Changeset 11638 for branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic

Timestamp:

12/03/14 17:04:46 (10 years ago)

Author:

bburlacu

Message:

#1772: Merged trunk changes. Updated PhenotypicSimilarityCalculator, updated FragmentGraphView.

Location:

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

Files:

• . (modified) (1 prop)
• 3.4/Analyzers/SymbolicDataAnalysisUsefulGenesAnalyzer.cs (modified) (1 diff)
• 3.4/Formatters/SymbolicDataAnalysisExpressionExcelFormatter.cs (modified) (1 diff)
• 3.4/HeuristicLab.Problems.DataAnalysis.Symbolic-3.4.csproj (modified) (8 diffs)
• 3.4/Matching/SymbolicExpressionTreeNodeComparer.cs (modified) (2 diffs)
• 3.4/SimilarityCalculators (modified) (1 prop)
• 3.4/SimilarityCalculators/BottomUpSimilarityCalculator.cs (modified) (1 prop)
• 3.4/SimilarityCalculators/PhenotypicSimilarityCalculator.cs (modified) (3 diffs)
• 3.4/Tracking/TraceCalculator.cs (modified) (1 diff)

branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisUsefulGenesAnalyzer.cs

@@ -219 +219 @@
       }
 
-      avgQualityImprovement /= replacedTrees;
-      avgLengthReduction = (int)Math.Round((double)avgLengthReduction / replacedTrees);
+      avgQualityImprovement = replacedTrees == 0 ? 0 : avgQualityImprovement / replacedTrees;
+      avgLengthReduction = replacedTrees == 0 ? 0 : (int)Math.Round((double)avgLengthReduction / replacedTrees);
 
       var results = ResultCollectionParameter.ActualValue;

branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Formatters/SymbolicDataAnalysisExpressionExcelFormatter.cs

@@ -203 +203 @@
         stringBuilder.Append(FormatRecursively(node.GetSubtree(1)));
         stringBuilder.Append(",0))");
+      } else if (symbol is IfThenElse) {
+        stringBuilder.Append("IF(");
+        stringBuilder.Append("(" + FormatRecursively(node.GetSubtree(0)) + " ) > 0");
+        stringBuilder.Append(",");
+        stringBuilder.Append(FormatRecursively(node.GetSubtree(1)));
+        stringBuilder.Append(",");
+        stringBuilder.Append(FormatRecursively(node.GetSubtree(2)));
+        stringBuilder.Append(")");
+      } else if (symbol is VariableCondition) {
+        VariableConditionTreeNode variableConditionTreeNode = node as VariableConditionTreeNode;
+        double threshold = variableConditionTreeNode.Threshold;
+        double slope = variableConditionTreeNode.Slope;
+        string p = "(1 / (1 + EXP(-" + slope.ToString(CultureInfo.InvariantCulture) + "* (" + GetColumnToVariableName(variableConditionTreeNode.VariableName) + "-" + threshold.ToString(CultureInfo.InvariantCulture) + "))))";
+        stringBuilder.Append("INT((");
+        stringBuilder.Append(FormatRecursively(node.GetSubtree(0)));
+        stringBuilder.Append("*");
+        stringBuilder.Append(p);
+        stringBuilder.Append(") + (");
+        stringBuilder.Append(FormatRecursively(node.GetSubtree(1)));
+        stringBuilder.Append("*(");
+        stringBuilder.Append("1 - " + p + ")");
+        stringBuilder.Append("))");
+      } else if (symbol is Xor) {
+        stringBuilder.Append("IF(");
+        stringBuilder.Append("XOR(");
+        stringBuilder.Append("(" + FormatRecursively(node.GetSubtree(0)) + ") > 0,");
+        stringBuilder.Append("(" + FormatRecursively(node.GetSubtree(1)) + ") > 0");
+        stringBuilder.Append("), 1.0, -1.0)");
+      } else if (symbol is Or) {
+        stringBuilder.Append("IF(");
+        stringBuilder.Append("OR(");
+        stringBuilder.Append("(" + FormatRecursively(node.GetSubtree(0)) + ") > 0,");
+        stringBuilder.Append("(" + FormatRecursively(node.GetSubtree(1)) + ") > 0");
+        stringBuilder.Append("), 1.0, -1.0)");
+      } else if (symbol is And) {
+        stringBuilder.Append("IF(");
+        stringBuilder.Append("AND(");
+        stringBuilder.Append("(" + FormatRecursively(node.GetSubtree(0)) + ") > 0,");
+        stringBuilder.Append("(" + FormatRecursively(node.GetSubtree(1)) + ") > 0");
+        stringBuilder.Append("), 1.0, -1.0)");
+      } else if (symbol is Not) {
+        stringBuilder.Append("IF(");
+        stringBuilder.Append(FormatRecursively(node.GetSubtree(0)));
+        stringBuilder.Append(" > 0, -1.0, 1.0)");
+      } else if (symbol is GreaterThan) {
+        stringBuilder.Append("IF((");
+        stringBuilder.Append(FormatRecursively(node.GetSubtree(0)));
+        stringBuilder.Append(") > (");
+        stringBuilder.Append(FormatRecursively(node.GetSubtree(1)));
+        stringBuilder.Append("), 1.0, -1.0)");
+      } else if (symbol is LessThan) {
+        stringBuilder.Append("IF((");
+        stringBuilder.Append(FormatRecursively(node.GetSubtree(0)));
+        stringBuilder.Append(") < (");
+        stringBuilder.Append(FormatRecursively(node.GetSubtree(1)));
+        stringBuilder.Append("), 1.0, -1.0)");
       } else {
         throw new NotImplementedException("Excel export of " + node.Symbol + " is not implemented.");

branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/HeuristicLab.Problems.DataAnalysis.Symbolic-3.4.csproj

@@ -11 +11 @@
     <RootNamespace>HeuristicLab.Problems.DataAnalysis.Symbolic</RootNamespace>
     <AssemblyName>HeuristicLab.Problems.DataAnalysis.Symbolic-3.4</AssemblyName>
-    <TargetFrameworkVersion>v4.0</TargetFrameworkVersion>
+    <TargetFrameworkVersion>v4.5</TargetFrameworkVersion>
     <TargetFrameworkProfile>
     </TargetFrameworkProfile>
@@ -46 +46 @@
     <WarningLevel>4</WarningLevel>
     <CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
+    <Prefer32Bit>false</Prefer32Bit>
   </PropertyGroup>
   <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|AnyCPU' ">
@@ -55 +56 @@
     <WarningLevel>4</WarningLevel>
     <CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
+    <Prefer32Bit>false</Prefer32Bit>
   </PropertyGroup>
   <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|x64' ">
@@ -64 +66 @@
     <ErrorReport>prompt</ErrorReport>
     <CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
+    <Prefer32Bit>false</Prefer32Bit>
   </PropertyGroup>
   <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|x64' ">
@@ -73 +76 @@
     <ErrorReport>prompt</ErrorReport>
     <CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
+    <Prefer32Bit>false</Prefer32Bit>
   </PropertyGroup>
   <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Debug|x86' ">
@@ -82 +86 @@
     <ErrorReport>prompt</ErrorReport>
     <CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
+    <Prefer32Bit>false</Prefer32Bit>
   </PropertyGroup>
   <PropertyGroup Condition=" '$(Configuration)|$(Platform)' == 'Release|x86' ">
@@ -91 +96 @@
     <ErrorReport>prompt</ErrorReport>
     <CodeAnalysisRuleSet>AllRules.ruleset</CodeAnalysisRuleSet>
+    <Prefer32Bit>false</Prefer32Bit>
   </PropertyGroup>
   <ItemGroup>
@@ -194 +200 @@
     </Compile>
     <Compile Include="Analyzers\SymbolicDataAnalysisUsefulGenesAnalyzer.cs" />
+    <Compile Include="Crossovers\SymbolicDataAnalysisExpressionDiversityPreservingCrossover.cs" />
     <Compile Include="Importer\SymbolicExpressionImporter.cs" />
     <Compile Include="Importer\Token.cs" />

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

@@ -1 @@
-using System;
+#region License Information
+/* HeuristicLab
+ * Copyright (C) 2002-2014 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
+ *
+ * This file is part of HeuristicLab.
+ *
+ * HeuristicLab is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * HeuristicLab is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with HeuristicLab. If not, see <http://www.gnu.org/licenses/>.
+ */
+#endregion
+
+using System;
 using HeuristicLab.Encodings.SymbolicExpressionTreeEncoding;
 
