/**
* @param isSimplifyEntity
* @param tokenWithPos
* @param senID
* @param sentence
* @param listEnt
* @param listRel
* @param listDependencies
* @param medtType
* @param isResolveOverlappingEntities
* @param relToBeConsidered
* @param arrClauseBoundOfSen
* @return
* @throws IOException
*/
public boolean setInpVectFromDepGraphOfPairsAndTrigger(
Relation objRel,
Sentence objCurSen,
int medtType,
boolean discardDepRelUsingProbabilityInReducedGraph,
boolean useWalkFeatures,
boolean useRegExPatterns,
boolean useDepPatterns,
boolean useTriggers,
boolean triggersFromWholeRGinsteadOfLCP,
boolean useNegativeCues,
Entity e1,
Entity e2)
throws IOException {
ArrayList<Integer> listFeatIndsOfCurInp = new ArrayList<Integer>(),
listFeatCountOfCurInp = new ArrayList<Integer>();
DepTreeNode
headOfEnt1 =
objCurSen.depTree.getHeadWordFromWordBoundaries(
e1.getAllWordIndexes(), true, objCurSen),
headOfEnt2 =
objCurSen.depTree.getHeadWordFromWordBoundaries(
e2.getAllWordIndexes(), true, objCurSen);
DepTreeNode dn = null;
// System.out.println(e1.id + " " + e2.id);
// All nodes in the shortest path connecting the target pairs must be retained
// All nodes satisfying the 3 rules of MEDT kernel must be retained
dn =
objCurSen
.depTree
.clone()
.findMinimalSubTreeWithEntities(false, headOfEnt1, medtType, headOfEnt2);
/*
* If there is no minimal subtree/path between target entities then we do not consider to generate
* instance for training/testing.
*/
if (dn == null) {
FileUtility.writeInFile(
GenericFeatVect.vectOutFile,
e1.id + " " + e1.name + "\t" + e2.id + " " + e2.name + "\n\n",
true);
FileUtility.writeInFile(GenericFeatVect.vectOutFile, objCurSen.text + "\n\n", true);
return false;
}
GenericFeatVect.listOfAllInstances.add(
e1.id + " " + e1.name + "\t" + e2.id + " " + e2.name + "\n\n" + objCurSen.text + "\n\n");
// Construct feature set using e-walks and v-walks
if (dn != null && useWalkFeatures) {
createNgramFeatures(objCurSen.depTree, 1, e1, listFeatIndsOfCurInp, listFeatCountOfCurInp);
createNgramFeatures(objCurSen.depTree, 1, e2, listFeatIndsOfCurInp, listFeatCountOfCurInp);
// System.out.println(objCurSen.senID + " " + dn.wordIndex);
objCurSen.depTree.replaceEntitiesWithDummies(
dn, e1.boundaries, e2.boundaries, new ArrayList<Integer>());
createFeaturesFromInputGraph(
objCurSen.depTree,
dn,
"",
listFeatIndsOfCurInp,
listFeatCountOfCurInp,
new ArrayList<Integer>(),
e1.boundaries,
e2.boundaries);
}
if (useRegExPatterns) {
matchPPIpatternOnSentence(
objCurSen.text, e1.name, e2.name, listFeatIndsOfCurInp, listFeatCountOfCurInp);
matchPPIpatternOnSentence(
objCurSen.text, e2.name, e1.name, listFeatIndsOfCurInp, listFeatCountOfCurInp);
}
ArrayList<String> listOfDepRelsInReducedGraph = new ArrayList<String>();
ArrayList<ArrayList<Integer>> listNodesAndLCP =
new PatternsDepRelFromGraph()
.extractDepRelsInReducedGraph(
objRel,
objCurSen,
listOfDepRelsInReducedGraph,
discardDepRelUsingProbabilityInReducedGraph,
false);
if (useDepPatterns)
extractDepPatternFeatures(
listOfDepRelsInReducedGraph, listFeatIndsOfCurInp, listFeatCountOfCurInp);
// NOTE: listNodesAndLCP has two elements - (0) all the nodes in Reduced graph, and (1) the
// least common parents (LCPs) in Reduced graph.
