Changeset 12891 for branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/TreeMatching

Timestamp:

08/22/15 14:27:37 (9 years ago)

Author:

bburlacu

Message:

#1772: Merge trunk changes. Remove dead code from the genealogy analyzer.

Location:

branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic

Files:

• . (modified) (1 prop)
• 3.4/TreeMatching/SymbolicExpressionTreeBottomUpSimilarityCalculator.cs (modified) (5 diffs)
• 3.4/TreeMatching/SymbolicExpressionTreeNodeComparer.cs (modified) (3 diffs)
• 3.4/TreeMatching/SymbolicExpressionTreePhenotypicSimilarityCalculator.cs (modified) (2 diffs)

branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/TreeMatching/SymbolicExpressionTreeBottomUpSimilarityCalculator.cs

@@ -1 +1 @@
 #region License Information
+
 /* HeuristicLab
  * Copyright (C) 2002-2015 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
@@ -18 +19 @@
  * along with HeuristicLab. If not, see <http://www.gnu.org/licenses/>.
  */
-#endregion
+
+#endregion License Information
 
 using System;
@@ -32 +34 @@
 
 namespace HeuristicLab.Problems.DataAnalysis.Symbolic {
+
   [StorableClass]
   [Item("SymbolicExpressionTreeBottomUpSimilarityCalculator", "A similarity calculator which uses the tree bottom-up distance as a similarity metric.")]
@@ -37 +40 @@
     private readonly HashSet<string> commutativeSymbols = new HashSet<string> { "Addition", "Multiplication", "Average", "And", "Or", "Xor" };
 
-    public SymbolicExpressionTreeBottomUpSimilarityCalculator() { }
+    public SymbolicExpressionTreeBottomUpSimilarityCalculator() {
+    }
+
     protected override bool IsCommutative { get { return true; } }
 
@@ -107 +112 @@
 
         // at this point we know that v and w are isomorphic, however, the mapping cannot be done directly
-        // (as in the paper) because the trees are unordered (subtree order might differ). the solution is 
+        // (as in the paper) because the trees are unordered (subtree order might differ). the solution is
         // to sort subtrees from under commutative labels (this will work because the subtrees are isomorphic!)
         // while iterating over the two subtrees

branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/TreeMatching/SymbolicExpressionTreeNodeComparer.cs

@@ -18 +18 @@
  * along with HeuristicLab. If not, see <http://www.gnu.org/licenses/>.
  */
-#endregion
+#endregion License Information
 
 using System;
@@ -29 +29 @@
   // - used for bringing subtrees to a "canonical" form when the operation allows reordering of arguments
   public class SymbolicExpressionTreeNodeComparer : ISymbolicExpressionTreeNodeComparer {
+
     public static int CompareNodes(ISymbolicExpressionTreeNode a, ISymbolicExpressionTreeNode b) {
       var ta = a as SymbolicExpressionTreeTerminalNode;
@@ -69 +70 @@
     }
   }
-
 }

branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/TreeMatching/SymbolicExpressionTreePhenotypicSimilarityCalculator.cs

@@ -65 +65 @@
 
       OnlineCalculatorError error;
-      var r2 = OnlinePearsonsRSquaredCalculator.Calculate(v1, v2, out error);
+      var r = OnlinePearsonsRCalculator.Calculate(v1, v2, out error);
+
+      var r2 = error == OnlineCalculatorError.None ? r * r : 0;
 
       if (r2 > 1.0)
         r2 = 1.0;
 
-      return error == OnlineCalculatorError.None ? r2 : 0;
+      return r2;
     }
 
@@ -87 +89 @@
 
       OnlineCalculatorError error;
-      var r2 = OnlinePearsonsRSquaredCalculator.Calculate(leftValues, rightValues, out error);
+      var r = OnlinePearsonsRCalculator.Calculate(leftValues, rightValues, out error);
+
+      var r2 = error == OnlineCalculatorError.None ? r * r : 0;
 
       if (r2 > 1.0)
-        r2 = 1.0; // sometimes due to fp errors it can happen that the r2 is over 1 (like 1.0000000009)
+        r2 = 1.0;
 
-      return error == OnlineCalculatorError.None ? r2 : 0;
+      return r2;
     }
   }