Changeset 9126 for branches/Sliding Window GP/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers

Timestamp:

01/08/13 15:36:13 (12 years ago)

Author:

mkommend

Message:

#1837: Updated sliding window GP branch with trunk changes.

Location:

branches/Sliding Window GP/HeuristicLab.Problems.DataAnalysis.Symbolic

Files:

• . (modified) (1 prop)
• 3.4 (modified) (1 prop)
• 3.4/Analyzers/SymbolicDataAnalysisAlleleFrequencyAnalyzer.cs (modified) (2 diffs)
• 3.4/Analyzers/SymbolicDataAnalysisComplexityAnalyzer.cs (deleted)
• 3.4/Analyzers/SymbolicDataAnalysisMultiObjectiveAnalyzer.cs (modified) (4 diffs)
• 3.4/Analyzers/SymbolicDataAnalysisSingleObjectiveAnalyzer.cs (modified) (4 diffs)
• 3.4/Analyzers/SymbolicDataAnalysisSingleObjectiveTrainingBestSolutionAnalyzer.cs (modified) (1 diff)
• 3.4/Analyzers/SymbolicDataAnalysisSingleObjectiveTrainingParetoBestSolutionAnalyzer.cs (modified) (6 diffs)
• 3.4/Analyzers/SymbolicDataAnalysisSingleObjectiveValidationAnalyzer.cs (modified) (1 diff)
• 3.4/Analyzers/SymbolicDataAnalysisSingleObjectiveValidationParetoBestSolutionAnalyzer.cs (modified) (7 diffs)
• 3.4/Analyzers/SymbolicDataAnalysisVariableFrequencyAnalyzer.cs (modified) (1 diff)

branches/Sliding Window GP/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4

@@ +1 @@
+*.user
+Plugin.cs
 bin
-*.user
-HeuristicLabProblemsDataAnalysisSymbolicPlugin.cs
 obj
-*.vs10x
-Plugin.cs

@@ +1 @@
+*.user
+Plugin.cs
 bin
-*.user
-HeuristicLabProblemsDataAnalysisSymbolicPlugin.cs
 obj
-*.vs10x
-Plugin.cs

branches/Sliding Window GP/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisAlleleFrequencyAnalyzer.cs

@@ -70 +70 @@
 
     protected override Allele[] CalculateAlleles(ISymbolicExpressionTree solution) {
-      return GetAllSubtreesOfDepth(solution, AlleleTreeDepth)
+      return CalculateAlleles(solution, AlleleTreeDepth);
+    }
+
+    public static Allele[] CalculateAlleles(ISymbolicExpressionTree solution, int alleleTreedepth) {
+      return GetAllSubtreesOfDepth(solution, alleleTreedepth)
         .AsParallel()
-        .Select(t => GetAlleleFromSubtreeOfDepth(t, AlleleTreeDepth))
+        .Select(t => GetAlleleFromSubtreeOfDepth(t, alleleTreedepth))
         .ToArray();
     }
 
-    private Allele GetAlleleFromSubtreeOfDepth(ISymbolicExpressionTreeNode tree, int d) {
+    private static Allele GetAlleleFromSubtreeOfDepth(ISymbolicExpressionTreeNode tree, int d) {
       string textualRepresentation = GetTextualRepresentationFromSubtreeOfDepth(tree, d);
       return new Allele(textualRepresentation);
     }
 
-    private string GetTextualRepresentationFromSubtreeOfDepth(ISymbolicExpressionTreeNode tree, int d) {
+    private static string GetTextualRepresentationFromSubtreeOfDepth(ISymbolicExpressionTreeNode tree, int d) {
       if (d == 0) return "";
       StringBuilder builder = new StringBuilder();
@@ -100 +104 @@
     }
 
