # if totalError > 9: # for mType in mentions.keys(): # print 'Type: %s, FP: %d, FN: %d, DUP: %d'%(mType, stats[mType].fp, stats[mType].fn, stats[mType].duplicates) # print self.sentence.abstract.id, 'Total error = ', totalError return totalError
def __init__(self, entityTypes): """ start computing RPF statistics for new set of abstracts """ self.irstats = {} self.entityTypes = entityTypes for mType in self.entityTypes: self.irstats[mType] = IRstats()
# if token.hasAnnotation(entityType): # verbRuleCounts[depToken.lemma].incTP() # else: # verbRuleCounts[depToken.lemma].incFP() for dep in token.governors: if dep.isRoot() == False and dep.type == 'pobj': depToken = token.sentence[dep.index] # print depToken.text, token.text for g in depToken.governors: if g.isRoot() == False:# and g.type == 'prep': gToken = token.sentence[g.index] # print gToken.text+'_'+g.type, depToken.text, token.text if gToken.pos[0:2] == 'VB': if gToken.lemma not in verbRuleCounts: verbRuleCounts[gToken.lemma] = IRstats() if token.hasAnnotation(entityType): verbRuleCounts[gToken.lemma].incTP() else: verbRuleCounts[gToken.lemma].incFP() for token in sentence: for type in entityTypes: if token.hasAnnotation(type): entityTokenCounts[type] += 1 # for token in sentence # for token in sentence: # if token.text != 'greater' and token.text != 'less': # continue