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Adding the likelihood assignment component.
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197 changes: 186 additions & 11 deletions
197
...rc/main/java/de/julielab/jcore/ae/likelihoodassignment/LikelihoodAssignmentAnnotator.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,34 +1,209 @@ | ||
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| package de.julielab.jcore.ae.likelihoodassignment; | ||
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| import de.julielab.jcore.types.ConceptMention; | ||
| import de.julielab.jcore.types.LikelihoodIndicator; | ||
| import de.julielab.jcore.types.Sentence; | ||
| import org.apache.uima.UimaContext; | ||
| import org.apache.uima.analysis_component.JCasAnnotator_ImplBase; | ||
| import org.apache.uima.analysis_engine.AnalysisEngineProcessException; | ||
| import org.apache.uima.cas.FSIterator; | ||
| import org.apache.uima.fit.descriptor.ResourceMetaData; | ||
| import org.apache.uima.fit.descriptor.TypeCapability; | ||
| import org.apache.uima.jcas.JCas; | ||
| import org.apache.uima.resource.ResourceInitializationException; | ||
| import org.slf4j.Logger; | ||
| import org.slf4j.LoggerFactory; | ||
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| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.NavigableMap; | ||
| import java.util.TreeMap; | ||
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| @ResourceMetaData(name="JCoRe Likelihood Assignment AE", description = "Analysis Engine to assign likelihood indicators to their corresponding entities and events.") | ||
| @TypeCapability(inputs="de.julielab.jcore.types.LikelihoodIndicator") | ||
| public class LikelihoodAssignmentAnnotator extends JCasAnnotator_ImplBase { | ||
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| private final static Logger log = LoggerFactory.getLogger(LikelihoodAssignmentAnnotator.class); | ||
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| private static final Logger LOGGER = LoggerFactory | ||
| .getLogger(LikelihoodAssignmentAnnotator.class); | ||
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| /** | ||
| * Maps sentence ends to sentence begins. | ||
| */ | ||
| private TreeMap<Integer, Integer> sentMap; | ||
| /** | ||
| * Maps concept mentions to their begins. | ||
| */ | ||
| private TreeMap<Integer, ArrayList<ConceptMention>> conceptMap; | ||
| /** | ||
| * Maps likelihood indicators to their begins. | ||
| */ | ||
| private TreeMap<Integer, LikelihoodIndicator> likelihoodMap; | ||
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| /** | ||
| * This method is called a single time by the framework at component | ||
| * creation. Here, descriptor parameters are read and initial setup is done. | ||
| * Quantifies likelihood values. | ||
| */ | ||
| private HashMap<String, Integer> likelihoodValueMap; | ||
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| public void initialize(UimaContext aContext) | ||
| throws ResourceInitializationException { | ||
| super.initialize(aContext); | ||
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| // ordinal scale for likelihood indicators; | ||
| // used when there are multiple occurrences (the lowest category is | ||
| // chosen) | ||
| likelihoodValueMap = new HashMap<>(); | ||
| likelihoodValueMap.put("negation", 1); | ||
| likelihoodValueMap.put("low", 2); | ||
| likelihoodValueMap.put("investigation", 3); | ||
| likelihoodValueMap.put("moderate", 4); | ||
| likelihoodValueMap.put("high", 5); | ||
| } | ||
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| @Override | ||
| public void initialize(final UimaContext aContext) throws ResourceInitializationException { | ||
| // TODO | ||
| public void process(JCas aJCas) throws AnalysisEngineProcessException { | ||
| assignLikelihood(aJCas); | ||
| } | ||
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| /** | ||
| * This method is called for each document going through the component. This | ||
| * is where the actual work happens. | ||
| * If a sentence contains a likelihood indicator, this indicator is assigned | ||
| * to all concept mentions occurring in the sentence. If a sentence does not | ||
| * contain a likelihood indicator, the default likelihood category (i.e. | ||