-    private IEnumerable<ISymbolicExpressionTreeNode> GetAllSubtreesOfDepth(ISymbolicExpressionTree solution, int d) {
+    private static IEnumerable<ISymbolicExpressionTreeNode> GetAllSubtreesOfDepth(ISymbolicExpressionTree solution, int d) {
       return from node in solution.IterateNodesPostfix()
              where node.GetDepth() >= d

branches/Sliding Window GP/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisMultiObjectiveAnalyzer.cs

@@ -20 +20 @@
 #endregion
 
-using System.Collections.Generic;
-using System.Linq;
 using HeuristicLab.Common;
 using HeuristicLab.Core;
 using HeuristicLab.Data;
-using HeuristicLab.Encodings.SymbolicExpressionTreeEncoding;
-using HeuristicLab.Operators;
 using HeuristicLab.Parameters;
 using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
-using HeuristicLab.Optimization;
 
 namespace HeuristicLab.Problems.DataAnalysis.Symbolic {
@@ -39 +34 @@
     private const string QualitiesParameterName = "Qualities";
     private const string MaximizationParameterName = "Maximization";
+    private const string ApplyLinearScalingParameterName = "ApplyLinearScaling";
     #region parameter properties
     public IScopeTreeLookupParameter<DoubleArray> QualitiesParameter {
@@ -45 +41 @@
     public ILookupParameter<BoolArray> MaximizationParameter {
       get { return (ILookupParameter<BoolArray>)Parameters[MaximizationParameterName]; }
+    }
+    public ILookupParameter<BoolValue> ApplyLinearScalingParameter {
+      get { return (ILookupParameter<BoolValue>)Parameters[ApplyLinearScalingParameterName]; }
     }
     #endregion
@@ -64 +63 @@
       Parameters.Add(new ScopeTreeLookupParameter<DoubleArray>(QualitiesParameterName, "The qualities of the trees that should be analyzed."));
       Parameters.Add(new LookupParameter<BoolArray>(MaximizationParameterName, "The directions of optimization for each dimension."));
+      Parameters.Add(new LookupParameter<BoolValue>(ApplyLinearScalingParameterName, "Flag that indicates if the individual should be linearly scaled before evaluating."));
+    }
+
+    [StorableHook(HookType.AfterDeserialization)]
+    private void AfterDeserialization() {
+      if (Parameters.ContainsKey(ApplyLinearScalingParameterName) && Parameters[ApplyLinearScalingParameterName] is LookupParameter<BoolValue>)
+        Parameters.Remove(ApplyLinearScalingParameterName);
+      if (!Parameters.ContainsKey(ApplyLinearScalingParameterName))
+        Parameters.Add(new LookupParameter<BoolValue>(ApplyLinearScalingParameterName, "Flag that indicates if the individual should be linearly scaled before evaluating."));
     }
   }

branches/Sliding Window GP/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisSingleObjectiveAnalyzer.cs

@@ -20 +20 @@
 #endregion
 
-using System.Collections.Generic;
-using System.Linq;
 using HeuristicLab.Common;
 using HeuristicLab.Core;
 using HeuristicLab.Data;
-using HeuristicLab.Encodings.SymbolicExpressionTreeEncoding;
-using HeuristicLab.Operators;
 using HeuristicLab.Parameters;
 using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
-using HeuristicLab.Optimization;
 
