public static void Evaluate(DiseasesData PredictionData, DiseasesData RealData, string wantedFileName = "")
{
//Object to write in JSON
Results results = new Results();
int RP = 0; //RealPositive general
int FP = 0; //FalsePositive general
int FN = 0; //FalseNegative general
//For each existent rare disease
foreach (string orphaNumber in PredictionData.DiseaseDataList.Select(x => x?.Disease?.OrphaNumber))
{
//Find THE diseaseData of ONE disease (real and predicted data)
DiseaseData RealDiseaseData = RealData.DiseaseDataList.Where(x => x?.Disease?.OrphaNumber == orphaNumber).FirstOrDefault();
DiseaseData PredictionDiseaseData = PredictionData.DiseaseDataList.Where(x => x?.Disease?.OrphaNumber == orphaNumber).FirstOrDefault();
//If we don't find the disease in both dataset, we shoud pass to another disease
if (RealDiseaseData != null && PredictionDiseaseData != null)
{
int RP_Disease = 0; //RealPositive of one disease
int FP_Disease = 0; //FalsePositive of one disease
int FN_Disease = 0; //FalseNegative of one disease
//Compute RP and FP
List <string> RelatedEntitiesNamesReal =
RealDiseaseData
.RelatedEntities.RelatedEntitiesList
.Select(x => x.Name)
.ToList();
for (int j = 0; j < PredictionDiseaseData.RelatedEntities.RelatedEntitiesList.Count; j++)
{
//Is my predicted related entity is present in the real data?
if (RelatedEntitiesNamesReal.IndexOf(PredictionDiseaseData.RelatedEntities.RelatedEntitiesList[j].Name) != -1)
{
RP++;
RP_Disease++;
}
else
{
FP++;
FP_Disease++;
}
}
//Compute FN
List <string> RelatedEntitiesNamesPred =
PredictionDiseaseData
.RelatedEntities.RelatedEntitiesList
.Select(x => x.Name)
.ToList();
for (int j = 0; j < RealDiseaseData.RelatedEntities.RelatedEntitiesList.Count; j++)
{
//Is my real related entity is present in the predicted data?
if (RelatedEntitiesNamesPred.IndexOf(RealDiseaseData.RelatedEntities.RelatedEntitiesList[j].Name) == -1)
{
FN++;
FN_Disease++;
}
}
//Compute Precision/recall and F_score
double PrecisionDisease = 0.0;
double RecallDisease = 0.0;
double F_ScoreDisease = 0.0;
if (RP_Disease + FP_Disease != 0)
{
PrecisionDisease = Math.Round((double)RP_Disease / (double)(RP_Disease + FP_Disease), 4);
}
if (RP_Disease + FN_Disease != 0)
{
RecallDisease = Math.Round((double)RP_Disease / (double)(RP_Disease + FN_Disease), 4);
}
if (PrecisionDisease + RecallDisease != 0.0)
{
F_ScoreDisease = Math.Round(2 * PrecisionDisease * RecallDisease / (PrecisionDisease + RecallDisease), 4);
}
//Construct results object
PerDisease OnePerDisease = new PerDisease(orphaNumber,
PredictionDiseaseData.Disease.NumberOfPublications,
PredictionData.Type.ToString(),
RP_Disease,
FP_Disease,
FN_Disease,
PrecisionDisease, //Precision
RecallDisease, //Recall
F_ScoreDisease
);
results.perDisease.Add(OnePerDisease);
}
}
//Compute Precision/recall and F_score general
double Precision = 0.0;
double Recall = 0.0;
double F_Score = 0.0;
if (RP + FP != 0)
{
Precision = Math.Round((double)RP / (double)(RP + FP), 4);
}
if (RP + FN != 0)
{
Recall = Math.Round((double)RP / (double)(RP + FN), 4);
}
if (Precision + Recall != 0.0)
{
F_Score = Math.Round(2 * Precision * Recall / (Precision + Recall), 4);