| * 'assertion') is assigned to all concept mentions occurring in the | ||
| * sentence. In case of multiple likelihood indicators the lowest likelihood | ||
| * category is chosen. | ||
| * | ||
| * @param aJCas | ||
| */ | ||
| @Override | ||
| public void process(final JCas aJCas) throws AnalysisEngineProcessException { | ||
| // TODO | ||
| private void assignLikelihood(JCas aJCas) { | ||
| buildTreeMaps(aJCas); | ||
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| // create default likelihood indicator for assertions (has begin = 0 and | ||
| // end = 0) | ||
| LikelihoodIndicator assertionIndicator = new LikelihoodIndicator(aJCas); | ||
| assertionIndicator.setLikelihood("assertion"); | ||
| assertionIndicator.setComponentId(this.getClass().getName()); | ||
| assertionIndicator.addToIndexes(); | ||
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| // iterate over sentences | ||
| for (int sentBegin : sentMap.keySet()) { | ||
| int sentEnd = sentMap.get(sentBegin); | ||
| boolean sentHasLikelihood = false; | ||
| boolean multipleLikelihood = false; | ||
| Integer firstLikelihoodBegin = 0; | ||
| Integer lastLikelihoodBegin = 0; | ||
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| // determine whether the sentence contains a likelihood indicator at | ||
| // all and whether it even contains multiple likelihood indicators | ||
| firstLikelihoodBegin = likelihoodMap.ceilingKey(sentBegin); | ||
| if (firstLikelihoodBegin != null) { | ||
| if (firstLikelihoodBegin > sentEnd) { | ||
| sentHasLikelihood = false; | ||
| } else { | ||
| sentHasLikelihood = true; | ||
| } | ||
| } | ||
| if (sentHasLikelihood == true) { | ||
| lastLikelihoodBegin = likelihoodMap.floorKey(sentEnd); | ||
| if (firstLikelihoodBegin == lastLikelihoodBegin) { | ||
| multipleLikelihood = false; | ||
| } else { | ||
| multipleLikelihood = true; | ||
| } | ||
| } | ||
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| // determine which likelihood category to assign to concept mentions | ||
| // in the sentence and create the corresponding likelihood indicator | ||
| LikelihoodIndicator assignedLikelihood = null; | ||
| if (sentHasLikelihood == true) { | ||
| if (multipleLikelihood = true) { | ||
| // determine the lowest likelihood category in the sentence | ||
| NavigableMap<Integer, LikelihoodIndicator> likelihoodSubMap = likelihoodMap | ||
| .subMap(firstLikelihoodBegin, true, | ||
| lastLikelihoodBegin, true); | ||
| int currentLikelihoodValue = 100; | ||
| for (int i : likelihoodSubMap.keySet()) { | ||
| LikelihoodIndicator likelihood = likelihoodSubMap | ||
| .get(i); | ||
| String likelihoodCat = likelihood.getLikelihood(); | ||
| int likelihoodValue = likelihoodValueMap | ||
| .get(likelihoodCat); | ||
| if (likelihoodValue < currentLikelihoodValue) { | ||
| assignedLikelihood = likelihood; | ||
| currentLikelihoodValue = likelihoodValue; | ||
| } | ||
| } | ||
| } else { | ||
| LikelihoodIndicator likelihood = likelihoodMap | ||
| .get(firstLikelihoodBegin); | ||
| assignedLikelihood = likelihood; | ||
| } | ||
| } else { | ||
| assignedLikelihood = assertionIndicator; | ||
| } | ||
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| // get all events in the sentence and assign the corresponding | ||
| // likelihood indicator | ||
| if (conceptMap.ceilingKey(sentBegin) != null) { | ||
| int firstConceptBegin = conceptMap.ceilingKey(sentBegin); | ||
| if (firstConceptBegin > sentEnd) { | ||
| continue; | ||
| } else { | ||
| int lastConceptBegin = conceptMap.floorKey(sentEnd); | ||
| NavigableMap<Integer, ArrayList<ConceptMention>> conceptSubMap = conceptMap | ||
| .subMap(firstConceptBegin, true, lastConceptBegin, | ||
| true); | ||
| for (int i : conceptSubMap.keySet()) { | ||
| ArrayList<ConceptMention> conceptList = conceptSubMap | ||
| .get(i); | ||
| for (ConceptMention concept : conceptList) { | ||
| concept.setLikelihood(assignedLikelihood); | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| @SuppressWarnings("rawtypes") | ||
| public void buildTreeMaps(JCas aJCas) { | ||
| FSIterator sentIt = aJCas.getAnnotationIndex(Sentence.type).iterator(); | ||
| FSIterator conceptIt = aJCas.getAnnotationIndex(ConceptMention.type) | ||
