override protected double LogLikelihoodOfEffects(QmrrPartialModel qmrrPartialModel, TrueCollection trueCollection, OptimizationParameterList qmrrParams)
{
Set <Hla> trueCollectionAsSet = trueCollection.CreateHlaAssignmentAsSet();
double logOneLessLeakProbability = Math.Log(1.0 - qmrrParams["leakProbability"].Value);
Dictionary <Hla, double> hlaToLogOneLessLink = new Dictionary <Hla, double>();
foreach (Hla hla in trueCollectionAsSet)
{
double logOneLessLink = Math.Log(1.0 - qmrrParams["link" + hla].Value);
hlaToLogOneLessLink.Add(hla, logOneLessLink);
}
double logLikelihood = 0.0;
foreach (KeyValuePair <string, Set <Hla> > patientAndHlaList in qmrrPartialModel.PatientList)
{
double logLikelihoodNoReactionInThisPatient = logOneLessLeakProbability;
foreach (Hla hla in patientAndHlaList.Value)
{
if (trueCollectionAsSet.Contains(hla))
{
double logOneLessLink = hlaToLogOneLessLink[hla];
logLikelihoodNoReactionInThisPatient += logOneLessLink;
}
}
bool didReact = qmrrPartialModel.PatientToAnyReaction.ContainsKey(patientAndHlaList.Key);
logLikelihood += LogLikelihoodOfThisPatient(logLikelihoodNoReactionInThisPatient, didReact);
}
return(logLikelihood);
}
private double LogLikelihoodOfCompleteModelConditionedOnKnownHlas(QmrrPartialModel qmrrPartialModel, TrueCollection trueCollection, OptimizationParameterList qmrrParams)
{
Set <Hla> trueHlaSet = trueCollection.CreateHlaAssignmentAsSet();
int reactionsCoveredCount = CountReactionsCovered(qmrrPartialModel, trueHlaSet);
SpecialFunctions.CheckCondition(reactionsCoveredCount < 1000);
int trueCount = trueCollection.Count;
SpecialFunctions.CheckCondition(trueCount < 1000);
int falseCount = qmrrPartialModel.HlaList.Count - trueCollection.Count;
SpecialFunctions.CheckCondition(falseCount < 1000);
string llAsString = string.Format("{0:000}.{1:000}{2:000}", reactionsCoveredCount, falseCount, trueCount);
double logLikelihood = double.Parse(llAsString);
return(logLikelihood);
}
virtual protected double LogLikelihoodOfEffects(QmrrPartialModel qmrrPartialModel, TrueCollection trueCollection, OptimizationParameterList qmrrParams)
{
double logOneLessLink = Math.Log(1.0 - qmrrParams["link"].Value);
double logOneLessLeakProbability = Math.Log(1.0 - qmrrParams["leakProbability"].Value);
double logLikelihood = 0.0;
Set <Hla> trueCollectionAsSet = trueCollection.CreateHlaAssignmentAsSet();
foreach (KeyValuePair <string, Set <Hla> > patientAndHlaList in qmrrPartialModel.PatientList)
{
double logLikelihoodNoReactionInThisPatient =
logOneLessLeakProbability
+ NumberOfPositiveHlas(patientAndHlaList.Value, trueCollectionAsSet) * logOneLessLink;
bool didReact = qmrrPartialModel.PatientToAnyReaction.ContainsKey(patientAndHlaList.Key);
logLikelihood += LogLikelihoodOfThisPatient(logLikelihoodNoReactionInThisPatient, didReact);
}
return(logLikelihood);
}