}
//Construct results object
results.general = new General(
DateTime.Now,
PredictionData.Type.ToString(),
RP,
FP,
FN,
Precision,
Recall,
F_Score);
//Write JSON FILE
WriteJSONFile(results, wantedFileName);
}
public static Results Evaluate(DiseasesData PredictionData, DiseasesData RealData,
Tuple <TFType, IDFType> WeightCombinaison,
double threshold = -1.0)
{
//Object to write in JSON
Results results = new Results();
int RP = 0; //RealPositive general
int FP = 0; //FalsePositive general
int FN = 0; //FalseNegative general
int NumberOfDiseasesWithKnownPhenotypes = RealData.DiseaseDataList.Count;
int NumberOfDiseasesWithPublicationsInPredictionData = PredictionData.DiseaseDataList.Count(x => x.Disease.NumberOfPublications != 0);
int NumberOfDiseasesEvaluatedForReal = 0;
//For each existent rare disease
foreach (string orphaNumber in PredictionData.DiseaseDataList.Select(x => x?.Disease?.OrphaNumber))
{
//Find THE diseaseData of ONE disease (real and predicted data)
DiseaseData RealDiseaseData = RealData.DiseaseDataList.Where(x => x?.Disease?.OrphaNumber == orphaNumber).FirstOrDefault();
DiseaseData PredictionDiseaseData = PredictionData.DiseaseDataList.Where(
x => x?.Disease?.OrphaNumber == orphaNumber &&
x.Disease.NumberOfPublications != 0).FirstOrDefault();
//If we don't find the disease in both dataset, we shoud pass to another disease
if (RealDiseaseData != null && PredictionDiseaseData != null)
{
NumberOfDiseasesEvaluatedForReal++;//Increase number of diseases evaluated
Dictionary <RelatedEntity, double> RealWeightOfPhenotypes = new Dictionary <RelatedEntity, double>();
List <RelatedEntity> RealPhenotypes = new List <RelatedEntity>();
double MR_Disease = 0.0; //MeanRank RealPhenotype of one disease
int RP_Disease = 0; //RealPositive of one disease
int FP_Disease = 0; //FalsePositive of one disease
int FN_Disease = 0; //FalseNegative of one disease
//Compute RP and FP
List <string> RelatedEntitiesNamesReal =
RealDiseaseData
.RelatedEntities.RelatedEntitiesList
.Select(x => x.Name)
.ToList();
int NumberOfRelatedEntitiesFound = PredictionDiseaseData.RelatedEntities.RelatedEntitiesList.Count;
for (int j = 0; j < NumberOfRelatedEntitiesFound; j++)
{
double realWeight = PredictionDiseaseData.RelatedEntities.RelatedEntitiesList[j]
.CalcFinalWeight(WeightCombinaison.Item1, WeightCombinaison.Item2);
RealWeightOfPhenotypes.Add(PredictionDiseaseData.RelatedEntities.RelatedEntitiesList[j], realWeight);
if (threshold == -1.0 || realWeight >= threshold)
{
//Is my predicted related entity is present in the real data?
if (RelatedEntitiesNamesReal.IndexOf(PredictionDiseaseData.RelatedEntities.RelatedEntitiesList[j].Name) != -1)
{
RP++;
RP_Disease++;
RealPhenotypes.Add(PredictionDiseaseData.RelatedEntities.RelatedEntitiesList[j]);
}
else
{
FP++;
FP_Disease++;
}
}
}
//Compute FN
List <string> RelatedEntitiesNamesPred =
PredictionDiseaseData
.RelatedEntities.RelatedEntitiesList
.Select(x => x.Name)
.ToList();
for (int j = 0; j < RealDiseaseData.RelatedEntities.RelatedEntitiesList.Count; j++)
{
//Is my real related entity is present in the predicted data?