| .iterator(); | ||
| FSIterator likelihoodIt = aJCas.getAnnotationIndex( | ||
| LikelihoodIndicator.type).iterator(); | ||
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| sentMap = new TreeMap<Integer, Integer>(); | ||
| while (sentIt.hasNext()) { | ||
| Sentence sent = (Sentence) sentIt.next(); | ||
| int sentBegin = sent.getBegin(); | ||
| int sentEnd = sent.getEnd(); | ||
| sentMap.put(sentBegin, sentEnd); | ||
| } | ||
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| conceptMap = new TreeMap<Integer, ArrayList<ConceptMention>>(); | ||
| while (conceptIt.hasNext()) { | ||
| ConceptMention concept = (ConceptMention) conceptIt.next(); | ||
| int conceptBegin = concept.getBegin(); | ||
| if (conceptMap.containsKey(conceptBegin)) { | ||
| ArrayList<ConceptMention> conceptList = conceptMap | ||
| .get(conceptBegin); | ||
| conceptList.add(concept); | ||
| conceptMap.put(conceptBegin, conceptList); | ||
| } else { | ||
| ArrayList<ConceptMention> conceptList = new ArrayList<ConceptMention>(); | ||
| conceptList.add(concept); | ||
| conceptMap.put(conceptBegin, conceptList); | ||
| } | ||
| } | ||
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| likelihoodMap = new TreeMap<Integer, LikelihoodIndicator>(); | ||
| while (likelihoodIt.hasNext()) { | ||
| LikelihoodIndicator likelihood = (LikelihoodIndicator) likelihoodIt | ||
| .next(); | ||
| int likelihoodBegin = likelihood.getBegin(); | ||
| likelihoodMap.put(likelihoodBegin, likelihood); | ||
| } | ||
| } | ||
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| } |
1 change: 0 additions & 1 deletion
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...signment-ae/src/main/resources/de/julielab/jcore/ae/likelihoodassignment/desc/PLACEHOLDER
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48 changes: 30 additions & 18 deletions
48
...sources/de/julielab/jcore/ae/likelihoodassignment/desc/jcore-likelihood-assignment-ae.xml
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,21 +1,33 @@ | ||
| <?xml version="1.0" encoding="UTF-8"?> | ||
| <analysisEngineDescription xmlns="http://uima.apache.org/resourceSpecifier"> | ||
| <frameworkImplementation>org.apache.uima.java</frameworkImplementation> | ||
| <primitive>true</primitive> | ||
| <annotatorImplementationName>LikelihoodAssignmentAnnotator</annotatorImplementationName> | ||
| <analysisEngineMetaData> | ||
| <name>JCoRe Likelihood Assignment AE</name> | ||
| <description/> | ||
| <version>2.3.0-SNAPSHOT</version> | ||
| <vendor>JULIE Lab Jena, Germany</vendor> | ||
| <configurationParameters/> | ||
| <configurationParameterSettings/> | ||
| <typeSystemDescription/> | ||
| <capabilities/> | ||
| <operationalProperties> | ||
| <modifiesCas>true</modifiesCas> | ||
| <multipleDeploymentAllowed>true</multipleDeploymentAllowed> | ||
| <outputsNewCASes>false</outputsNewCASes> | ||
| </operationalProperties> | ||
| </analysisEngineMetaData> | ||
| <frameworkImplementation>org.apache.uima.java</frameworkImplementation> | ||
| <primitive>true</primitive> | ||
| <annotatorImplementationName>de.julielab.jcore.ae.likelihoodassignment.LikelihoodAssignmentAnnotator</annotatorImplementationName> | ||
| <analysisEngineMetaData> | ||
| <name>JCoRe Likelihood Assignment AE</name> | ||
| <description>Analysis Engine to assign likelihood indicators to their corresponding entities and events.</description> | ||
| <version>2.3.0</version> | ||
| <configurationParameters/> | ||
| <configurationParameterSettings/> | ||
| <typeSystemDescription> | ||
| <imports> | ||
| <import name="de.julielab.jcore.types.jcore-semantics-mention-types"/> | ||
| </imports> | ||
| </typeSystemDescription> | ||
| <fsIndexCollection/> | ||
| <capabilities> | ||
| <capability> | ||
| <inputs> | ||
| <type>de.julielab.jcore.types.LikelihoodIndicator</type> | ||
| </inputs> | ||
| <outputs/> | ||
| <languagesSupported/> | ||
| </capability> | ||
| </capabilities> | ||
| <operationalProperties> | ||
| <modifiesCas>true</modifiesCas> | ||
| <multipleDeploymentAllowed>true</multipleDeploymentAllowed> | ||
| <outputsNewCASes>false</outputsNewCASes> | ||
| </operationalProperties> | ||
| </analysisEngineMetaData> | ||
| </analysisEngineDescription> |
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