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Changeset 11672 for branches

Timestamp:

12/09/14 14:25:57 (10 years ago)

Author:

bgoldman

Message:

#2282 Commenting, added some basic unit tests for P3.

Location:

branches/Parameter-less Population Pyramid

Files:

-                      r11668
+                      r11672
   [StorableClass]
   [Creatable("Parameterless Population Pyramid")]
+  // In the GECCO paper, Section 2.1
   public class HillClimber : AlgorithmBase {
     [Storable]
 …
+      }
+    }
     public static double ImproveToLocalOptimum(IBinaryVectorProblem problem, bool[] solution, double fitness, IRandom rand) {
       var tried = new HashSet<int>();

r11667	r11672
29	29	namespace HeuristicLab.Algorithms.ParameterlessPopulationPyramid {
30	30	public static class LinkageCrossover {
31
	31	// In the GECCO paper, Figure 3
32	32	public static double ImproveUsingTree(LinkageTree tree, IList<bool[]> donors, bool[] solution, double fitness, IBinaryVectorProblem problem, IRandom rand) {
33	33	var options = Enumerable.Range(0, donors.Count).ToArray();

-                      r11669
+                      r11672
     // While "total" always has an integer value, it is a double to reduce
     // how often type casts are needed to prevent integer divison
+    // In the GECCO paper, calculates Equation 2
     private static double NegativeEntropy(int[] counts, double total) {
       double sum = 0;
 …
+    }
+    // Uses the frequency table to calcuate the entropy distance between two indices.
+    // In the GECCO paper, calculates Equation 1
     private double EntropyDistance(int i, int j) {
       // This ensures you are using the lower triangular part of "occurances"
 …
+    }
+    // Performs O(N^2) clustering based on the method described in:
+    // "Optimal implementations of UPGMA and other common clustering algorithms"
+    // by I. Gronau and S. Moran
+    // In the GECCO paper, Figure 2 is a simplified version of this algorithm.
     private void Rebuild() {
       // Keep track of which clusters have not been merged
 …
           topLevel.Swap(end_of_path, best_index);
           end_of_path++;
+        }
         // Last two elements in the path are the clusters to join

r11669	r11672
31	31	[StorableClass]
32	32	[Creatable("Parameterless Population Pyramid")]
	33	// In the GECCO paper, Section 4.1
33	34	public class DeceptiveStepTrapProblem : DeceptiveTrapProblem {
34	35	[StorableConstructor]

-                      r11669
+                      r11672
   [StorableClass]
   [Creatable("Parameterless Population Pyramid")]
+  // In the GECCO paper, Section 4.1
   public class DeceptiveTrapProblem : BinaryVectorProblem {
     [StorableConstructor]
 …
+    }
+    // In the GECCO paper, calculates Equation 3
     protected virtual int Score(bool[] individual, int trapIndex) {
       int result = 0;
+      // count number of bits in trap set to 1
       for (int index = trapIndex; index < trapIndex + TrapSize; index++) {
         if (individual[index]) result++;

-                      r11669
+                      r11672
 using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
 namespace HeuristicLab.Algorithms.ParameterlessPopulationPyramid.Problems {
+namespace HeuristicLab.Algorithms.ParameterlessPopulationPyramid {
   [Item("Hierararchical If and only If problem", "Genome evaluated in nested subsets to see if each subset contains either all 0s or all 1s.")]
   [StorableClass]
   [Creatable("Parameterless Population Pyramid")]
+  // In the GECCO paper, Section 4.1
   public class HIFFProblem : BinaryVectorProblem {
     [StorableConstructor]

-                      r11667
+                      r11672
       <HintPath>..\HeuristicLab.Algorithms.ParameterlessPopulationPyramid\3.3\obj\Release\HeuristicLab.Algorithms.ParameterlessPopulationPyramid-3.3.dll</HintPath>
     </Reference>
+    <Reference Include="HeuristicLab.Analysis-3.3">
+      <HintPath>..\..\..\trunk\sources\bin\HeuristicLab.Analysis-3.3.dll</HintPath>
+    </Reference>
     <Reference Include="HeuristicLab.Common-3.3">
       <HintPath>..\..\..\trunk\sources\bin\HeuristicLab.Common-3.3.dll</HintPath>
 …
     <Reference Include="HeuristicLab.Core-3.3">
       <HintPath>..\..\..\trunk\sources\bin\HeuristicLab.Core-3.3.dll</HintPath>
+    </Reference>
+    <Reference Include="HeuristicLab.Encodings.BinaryVectorEncoding-3.3">
+      <HintPath>..\..\..\trunk\sources\bin\HeuristicLab.Encodings.BinaryVectorEncoding-3.3.dll</HintPath>
+    </Reference>
+    <Reference Include="HeuristicLab.Optimization-3.3">
+      <HintPath>..\..\..\trunk\sources\bin\HeuristicLab.Optimization-3.3.dll</HintPath>
     </Reference>
     <Reference Include="HeuristicLab.Random-3.3">
 …
     <Compile Include="EnumerableBoolEqualityComparerTest.cs" />
     <Compile Include="LinkageTreeTest.cs" />
+    <Compile Include="ParameterlessPopulationPyramidTest.cs" />
     <Compile Include="Properties\AssemblyInfo.cs" />
   </ItemGroup>

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