Changeset 7783 for branches/FitnessLandscapeAnalysis/HeuristicLab.Analysis.FitnessLandscape/Analysis

Timestamp:

05/07/12 15:14:47 (13 years ago)

Author:

epitzer

Message:

#1696 add neutrality breadth analysis by including and analyzing the number of possible neutral neighbors both overall and inside neutral areas

File:

• branches/FitnessLandscapeAnalysis/HeuristicLab.Analysis.FitnessLandscape/Analysis/NeutralityAnalyzer.cs (modified) (6 diffs)

branches/FitnessLandscapeAnalysis/HeuristicLab.Analysis.FitnessLandscape/Analysis/NeutralityAnalyzer.cs

@@ -48 +48 @@
       get { return (LookupParameter<DoubleValue>)Parameters["CurrentNeutralDistance"]; }
     }
+    public LookupParameter<DoubleValue> CurrentFractionOfNeutralNeighborsParameter {
+      get { return (LookupParameter<DoubleValue>)Parameters["CurrentFractionOfNeutralNeighbors"]; }
+    }
     public LookupParameter<DataTable> NeutralWalkDistancesTableParameter {
       get { return (LookupParameter<DataTable>)Parameters["NeutralWalkDistancesTable"]; }
@@ -57 +60 @@
       get { return (LookupParameter<DoubleValue>)Parameters["AverageNeutralWalkDistance"]; }
     }
+    public LookupParameter<DoubleValue> AverageNeutralNeighborFractionParameter {
+      get { return (LookupParameter<DoubleValue>)Parameters["AverageNeutralNeighborFraction"]; }
+    }
+    public LookupParameter<DoubleValue> AverageInnerNeutralNeighborFractionParameter {
+      get { return (LookupParameter<DoubleValue>)Parameters["AverageInnerNeutralNeighborFraction"]; }
+    }
     public LookupParameter<DoubleValue> NeutralWalkLengthVarianceParameter {
       get { return (LookupParameter<DoubleValue>)Parameters["NeutralWalkLengthVariance"]; }
@@ -63 +72 @@
       get { return (LookupParameter<DoubleValue>)Parameters["NeutralWalkDistanceVariance"]; }
     }        
+    public LookupParameter<DoubleValue> NeutralNeighborFractionVarianceParameter {
+      get { return (LookupParameter<DoubleValue>)Parameters["NeutralNeighborFractionVariance"]; }
+    }
+    public LookupParameter<DoubleValue> InnerNeutralNeighborFractionVarianceParameter {
+      get { return (LookupParameter<DoubleValue>)Parameters["InnerNeutralNeighborFractionVariance"]; }
+    }
     public LookupParameter<VariableCollection> ResultsParameter {
       get { return (LookupParameter<VariableCollection>)Parameters["Results"]; }
@@ -75 +90 @@
       Parameters.Add(new LookupParameter<DoubleValue>("Quality", "The current quality"));
       Parameters.Add(new LookupParameter<DoubleValue>("CurrentNeutralDistance", "The distance of the current solution to the starting point of the neutral (portion of the) walk."));
+      Parameters.Add(new LookupParameter<DoubleValue>("CurrentFractionOfNeutralNeighbors", "The current fraction of neighbors with the same fitness (within epsilon)"));
       Parameters.Add(new LookupParameter<DataTable>("NeutralWalkDistancesTable", "The historical values of the current neutral distance."));
       Parameters.Add(new LookupParameter<DoubleValue>("AverageNeutralWalkLength", "The average length of a neutral walk"));
       Parameters.Add(new LookupParameter<DoubleValue>("AverageNeutralWalkDistance", "The average distance of the neutral walk to the starting point."));
+      Parameters.Add(new LookupParameter<DoubleValue>("AverageNeutralNeighborFraction", "The average fraction of neutral neighbors overall."));
+      Parameters.Add(new LookupParameter<DoubleValue>("AverageInnerNeutralNeighborFraction", "The average fraction of neutral neighbors within a neutral area."));
       Parameters.Add(new LookupParameter<DoubleValue>("NeutralWalkLengthVariance", "The variance of the neutral walks lengths"));
       Parameters.Add(new LookupParameter<DoubleValue>("NeutralWalkDistanceVariance", "The varaince of the neutral walks distances"));
+      Parameters.Add(new LookupParameter<DoubleValue>("NeutralNeighborFractionVariance", "The average fraction of neutral neighbors overall."));
+      Parameters.Add(new LookupParameter<DoubleValue>("InnerNeutralNeighborFractionVariance", "The average fraction of neutral neighbors within a neutral area."));
 
