public override PartialModelDelegate PartialModelDelegateFactory(QmrrPartialModel qmrrPartialModel)
{
return(delegate(TrueCollection trueCollection, OptimizationParameterList qmrrParams)
{
return LogLikelihoodOfCompleteModelConditionedOnKnownHlas(qmrrPartialModel, trueCollection, qmrrParams);
});
}
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);
}
static public QmrrPartialModel GetInstance(ModelLikelihoodFactories modelLikelihoodFactories,
string peptide,
Dictionary <string, double> patientToAnyReaction,
Set <Hla> knownHlaSet,
Dictionary <string, Set <Hla> > patientList,
OptimizationParameterList qmrrParamsStart
)
{
QmrrPartialModel aQmrrPartialModel = new QmrrPartialModel();
aQmrrPartialModel.QmrrParamsStart = qmrrParamsStart;
aQmrrPartialModel.Peptide = peptide;
aQmrrPartialModel.PatientToAnyReaction = patientToAnyReaction;
aQmrrPartialModel.PatientList = patientList;
aQmrrPartialModel.KnownHlaSet = knownHlaSet;
aQmrrPartialModel.CreateHlaList();
aQmrrPartialModel.CreateSwitchableHlasWithRespondingPatients();
aQmrrPartialModel.ModelLikelihoodFactories = modelLikelihoodFactories;
if (modelLikelihoodFactories != null)
{
aQmrrPartialModel.LogLikelihoodOfCompleteModelConditionedOnKnownHlas = modelLikelihoodFactories.PartialModelDelegateFactory(aQmrrPartialModel);
}
else
{
aQmrrPartialModel.LogLikelihoodOfCompleteModelConditionedOnKnownHlas = null;
}
return(aQmrrPartialModel);
}
virtual protected double LogLikelihoodOfCompleteModelConditionedOnKnownHlas(QmrrPartialModel qmrrPartialModel, TrueCollection trueCollection, OptimizationParameterList qmrrParams)
{
double logLikelihood =
LogLikelihoodOfCausesConditionedOnKnownHlas(qmrrPartialModel, trueCollection, qmrrParams)
+ LogLikelihoodOfEffects(qmrrPartialModel, trueCollection, qmrrParams);
return(logLikelihood);
}
virtual public MissingParametersDelegate MissingParametersDelegateFactory(QmrrPartialModel qmrrPartialModel, TrueCollection trueCollection)
{
PartialModelDelegate LogLikelihoodOfCompleteModelConditionedOnKnownHlas = PartialModelDelegateFactory(qmrrPartialModel);
return(delegate(OptimizationParameterList parameterList)
{
return LogLikelihoodOfCompleteModelConditionedOnKnownHlas(trueCollection, parameterList);
});
}
private int CountReactionsCovered(QmrrPartialModel qmrrPartialModel, Set <Hla> trueHlaSet)
{
int reactionsCoveredCount = 0;
foreach (string patient in qmrrPartialModel.PatientToAnyReaction.Keys)
{
if (NonEmptyIntersection(qmrrPartialModel.PatientList[patient], trueHlaSet))
{
++reactionsCoveredCount;
}
}
return(reactionsCoveredCount);
}
virtual protected double LogLikelihoodOfCausesConditionedOnKnownHlas(QmrrPartialModel qmrrPartialModel, TrueCollection trueCollection, OptimizationParameterList qmrrParams)
{
double logCausePrior = Math.Log(qmrrParams["causePrior"].Value);
double logOneLessCausePrior = Math.Log(1.0 - qmrrParams["causePrior"].Value);
int trueCountLessKnown = trueCollection.Count - qmrrPartialModel.KnownHlaSet.Count;
Debug.Assert(trueCountLessKnown >= 0); // real assert
int falseCount = qmrrPartialModel.HlaList.Count - trueCollection.Count;
double logLikelihood =
(double)trueCountLessKnown * logCausePrior
+ (double)falseCount * logOneLessCausePrior;
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);
}
protected QmmrModelOnePeptide QmmrModelOnePeptideGetInstance(QmrrPartialModel qmrrPartialModel, OptimizationParameterList qmrrParams, double depth)
{
QmmrModelOnePeptide aQmmrModelOnePeptide = new QmmrModelOnePeptide();
aQmmrModelOnePeptide.QmrrModelMissingAssignment = QmrrModelMissingAssignment.GetInstance(ModelLikelihoodFactories, qmrrPartialModel, qmrrParams);
aQmmrModelOnePeptide.CreateNoSwitchablesHlaAssignment();
if (depth == 0)
{
// do nothing
}
else if (depth == Math.Floor(depth))
{
SpecialFunctions.CheckCondition(depth > 0);