if (listNodesAndLCP == null) listNodesAndLCP = new ArrayList<ArrayList<Integer>>();
if (useTriggers && listNodesAndLCP.size() > 0) {
if (triggersFromWholeRGinsteadOfLCP)
for (int i = 0; i < listNodesAndLCP.get(0).size(); i++)
addTriggerWordFeatures(
objCurSen.depGraph.allNodesByWordIndex[listNodesAndLCP.get(0).get(i)].word,
listFeatIndsOfCurInp,
listFeatCountOfCurInp);
else
for (int i = 0; i < listNodesAndLCP.get(1).size(); i++)
addTriggerWordFeatures(
objCurSen.depGraph.allNodesByWordIndex[listNodesAndLCP.get(1).get(i)].word,
listFeatIndsOfCurInp,
listFeatCountOfCurInp);
}
// *
if (useNegativeCues && listNodesAndLCP.size() > 0) {
for (int i = 0; i < listNodesAndLCP.get(0).size(); i++) {
// System.out.println(objCurSen.senID + " " + dn.wordIndex);
// addNegativeWordFeatures( graph.allNodesByWordIndex[listNodesAndLCP.get(0).get(i)].word,
// listFeatIndsOfCurInp, listFeatCountOfCurInp);
if (Triggers.listOfNegativeWords.contains(
objCurSen.depGraph.allNodesByWordIndex[listNodesAndLCP.get(0).get(i)].lemma)) {
// add a feature indicating that there is a negative word in the reduced graph
String[] feature =
new String[] {
"HasNegWord@$"
+ objCurSen.depGraph.allNodesByWordIndex[listNodesAndLCP.get(0).get(i)].lemma,
};
GenericFeatVect.addNewFeatureInList(
feature, 1, listFeatIndsOfCurInp, listFeatCountOfCurInp, 1);
if (objCurSen.depGraph.allNodesByWordIndex[listNodesAndLCP.get(0).get(i) + 1].lemma
.equalsIgnoreCase("be")
|| objCurSen.depGraph.allNodesByWordIndex[listNodesAndLCP.get(0).get(i) + 1].pos
.equalsIgnoreCase("IN")) {
feature =
new String[] {
"WordNextToNegCue@$"
+ objCurSen
.depGraph
.allNodesByWordIndex[listNodesAndLCP.get(0).get(i) + 2]
.lemma,
};
} else {
feature =
new String[] {
"WordNextToNegCue@$"
+ objCurSen
.depGraph
.allNodesByWordIndex[listNodesAndLCP.get(0).get(i) + 1]
.lemma,
};
}
GenericFeatVect.addNewFeatureInList(
feature, 1, listFeatIndsOfCurInp, listFeatCountOfCurInp, 1);
// *
// extract negation scope features
if (objCurSen.depGraph.allNodesByWordIndex[listNodesAndLCP.get(0).get(i)].lemma.matches(
"(no|not)"))
extractNegationScopeFeatures(
objCurSen,
listFeatIndsOfCurInp,
listFeatCountOfCurInp,
e1,
e2,
listNodesAndLCP.get(0).get(i),
listNodesAndLCP.get(0));
// */
}
}
}
// */
// add Zhou et al. 2005 features
new ExtAceFeatVect()
.getZhouEtAl2005FeatVal(objCurSen, e1, e2, listFeatIndsOfCurInp, listFeatCountOfCurInp);
extractNonTargetEntityFeatures(objCurSen, listFeatIndsOfCurInp, listFeatCountOfCurInp, e1, e2);
GenericFeatVect.sortFeatValByIndx(listFeatIndsOfCurInp, listFeatCountOfCurInp);
GenericFeatVect.listOfAllInstancesWithFeat.add(listFeatIndsOfCurInp);
GenericFeatVect.listOfAllInstancesWithFeatCount.add(listFeatCountOfCurInp);
return true;
}
/**
* @param isSimplifyEntity
* @param parsedFileName
* @param aimedDataFileName
* @param outputFile
* @param medtType
* @param isRemoveOverlappingEntities
* @throws Exception
*/
public void generateTPWFvectorOutput(
ArrayList<Sentence> listSentence,
String outputFile,
int medtType,
String entPairFileName,
ClauseAnalyser.eDataFilterOption relToBeConsidered,
String inClauseBoundFileName)
throws Exception {
boolean useWalkFeatures = true,
useRegExPatterns = false,
useDepPatterns = true,
useTriggers = true,
useNegativeCues = true,
discardDepRelUsingProbabilityInReducedGraph = false,
triggersFromWholeRGinsteadOfLCP = true;
if (TextUtility.isEmptyString(TKOutputGenerator.triggerFileName)) useTriggers = false;
String str = "";
if (discardDepRelUsingProbabilityInReducedGraph)
