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package com.wcohen.ss.abbvGapsHmm;
import java.util.ArrayList;
import java.util.List;
import com.wcohen.ss.abbvGapsHmm.AbbvGapsHMM.*;
/**
* @author Dana Movshovitz-Attias
*/
public class AbbvGapsHmmBackwardsViterbiEvaluator
extends
AbbvGapsHmmBackwardsEvaluator {
protected Matrix3D _alpha;
protected Matrix3D _beta;
protected Matrix3D _emissions;
protected Matrix3D _states;
protected Matrix3D _prevSF;
protected Matrix3D _prevLF;
protected Matrix3D _prevSF_stringPos;
protected Matrix3D _prevLF_stringPos;
protected Double _bestProb;
protected Double _currProb;
public AbbvGapsHmmBackwardsViterbiEvaluator(AbbvGapsHMM abbvGapsHMM) {
super(abbvGapsHMM);
}
public AbbreviationAlignmentContainer<AbbvGapsHMM.Emissions, AbbvGapsHMM.States> backwardViterbiEvaluate(Acronym acronym, List<Double> transitionParams, List<Double> emissionParams){
_transitionParams = transitionParams;
_emissionParams = emissionParams;
super.evaluate(acronym);
return findMostProbablePathBackwards(acronym);
}
/* (non-Javadoc)
* @see Structures.AbbvGapsHMMEvaluator#initEvalMat()
*/
@Override
protected void initEvalMat() {
_emissions = new Matrix3D(_evalMat.dimension1(), _evalMat.dimension2(), _evalMat.dimension3());
_states = new Matrix3D(_evalMat.dimension1(), _evalMat.dimension2(), _evalMat.dimension3());
_prevSF = new Matrix3D(_evalMat.dimension1(), _evalMat.dimension2(), _evalMat.dimension3());
_prevLF = new Matrix3D(_evalMat.dimension1(), _evalMat.dimension2(), _evalMat.dimension3());
_prevSF_stringPos = new Matrix3D(_evalMat.dimension1(), _evalMat.dimension2(), _evalMat.dimension3());
_prevLF_stringPos = new Matrix3D(_evalMat.dimension1(), _evalMat.dimension2(), _evalMat.dimension3());
super.initEvalMat();
}
protected int getLegalStringPos(int strPos, String str){
int legalStrPos = strPos;
if(strPos > str.length() || strPos == -1){
legalStrPos = str.length();
}
return legalStrPos;
}
public AbbreviationAlignmentContainer<AbbvGapsHMM.Emissions, AbbvGapsHMM.States> findMostProbablePathBackwards(Acronym acronym){
int sPos = _sParam.getRangeEnd();
int lPos = _lParam.getRangeEnd();
int state = States.S.ordinal();
int stringPosS = -1;
int stringPosL = -1;
if(_evalMat.at(0, 0, States.S.ordinal()) == 0){
return null;
}
List<Emissions> emmisionsPath = new ArrayList<AbbvGapsHMM.Emissions>();
List<States> statesPath = new ArrayList<AbbvGapsHMM.States>();
List<String> lAlign = new ArrayList<String>();
List<String> sAlign = new ArrayList<String>();
Emissions[] emissionValues = Emissions.values();
States[] stateValues = States.values();
Emissions currEmission;
Integer currSF;
Integer currLF;
Integer currState;
Integer currSF_stringPos;
Integer currLF_stringPos;
while(sPos < _sParam.getEvalMatrixSize()-1 || lPos < _lParam.getEvalMatrixSize()-1){
currEmission = emissionValues[ (int) Math.round(_emissions.at(sPos, lPos, state)) ];
currSF = (int) Math.round(_prevSF.at(sPos, lPos, state));
currLF = (int) Math.round(_prevLF.at(sPos, lPos, state));
currState = (int) Math.round(_states.at(sPos, lPos, state));
currSF_stringPos = (int) Math.round(_prevSF_stringPos.at(sPos, lPos, state));
currLF_stringPos = (int) Math.round(_prevLF_stringPos.at(sPos, lPos, state));
if(stringPosS != -1 && stringPosL != -1){
stringPosS = getLegalStringPos(stringPosS, acronym._shortForm);
stringPosL = getLegalStringPos(stringPosL, acronym._longForm);
lAlign.add(acronym._longForm.substring(stringPosL, currLF_stringPos));
sAlign.add(acronym._shortForm.substring(stringPosS, currSF_stringPos));
}
emmisionsPath.add(currEmission);
statesPath.add(stateValues[currState]);
sPos = currSF;
lPos = currLF;
state = currState;
stringPosS = currSF_stringPos;
stringPosL = currLF_stringPos;
}
return new AbbreviationAlignmentContainer<AbbvGapsHMM.Emissions, AbbvGapsHMM.States>(sAlign, lAlign, emmisionsPath, statesPath, _evalMat.at(0, 0, States.S.ordinal()));
}
protected void updateLegalOutgoingEdges(
int currS, int currL, States currState,
int prevS, int prevL, States prevState,
Transitions transition, Emissions emission
){
Double prevProb = _evalMat.at(currS, currL, prevState.ordinal());
Double currProb = _evalMat.at(prevS, prevL, currState.ordinal())*_emissionParams.get(emission.ordinal())*_transitionParams.get(transition.ordinal());
if(prevProb.compareTo(currProb) < 0){
// Save best probability
_evalMat.set(currS, currL, prevState.ordinal(), currProb);
// Save emission with best probability
_emissions.set(currS, currL, prevState.ordinal(), emission.ordinal());
// Save previous location that produced best probability
_states.set(currS, currL, prevState.ordinal(), currState.ordinal());
_prevSF.set(currS, currL, prevState.ordinal(), prevS);
_prevLF.set(currS, currL, prevState.ordinal(), prevL);
_prevSF_stringPos.set(currS, currL, prevState.ordinal(), _sParam.getEvalStringPos());
_prevLF_stringPos.set(currS, currL, prevState.ordinal(), _lParam.getEvalStringPos());
}
}
}
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