       var resultsCollector = new ResultsCollector();
       resultsCollector.CollectedValues.Add(new LookupParameter<DoubleValue>(CurrentNeutralDistanceParameter.ActualName));
+      resultsCollector.CollectedValues.Add(new LookupParameter<DoubleValue>(CurrentFractionOfNeutralNeighborsParameter.ActualName));
       resultsCollector.CollectedValues.Add(new LookupParameter<DataTable>(NeutralWalkDistancesTableParameter.Name));
       resultsCollector.CollectedValues.Add(new LookupParameter<DoubleValue>(AverageNeutralWalkLengthParameter.Name));
       resultsCollector.CollectedValues.Add(new LookupParameter<DoubleValue>(AverageNeutralWalkDistanceParameter.Name));
+      resultsCollector.CollectedValues.Add(new LookupParameter<DoubleValue>(AverageNeutralNeighborFractionParameter.Name));
+      resultsCollector.CollectedValues.Add(new LookupParameter<DoubleValue>(AverageInnerNeutralNeighborFractionParameter.Name));
       resultsCollector.CollectedValues.Add(new LookupParameter<DoubleValue>(NeutralWalkLengthVarianceParameter.Name));
       resultsCollector.CollectedValues.Add(new LookupParameter<DoubleValue>(NeutralWalkDistanceVarianceParameter.Name));
+      resultsCollector.CollectedValues.Add(new LookupParameter<DoubleValue>(NeutralNeighborFractionVarianceParameter.Name));
+      resultsCollector.CollectedValues.Add(new LookupParameter<DoubleValue>(InnerNeutralNeighborFractionVarianceParameter.Name));
 
       OperatorGraph.InitialOperator = resultsCollector;
@@ -99 +124 @@
     public override IOperation Apply() {
       DataTable distanceTable = GetOrCreateDistanceTable();
-      var values = distanceTable.Rows["Neutral Walk Distances"].Values;
-      values.Add(CurrentNeutralDistanceParameter.ActualValue == null ? 0 : CurrentNeutralDistanceParameter.ActualValue.Value);
-      List<double> lenghts = new List<double>();
-      List<double> distances = new List<double>();
+      var distanceValues = distanceTable.Rows["Neutral Walk Distances"].Values;
+      var fractionValues = distanceTable.Rows["Neutral Neighbor Fractions"].Values;
+      distanceValues.Add(CurrentNeutralDistanceParameter.ActualValue == null ? 0 : CurrentNeutralDistanceParameter.ActualValue.Value);
+      fractionValues.Add(CurrentFractionOfNeutralNeighborsParameter.ActualValue == null ? 0 : CurrentFractionOfNeutralNeighborsParameter.ActualValue.Value);
+      var lengths = new List<double>();
+      var distances = new List<double>();
+      var innerFractions = new List<double>();
       double lastValue = -1;
       int lastStart = 0;
-      for (int i = 0; i<values.Count; i++) {
-        if (values[i] < lastValue) {
-          lenghts.Add(i - lastStart - 1);
+      for (int i = 0; i<distanceValues.Count; i++) {
+        if (distanceValues[i] < lastValue) { // restart
+          lengths.Add(i - lastStart - 1);
           distances.Add(lastValue);
           lastStart = i;
+        } else { // inside neutral area
+          innerFractions.Add(fractionValues[i]);
         }
-        lastValue = values[i];
+        lastValue = distanceValues[i];
       }
-      if (distances.Count > 0 && lenghts.Count > 0) {
+      if (lastStart != distanceValues.Count-1) {
+        lengths.Add(distanceValues.Count - lastStart - 1);
+        distances.Add(lastValue);
+      }
+      if (distances.Count > 0 && lengths.Count > 0) {
         AverageNeutralWalkDistanceParameter.ActualValue = new DoubleValue(distances.Average());
         NeutralWalkDistanceVarianceParameter.ActualValue = new DoubleValue(distances.Variance());
-        AverageNeutralWalkLengthParameter.ActualValue = new DoubleValue(lenghts.Average());
-        NeutralWalkLengthVarianceParameter.ActualValue = new DoubleValue(lenghts.Variance());
+        AverageNeutralWalkLengthParameter.ActualValue = new DoubleValue(lengths.Average());
+        NeutralWalkLengthVarianceParameter.ActualValue = new DoubleValue(lengths.Variance());
+        AverageNeutralNeighborFractionParameter.ActualValue = new DoubleValue(fractionValues.Average());
+        NeutralNeighborFractionVarianceParameter.ActualValue = new DoubleValue(fractionValues.Variance());
+        AverageInnerNeutralNeighborFractionParameter.ActualValue = new DoubleValue(innerFractions.Average());
+        InnerNeutralNeighborFractionVarianceParameter.ActualValue = new DoubleValue(innerFractions.Variance());
       }
       return base.Apply();
@@ -127 +165 @@
         distancesTable = new DataTable("Neutral Walk Distances");
         NeutralWalkDistancesTableParameter.ActualValue = distancesTable;
-        var row = new DataRow("Neutral Walk Distances");
-        distancesTable.Rows.Add(row);
+        distancesTable.Rows.Add(new DataRow("Neutral Walk Distances"));
+        distancesTable.Rows.Add(new DataRow("Neutral Neighbor Fractions") {VisualProperties = {SecondYAxis = true}});
       }
       return distancesTable;