From 57b63669a31c8e6b1b79954d5093713e79028afa Mon Sep 17 00:00:00 2001
From: Michael Stachowicz <15214467+ethiril@users.noreply.github.com>
Date: Thu, 8 Dec 2022 15:41:41 +0000
Subject: [PATCH 1/2] Create GPTGeneratedFitness.cs

---
 .../SNP_Evolution/GPTGeneratedFitness.cs      | 59 +++++++++++++++++++
 1 file changed, 59 insertions(+)
 create mode 100644 SNP_Evolution/SNP_Evolution/GPTGeneratedFitness.cs

diff --git a/SNP_Evolution/SNP_Evolution/GPTGeneratedFitness.cs b/SNP_Evolution/SNP_Evolution/GPTGeneratedFitness.cs
new file mode 100644
index 0000000..c943903
--- /dev/null
+++ b/SNP_Evolution/SNP_Evolution/GPTGeneratedFitness.cs
@@ -0,0 +1,59 @@
+private static float FitnessFunction(int index, Func<List<int>, List<int>, float> fitnessAlgorithm)
+{
+    DNA dna = ga.Population[index];
+    List<int> output = SNPRun(dna.Genes);
+    float fitness = fitnessAlgorithm(output, expectedSet);
+
+    if (fitness >= 0.985 && fitness <= 1)
+    {
+        Console.WriteLine("Testing the best fitness for repeated success.");
+        if (TestBestNetwork(ga.BestGenes, ga.BestFitness))
+        {
+            Console.WriteLine("Fitness over 0.985, stopping . . .");
+            active = false;
+        }
+    }
+
+    return fitness;
+}
+
+private static float CalculateF1Score(List<int> output, List<int> expectedSet)
+{
+    if (output.Count == 0)
+    {
+        return 0;
+    }
+
+    int truePositives = expectedSet.Intersect(output).Count();
+    int falsePositives = output.Count - truePositives;
+
+    float sensitivity = truePositives / (float)expectedSet.Count;
+    float precision = truePositives / (truePositives + falsePositives);
+
+    return 2 * ((precision * sensitivity) / (precision + sensitivity));
+}
+
+private static float CalculateJaccardIndex(List<int> output, List<int> expectedSet)
+{
+    if (output.Count == 0)
+    {
+        return 0;
+    }
+
+    return (float)expectedSet.Intersect(output).Count() / expectedSet.Union(output).Count();
+}
+
+private static float CalculateMatthewsCorrelationCoefficient(List<int> output, List<int> expectedSet)
+{
+    if (output.Count == 0)
+    {
+        return 0;
+    }
+
+    int truePositives = expectedSet.Intersect(output).Count();
+    int falsePositives = output.Count - truePositives;
+    int falseNegatives = expectedSet.Count - truePositives;
+
+    return (truePositives * truePositives - falsePositives * falseNegatives) /
+        (float)(Math.Sqrt((truePositives + falsePositives) * (truePositives + falseNegatives) * (falsePositives + truePositives) * (falsePositives + falseNegatives)));
+}

From 87c0a10afa7088461d0464ed665d959cb948652d Mon Sep 17 00:00:00 2001
From: Michael Stachowicz <15214467+ethiril@users.noreply.github.com>
Date: Tue, 18 Apr 2023 16:17:45 +0100
Subject: [PATCH 2/2] Update GPTGeneratedFitness.cs

---
 SNP_Evolution/SNP_Evolution/GPTGeneratedFitness.cs | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/SNP_Evolution/SNP_Evolution/GPTGeneratedFitness.cs b/SNP_Evolution/SNP_Evolution/GPTGeneratedFitness.cs
index c943903..82c8d4f 100644
--- a/SNP_Evolution/SNP_Evolution/GPTGeneratedFitness.cs
+++ b/SNP_Evolution/SNP_Evolution/GPTGeneratedFitness.cs
@@ -4,7 +4,7 @@ private static float FitnessFunction(int index, Func<List<int>, List<int>, float
     List<int> output = SNPRun(dna.Genes);
     float fitness = fitnessAlgorithm(output, expectedSet);
 
-    if (fitness >= 0.985 && fitness <= 1)
+    if (fitness >= 0.985f && fitness <= 1f)
     {
         Console.WriteLine("Testing the best fitness for repeated success.");
         if (TestBestNetwork(ga.BestGenes, ga.BestFitness))
@@ -27,10 +27,10 @@ private static float CalculateF1Score(List<int> output, List<int> expectedSet)
     int truePositives = expectedSet.Intersect(output).Count();
     int falsePositives = output.Count - truePositives;
 
-    float sensitivity = truePositives / (float)expectedSet.Count;
-    float precision = truePositives / (truePositives + falsePositives);
+    float sensitivity = (float)truePositives / expectedSet.Count;
+    float precision = (float)truePositives / (truePositives + falsePositives);
 
-    return 2 * ((precision * sensitivity) / (precision + sensitivity));
+    return 2f * ((precision * sensitivity) / (precision + sensitivity));
 }
 
 private static float CalculateJaccardIndex(List<int> output, List<int> expectedSet)
@@ -54,6 +54,8 @@ private static float CalculateMatthewsCorrelationCoefficient(List<int> output, L
     int falsePositives = output.Count - truePositives;
     int falseNegatives = expectedSet.Count - truePositives;
 
-    return (truePositives * truePositives - falsePositives * falseNegatives) /
-        (float)(Math.Sqrt((truePositives + falsePositives) * (truePositives + falseNegatives) * (falsePositives + truePositives) * (falsePositives + falseNegatives)));
+    float numerator = (truePositives * truePositives) - (falsePositives * falseNegatives);
+    float denominator = (float)Math.Sqrt((truePositives + falsePositives) * (truePositives + falseNegatives) * (falsePositives + truePositives) * (falsePositives + falseNegatives));
+
+    return numerator / denominator;
 }