 namespace HeuristicLab.Problems.DataAnalysis.Symbolic {
@@ -39 +34 @@
     private const string QualityParameterName = "Quality";
     private const string MaximizationParameterName = "Maximization";
+    private const string ApplyLinearScalingParameterName = "ApplyLinearScaling";
+
     #region parameter properties
     public IScopeTreeLookupParameter<DoubleValue> QualityParameter {
@@ -45 +42 @@
     public ILookupParameter<BoolValue> MaximizationParameter {
       get { return (ILookupParameter<BoolValue>)Parameters[MaximizationParameterName]; }
+    }
+    public ILookupParameter<BoolValue> ApplyLinearScalingParameter {
+      get { return (ILookupParameter<BoolValue>)Parameters[ApplyLinearScalingParameterName]; }
     }
     #endregion
@@ -64 +64 @@
       Parameters.Add(new ScopeTreeLookupParameter<DoubleValue>(QualityParameterName, "The qualities of the trees that should be analyzed."));
       Parameters.Add(new LookupParameter<BoolValue>(MaximizationParameterName, "The direction of optimization."));
+      Parameters.Add(new LookupParameter<BoolValue>(ApplyLinearScalingParameterName, "Flag that indicates if the individual should be linearly scaled before evaluating."));
+    }
+
+    [StorableHook(HookType.AfterDeserialization)]
+    private void AfterDeserialization() {
+      if (Parameters.ContainsKey(ApplyLinearScalingParameterName) && !(Parameters[ApplyLinearScalingParameterName] is LookupParameter<BoolValue>))
+        Parameters.Remove(ApplyLinearScalingParameterName);
+      if (!Parameters.ContainsKey(ApplyLinearScalingParameterName))
+        Parameters.Add(new LookupParameter<BoolValue>(ApplyLinearScalingParameterName, "Flag that indicates if the individual should be linearly scaled before evaluating."));
     }
   }

branches/Sliding Window GP/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisSingleObjectiveTrainingBestSolutionAnalyzer.cs

@@ -85 +85 @@
 
       var results = ResultCollection;
-      if (TrainingBestSolutionQuality == null ||
-        IsBetter(bestQuality, TrainingBestSolutionQuality.Value, Maximization.Value)) {
+      if (bestTree != null && (TrainingBestSolutionQuality == null ||
+        IsBetter(bestQuality, TrainingBestSolutionQuality.Value, Maximization.Value))) {
         TrainingBestSolution = CreateSolution(bestTree, bestQuality);
         TrainingBestSolutionQuality = new DoubleValue(bestQuality);

branches/Sliding Window GP/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisSingleObjectiveTrainingParetoBestSolutionAnalyzer.cs

@@ -20 +20 @@
 #endregion
 
+using System;
 using System.Collections.Generic;
 using System.Linq;
@@ -26 +27 @@
 using HeuristicLab.Data;
 using HeuristicLab.Encodings.SymbolicExpressionTreeEncoding;
-using HeuristicLab.Operators;
 using HeuristicLab.Optimization;
 using HeuristicLab.Parameters;
 using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
-using System;
 
 namespace HeuristicLab.Problems.DataAnalysis.Symbolic {
@@ -38 +37 @@
   [Item("SymbolicDataAnalysisSingleObjectiveTrainingParetoBestSolutionAnalyzer", "An operator that analyzes the Pareto-best symbolic data analysis solution for single objective symbolic data analysis problems.")]
   [StorableClass]
-  public abstract class SymbolicDataAnalysisSingleObjectiveTrainingParetoBestSolutionAnalyzer<T> : SymbolicDataAnalysisSingleObjectiveAnalyzer
-    where T : class, ISymbolicDataAnalysisSolution {
+  public abstract class SymbolicDataAnalysisSingleObjectiveTrainingParetoBestSolutionAnalyzer<S, T> : SymbolicDataAnalysisSingleObjectiveAnalyzer, ISymbolicDataAnalysisInterpreterOperator, ISymbolicDataAnalysisBoundedOperator
+    where T : class, ISymbolicDataAnalysisSolution
+    where S : class, IDataAnalysisProblemData {
+    private const string ProblemDataParameterName = "ProblemData";
     private const string TrainingBestSolutionsParameterName = "Best training solutions";
     private const string TrainingBestSolutionQualitiesParameterName = "Best training solution qualities";
     private const string ComplexityParameterName = "Complexity";
+    private const string SymbolicDataAnalysisTreeInterpreterParameterName = "SymbolicDataAnalysisTreeInterpreter";
+    private const string EstimationLimitsParameterName = "EstimationLimits";
 
