Changeset 11672 for branches/Parameter-less Population Pyramid/HeuristicLab.Algorithms.ParameterlessPopulationPyramid/3.3/LinkageTree.cs

Timestamp:

12/09/14 14:25:57 (9 years ago)

Author:

bgoldman

Message:

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

File:

• branches/Parameter-less Population Pyramid/HeuristicLab.Algorithms.ParameterlessPopulationPyramid/3.3/LinkageTree.cs (modified) (4 diffs)

branches/Parameter-less Population Pyramid/HeuristicLab.Algorithms.ParameterlessPopulationPyramid/3.3/LinkageTree.cs

@@ -75 +75 @@
     // 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;
@@ -85 +86 @@
     }
 
+    // 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"
@@ -111 +114 @@
     }
 
+    // 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
@@ -160 +167 @@
           topLevel.Swap(end_of_path, best_index);
           end_of_path++;
-
         }
         // Last two elements in the path are the clusters to join