@@ -9 +30 @@
   public class SymbolicExpressionTreeNodeComparer : ISymbolicExpressionTreeNodeComparer {
     public int Compare(ISymbolicExpressionTreeNode a, ISymbolicExpressionTreeNode b) {
-      if (!(a is SymbolicExpressionTreeTerminalNode)) {
-        return b is SymbolicExpressionTreeTerminalNode
-          ? -1
-          : string.Compare(a.Symbol.Name, b.Symbol.Name, StringComparison.Ordinal);
-      }
-      if (!(b is SymbolicExpressionTreeTerminalNode)) return 1;
-      // at this point we know a and b are terminal nodes
+      var ta = a as SymbolicExpressionTreeTerminalNode;
+      var tb = b as SymbolicExpressionTreeTerminalNode;
+
+      if (ta == null)
+        return tb == null ? String.CompareOrdinal(a.Symbol.Name, b.Symbol.Name) : -1;
+
+      if (tb == null)
+        return 1;
+
+      // at this point we know a and b are both terminals
       var va = a as VariableTreeNode;
-      if (va != null) {
-        if (b is ConstantTreeNode) return -1;
-        var vb = (VariableTreeNode)b;
-        return (va.VariableName.Equals(vb.VariableName)
-          ? va.Weight.CompareTo(vb.Weight)
-          : string.Compare(va.VariableName, vb.VariableName, StringComparison.Ordinal));
-      }
-      // at this point we know for sure that a is a constant tree node
-      if (b is VariableTreeNode) return 1;
-      var ca = (ConstantTreeNode)a;
-      var cb = (ConstantTreeNode)b;
-      return ca.Value.CompareTo(cb.Value);
+      var vb = b as VariableTreeNode;
+
+      if (va != null)
+        return vb == null ? -1 : CompareVariables(va, vb);
+
+      if (vb != null)
+        return 1;
+
+      // at this point we know a and b are not variables
+      var ca = a as ConstantTreeNode;
+      var cb = b as ConstantTreeNode;
+
+      if (ca != null && cb != null)
+        return ca.Value.CompareTo(cb.Value);
+
+      // for other unknown terminal types, compare strings
+      return string.CompareOrdinal(a.ToString(), b.ToString());
+    }
+
+    private static int CompareVariables(VariableTreeNode a, VariableTreeNode b) {
+      int result = string.CompareOrdinal(a.VariableName, b.VariableName);
+      return result == 0 ? a.Weight.CompareTo(b.Weight) : result;
     }
   }
+
 }

branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/SimilarityCalculators/PhenotypicSimilarityCalculator.cs

@@ -31 +31 @@
   [StorableClass]
   public class PhenotypicSimilarityCalculator : SingleObjectiveSolutionSimilarityCalculator, ISymbolicDataAnalysisExpressionSimilarityCalculator {
+    public IDataAnalysisProblemData ProblemData { get; set; }
+    public ISymbolicDataAnalysisExpressionTreeInterpreter Interpreter { get; set; }
+
     public PhenotypicSimilarityCalculator(PhenotypicSimilarityCalculator original, Cloner cloner)
       : base(original, cloner) {
@@ -45 +48 @@
 
     public double CalculateSimilarity(ISymbolicExpressionTree t1, ISymbolicExpressionTree t2) {
-      throw new System.NotImplementedException();
+      var v1 = Interpreter.GetSymbolicExpressionTreeValues(t1, ProblemData.Dataset, ProblemData.TrainingIndices);
+      var v2 = Interpreter.GetSymbolicExpressionTreeValues(t2, ProblemData.Dataset, ProblemData.TrainingIndices);
+
+      OnlineCalculatorError error;
+      var r2 = OnlinePearsonsRSquaredCalculator.Calculate(v1, v2, out error);
+
+      if (r2 > 1.0)
+        r2 = 1.0;
+
+      return error == OnlineCalculatorError.None ? r2 : 0;
     }
 
@@ -57 +69 @@
         r2 = 1.0; // sometimes due to fp errors it can happen that the r2 is over 1 (like 1.0000000009)
 
-      return error != OnlineCalculatorError.None ? 0 : r2;
+      return error == OnlineCalculatorError.None ? r2 : 0;
     }
   }

branches/HeuristicLab.EvolutionTracking/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Tracking/TraceCalculator.cs

@@ -90 +90 @@
         var fragment = (IFragment<ISymbolicExpressionTreeNode>)g.InArcs.Last().Data;
         if (fragment == null) {
+          //          if (parents.Count == 2)
+          //            throw new Exception("There should always be a crossover fragment.");
           // the node is either an elite node or (in rare cases) no fragment was transferred
           g = parents[0];