aQmmrModelOnePeptide.SetForDepthSearch((int)Math.Floor(depth));
}
else
{
SpecialFunctions.CheckCondition(depth == 1.5);
aQmmrModelOnePeptide.SetForBitFlipsAnd1Replacement();
}
return(aQmmrModelOnePeptide);
}
protected override double LogLikelihoodOfCausesConditionedOnKnownHlas(QmrrPartialModel qmrrPartialModel, TrueCollection trueCollection, OptimizationParameterList qmrrParams)
{
//!!!This could be calculated during the construction of qmrrPartialModel
Set <Hla> fitUniverse = SpecialFunctions.GetValueOrDefault(PeptideToFitUniverse, qmrrPartialModel.Peptide);
//Compute with priors
double unfitCausePrior = qmrrParams["causePrior"].Value;
double fitFactor = qmrrParams["fitFactor"].Value;
double fitCausePrior = unfitCausePrior * fitFactor;
double logUnfitCausePrior = Math.Log(unfitCausePrior);
double logOneLessUnfitCausePrior = Math.Log(1.0 - unfitCausePrior);
double logFitCausePrior = Math.Log(fitCausePrior);
double logOneLessFitCausePrior = Math.Log(1.0 - fitCausePrior);
//Tabulate counts
int unfitTotalCount = qmrrPartialModel.HlaList.Count - fitUniverse.Count;
int trueCountLessKnown = trueCollection.Count - qmrrPartialModel.KnownHlaSet.Count;
int falseCount = qmrrPartialModel.HlaList.Count - trueCollection.Count;
int knownFitCount = KnownFitCount(fitUniverse, qmrrPartialModel.KnownHlaSet); //!!!could be pretabulated
int knownUnfitCount = qmrrPartialModel.KnownHlaSet.Count - knownFitCount;
int fitTrueCountLessKnown = FitTrueCount(fitUniverse, trueCollection) - knownFitCount;
int unfitTrueCountLessKnown = trueCountLessKnown - fitTrueCountLessKnown;
int fitFalseCount = fitUniverse.Count - fitTrueCountLessKnown - knownFitCount;
int unfitFalseCount = unfitTotalCount - unfitTrueCountLessKnown - knownUnfitCount;
//Compute logLikelihood
double logLikelihood =
(double)unfitTrueCountLessKnown * logUnfitCausePrior
+ (double)unfitFalseCount * logOneLessUnfitCausePrior
+ (double)fitTrueCountLessKnown * logFitCausePrior
+ (double)fitFalseCount * logOneLessFitCausePrior;
return(logLikelihood);
}
internal static QmrrlModelMissingParameters GetInstance(ModelLikelihoodFactories modelLikelihoodFactories, QmrrPartialModel qmrrPartialModel, BestSoFar <double, TrueCollection> bestSoFar)
{
QmrrlModelMissingParameters aQmrrlModelMissingParameters = new QmrrlModelMissingParameters();
aQmrrlModelMissingParameters.QmrrPartialModel = qmrrPartialModel;
aQmrrlModelMissingParameters.TrueCollection = bestSoFar.Champ;
aQmrrlModelMissingParameters.ModelLikelihoodFactories = modelLikelihoodFactories;
aQmrrlModelMissingParameters.LogLikelihoodOfCompleteModelConditionedOnKnownHlas = modelLikelihoodFactories.MissingParametersDelegateFactory(qmrrPartialModel, bestSoFar.Champ);
return(aQmrrlModelMissingParameters);
}
abstract public PartialModelDelegate PartialModelDelegateFactory(QmrrPartialModel qmrrPartialModel);
public static QmrrModelMissingAssignment GetInstance(ModelLikelihoodFactories modelLikelihoodFactories, QmrrPartialModel qmrrPartialModel, OptimizationParameterList qmrrParams)
{
QmrrModelMissingAssignment aQmrrModelMissingAssignment = new QmrrModelMissingAssignment();
aQmrrModelMissingAssignment.QmrrPartialModel = qmrrPartialModel;
aQmrrModelMissingAssignment.OptimizationParameterList = qmrrParams;
aQmrrModelMissingAssignment.KnownHlaSet = qmrrPartialModel.KnownHlaSet;
aQmrrModelMissingAssignment.SwitchableHlasOfRespondingPatients = qmrrPartialModel.SwitchableHlasOfRespondingPatients;
aQmrrModelMissingAssignment.ModelLikelihoodFactories = modelLikelihoodFactories;
aQmrrModelMissingAssignment.LogLikelihoodOfCompleteModelConditionedOnKnownHlas = modelLikelihoodFactories.MissingAssignmentDelegateFactory(qmrrPartialModel, qmrrParams);
return(aQmrrModelMissingAssignment);
//SetOfAllHlasCount = qmrrPartialModel.HlaList.Count;
}