str += "discardDepRelUsingProbabilityInReducedGraph ";
if (useWalkFeatures) str += "WalkFeatures ";
if (useRegExPatterns) str += "RegExPatterns ";
if (useDepPatterns) str += "DepPatterns ";
if (useTriggers) str += "Triggers ";
if (triggersFromWholeRGinsteadOfLCP) str += "TriggersFromWholeRGinsteadOfLCP ";
if (useNegativeCues) str += "NegativeCues ";
System.out.println(str);
PatternsDepRelFromGraph clsWVG = new PatternsDepRelFromGraph();
if (PatternsDepRelFromGraph.listOfAllPatterns.size() == 0) {
clsWVG.collectAllDepRelPatternsFromTrainData(
listSentence, discardDepRelUsingProbabilityInReducedGraph);
}
int[][] arrClauseBoundOfSen = new TKOutputPST().getClauseBoundOfAllSen(inClauseBoundFileName);
FileUtility.writeInFile(outputFile, "", false);
// read trigger word list
Triggers.readTriggersAndNegativeWord();
for (int s = 0; s < listSentence.size(); s++) {
Sentence objCurSen = listSentence.get(s);
int senIndex = TKOutputPST.listAllSenIDs.indexOf(objCurSen.senID);
// only those sentences are taken into account which has more than one entity annotations
if (objCurSen.listOfEntities.size() > 1) {
generateVectorForSen(
objCurSen,
medtType,
entPairFileName,
discardDepRelUsingProbabilityInReducedGraph,
useWalkFeatures,
useRegExPatterns,
useDepPatterns,
useTriggers,
triggersFromWholeRGinsteadOfLCP,
useNegativeCues,
relToBeConsidered,
senIndex > 0 ? arrClauseBoundOfSen[senIndex] : null);
}
}
FileUtility.writeInFile(outputFile, GenericFeatVect.getInstanceVectors(), false);
}
/**
* @param tokenWithPos
* @param senID
* @param sentence
* @param listEnt
* @param listRel
* @param listDependencies
* @param medtType
* @param entPairFileName
* @return
* @throws IOException
*/
private void generateVectorForSen(
Sentence objCurSen,
int medtType,
String entPairFileName,
boolean discardDepRelUsingProbabilityInReducedGraph,
boolean useWalkFeatures,
boolean useRegExPatterns,
boolean useDepPatterns,
boolean useTriggers,
boolean triggersFromWholeRGinsteadOfLCP,
boolean useNegativeCues,
ClauseAnalyser.eDataFilterOption relToBeConsidered,
int[] arrClauseBoundOfSen)
throws IOException {
// for each pair of entities, find minimal subtrees and output it with 1 or 0
// 1 represents there exists a relation between those entities
for (int r = 0; r < objCurSen.listRels.size(); r++) {
Entity e1 = objCurSen.getEntityById(objCurSen.listRels.get(r).arg1);
Entity e2 = objCurSen.getEntityById(objCurSen.listRels.get(r).arg2);
// checking relation type
if (TKOutputPST.skipInstance(arrClauseBoundOfSen, relToBeConsidered, e1, e2, objCurSen, r))
continue;
if (!objCurSen.listRels.get(r).isPositive) TKOutputPST.totalRelNeg++;
else TKOutputPST.totalRelPos++;
boolean isSet =
setInpVectFromDepGraphOfPairsAndTrigger(
objCurSen.listRels.get(r),
objCurSen,
medtType,
discardDepRelUsingProbabilityInReducedGraph,
useWalkFeatures,
useRegExPatterns,
useDepPatterns,
useTriggers,
triggersFromWholeRGinsteadOfLCP,
useNegativeCues,
e1,
e2);
if (isSet)
GenericFeatVect.listOfAllInstancePolarity.add(
objCurSen.listRels.get(r).isPositive ? 1 : -1);
// */
if (!TextUtility.isEmptyString(entPairFileName)) {
if (isSet) FileUtility.writeInFile(entPairFileName, e1.id + "\t" + e2.id + "\n", true);
/*
//if ( !str.isEmpty() )
if ( !isSet )
FileUtility.writeInFile(entPairFileName, objCurSen.listRels.get(r).printString() + "\tFOUND\n", true);
else {
FileUtility.writeInFile(entPairFileName, objCurSen.listRels.get(r).printString() + "\tNOT_FOUND\n", true);
}
*/
}
}
}