if (RelatedEntitiesNamesPred.IndexOf(RealDiseaseData.RelatedEntities.RelatedEntitiesList[j].Name) == -1)
{
FN++;
FN_Disease++;
}
}
//Compute Precision/recall and F_score
double PrecisionDisease = 0.0;
double RecallDisease = 0.0;
double F_ScoreDisease = 0.0;
if (RP_Disease + FP_Disease != 0)
{
PrecisionDisease = Math.Round((double)RP_Disease / (double)(RP_Disease + FP_Disease), 4);
}
if (RP_Disease + FN_Disease != 0)
{
RecallDisease = Math.Round((double)RP_Disease / (double)(RP_Disease + FN_Disease), 4);
}
if (PrecisionDisease + RecallDisease != 0.0)
{
F_ScoreDisease = Math.Round(2 * PrecisionDisease * RecallDisease / (PrecisionDisease + RecallDisease), 4);
}
////////////////////
//Compute MeanRank//
////////////////////
//Compute Ranks
Dictionary <RelatedEntity, double> RanksPhenotypes = new Dictionary <RelatedEntity, double>();
RanksPhenotypes = RealWeightOfPhenotypes.OrderByDescending(p => p.Value).Select((p, i) => new KeyValuePair <RelatedEntity, double>(p.Key, i + 1.0)).ToDictionary(p => p.Key, p => p.Value);
//Keep Only real Phenotypes
RanksPhenotypes =
RanksPhenotypes
.Where(elem => RealPhenotypes.Select(x => x.Name).ToList().IndexOf(elem.Key.Name) != -1)
.ToDictionary(p => p.Key, p => p.Value);
//MeanRank of Real Phenotypes in one disease
if (RanksPhenotypes.Count != 0)
{
MR_Disease = RanksPhenotypes.Average(p => p.Value);
}
//Construct results object
PerDisease OnePerDisease = new PerDisease(orphaNumber,
PredictionDiseaseData.Disease.NumberOfPublications,
PredictionData.Type,
NumberOfRelatedEntitiesFound,
RP_Disease,
FP_Disease,
FN_Disease,
PrecisionDisease, //Precision
RecallDisease, //Recall
F_ScoreDisease,
MR_Disease
);
results.perDisease.Add(OnePerDisease);
}
}
//Compute Precision/recall and F_score general
double Precision = 0.0;
double Recall = 0.0;
double F_Score = 0.0;
if (RP + FP != 0)
{
Precision = Math.Round((double)RP / (double)(RP + FP), 4);
}
if (RP + FN != 0)
{
Recall = Math.Round((double)RP / (double)(RP + FN), 4);
}
if (Precision + Recall != 0.0)
{
F_Score = Math.Round(2 * Precision * Recall / (Precision + Recall), 4);
}
//Compute MeanRank general
double MeanRankRealPositiveGeneral = 0.0;//MeanRank RealPhenotype general
//Compute standard deviation
double StandardDeviationRankRealPositivesGeneral = 0.0;
//Filter PerDisease where MeanRankRealPositives = 0.0
List <PerDisease> perdiseasesFiltered = results.perDisease.Where(pd => pd.MeanRankRealPositives != 0.0).ToList();
if (perdiseasesFiltered.Count != 0)
{
MeanRankRealPositiveGeneral = perdiseasesFiltered.Average(pd => pd.MeanRankRealPositives);
StandardDeviationRankRealPositivesGeneral =
Math.Sqrt
(
perdiseasesFiltered.Average
(
pd => Math.Pow(pd.MeanRankRealPositives - MeanRankRealPositiveGeneral, 2)
)
);
}
//Compute MeanNumberOfRelatedEntitiesFound
double MeanNumberOfRelatedEntitiesFound = results.perDisease.Average(pd => pd.NumberOfRelatedEntitiesFound);
//Compute standard deviation
double StandardDeviationNumberOfRelatedEntitiesFound =
Math.Sqrt
(
results.perDisease.Average
(
pd => Math.Pow(pd.NumberOfRelatedEntitiesFound - MeanNumberOfRelatedEntitiesFound, 2)
)
);
//Construct results object
results.general = new General(
DateTime.Now,
NumberOfDiseasesWithKnownPhenotypes,
NumberOfDiseasesWithPublicationsInPredictionData,
NumberOfDiseasesEvaluatedForReal,
PredictionData.Type,
MeanNumberOfRelatedEntitiesFound,
StandardDeviationNumberOfRelatedEntitiesFound,
WeightCombinaison.Item1,
WeightCombinaison.Item2,
threshold,
RP,
FP,
FN,
Precision,
Recall,
F_Score,
MeanRankRealPositiveGeneral,
StandardDeviationRankRealPositivesGeneral);
return(results);
}
