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* Licensed to the Apache Software Foundation (ASF) under one
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* distributed with this work for additional information
* regarding copyright ownership. The ASF licenses this file
* to you under the Apache License, Version 2.0 (the
* "License"); you may not use this file except in compliance
* with the License. You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing,
* software distributed under the License is distributed on an
* "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
* KIND, either express or implied. See the License for the
* specific language governing permissions and limitations
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package org.apache.ctakes.assertion.medfacts.cleartk;
import java.io.File;
import java.io.IOException;
import java.net.URI;
import java.util.ArrayList;
import org.apache.ctakes.assertion.attributes.features.selection.Chi2FeatureSelection;
import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
import org.apache.ctakes.assertion.medfacts.cleartk.extractors.AboveLeftFragmentExtractor;
import org.apache.ctakes.assertion.medfacts.cleartk.extractors.ContextWordWindowExtractor;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.resource.ResourceInitializationException;
import org.cleartk.classifier.Instance;
import org.cleartk.classifier.feature.extractor.simple.SimpleFeatureExtractor;
public class UncertaintyCleartkAnalysisEngine extends AssertionCleartkAnalysisEngine {
@Override
public void initialize(UimaContext context) throws ResourceInitializationException {
super.initialize(context);
probabilityOfKeepingADefaultExample = 0.1;
if(this.entityFeatureExtractors == null){
this.entityFeatureExtractors = new ArrayList<SimpleFeatureExtractor>();
}
this.entityFeatureExtractors.add(new ContextWordWindowExtractor("org/apache/ctakes/assertion/models/uncertainty.txt"));
this.entityFeatureExtractors.add(new AboveLeftFragmentExtractor("ALUncertainty", "org/apache/ctakes/assertion/models/sharpUncertaintyFrags.txt"));
initializeFeatureSelection();
}
@Override
public void setClassLabel(IdentifiedAnnotation entityOrEventMention, Instance<String> instance) throws AnalysisEngineProcessException {
if (this.isTraining())
{
String uncertainty = (entityOrEventMention.getUncertainty() == 1) ? "uncertain" : "certain";
// downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling
if ("certain".equals(uncertainty)
&& coin.nextDouble() >= this.probabilityOfKeepingADefaultExample) {
return;
}
instance.setOutcome(uncertainty);
// this.dataWriter.write(instance);
} else
{
String label = this.classifier.classify(instance.getFeatures());
int uncertainty = 0;
if (label!= null && label.equals("uncertain"))
{
uncertainty = 1;
} else if (label != null && label.equals("certain"))
{
uncertainty = 0;
}
entityOrEventMention.setUncertainty(uncertainty);
}
}
public static FeatureSelection<String> createFeatureSelection(double threshold) {
return new Chi2FeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME, threshold, false);
// return new MutualInformationFeatureSelection<String>(AssertionCleartkAnalysisEngine.FEATURE_SELECTION_NAME);
}
public static URI createFeatureSelectionURI(File outputDirectoryName) {
return new File(outputDirectoryName, FEATURE_SELECTION_NAME + "_Chi2_extractor.dat").toURI();
}
@Override
protected void initializeFeatureSelection() throws ResourceInitializationException {
if (featureSelectionThreshold == 0) {
this.featureSelection = null;
} else {
this.featureSelection = this.createFeatureSelection(this.featureSelectionThreshold);
// if ( (new File(this.featureSelectionURI)).exists() ) {
// try {
// this.featureSelection.load(this.featureSelectionURI);
// } catch (IOException e) {
// throw new ResourceInitializationException(e);
// }
// }
}
}
}