     public override bool EnabledByDefault {
@@ -58 +61 @@
       get { return (IScopeTreeLookupParameter<DoubleValue>)Parameters[ComplexityParameterName]; }
     }
+    public ILookupParameter<ISymbolicDataAnalysisExpressionTreeInterpreter> SymbolicDataAnalysisTreeInterpreterParameter {
+      get { return (ILookupParameter<ISymbolicDataAnalysisExpressionTreeInterpreter>)Parameters[SymbolicDataAnalysisTreeInterpreterParameterName]; }
+    }
+    public ILookupParameter<S> ProblemDataParameter {
+      get { return (ILookupParameter<S>)Parameters[ProblemDataParameterName]; }
+    }
+    public IValueLookupParameter<DoubleLimit> EstimationLimitsParameter {
+      get { return (IValueLookupParameter<DoubleLimit>)Parameters[EstimationLimitsParameterName]; }
+    }
     #endregion
     #region properties
@@ -72 +84 @@
     [StorableConstructor]
     protected SymbolicDataAnalysisSingleObjectiveTrainingParetoBestSolutionAnalyzer(bool deserializing) : base(deserializing) { }
-    protected SymbolicDataAnalysisSingleObjectiveTrainingParetoBestSolutionAnalyzer(SymbolicDataAnalysisSingleObjectiveTrainingParetoBestSolutionAnalyzer<T> original, Cloner cloner) : base(original, cloner) { }
+    protected SymbolicDataAnalysisSingleObjectiveTrainingParetoBestSolutionAnalyzer(SymbolicDataAnalysisSingleObjectiveTrainingParetoBestSolutionAnalyzer<S, T> original, Cloner cloner) : base(original, cloner) { }
     public SymbolicDataAnalysisSingleObjectiveTrainingParetoBestSolutionAnalyzer()
       : base() {
+      Parameters.Add(new LookupParameter<S>(ProblemDataParameterName, "The problem data for the symbolic data analysis solution."));
       Parameters.Add(new LookupParameter<ItemList<T>>(TrainingBestSolutionsParameterName, "The training best (Pareto-optimal) symbolic data analysis solutions."));
       Parameters.Add(new LookupParameter<ItemList<DoubleArray>>(TrainingBestSolutionQualitiesParameterName, "The qualities of the training best (Pareto-optimal) solutions."));
       Parameters.Add(new ScopeTreeLookupParameter<DoubleValue>(ComplexityParameterName, "The complexity of each tree."));
+      Parameters.Add(new LookupParameter<ISymbolicDataAnalysisExpressionTreeInterpreter>(SymbolicDataAnalysisTreeInterpreterParameterName, "The symbolic data analysis tree interpreter for the symbolic expression tree."));
+      Parameters.Add(new ValueLookupParameter<DoubleLimit>(EstimationLimitsParameterName, "The lower and upper limit for the estimated values produced by the symbolic classification model."));
     }
 
@@ -100 +115 @@
 
       List<double> complexities;
-      if (ComplexityParameter.ActualValue != null) {
+      if (ComplexityParameter.ActualValue != null && ComplexityParameter.ActualValue.Length == qualities.Count) {
         complexities = ComplexityParameter.ActualValue.Select(x => x.Value).ToList();
       } else {

branches/Sliding Window GP/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisSingleObjectiveValidationAnalyzer.cs

@@ -76 +76 @@
       : base(original, cloner) {
     }
-    public SymbolicDataAnalysisSingleObjectiveValidationAnalyzer()
-      : base() {
+
+    protected SymbolicDataAnalysisSingleObjectiveValidationAnalyzer(): base() {
       Parameters.Add(new LookupParameter<IRandom>(RandomParameterName, "The random generator."));
       Parameters.Add(new LookupParameter<U>(ProblemDataParameterName, "The problem data of the symbolic data analysis problem."));
       Parameters.Add(new LookupParameter<T>(EvaluatorParameterName, "The operator to use for fitness evaluation on the validation partition."));
       Parameters.Add(new LookupParameter<ISymbolicDataAnalysisExpressionTreeInterpreter>(SymbolicDataAnalysisTreeInterpreterParameterName, "The interpreter for symbolic data analysis expression trees."));
-      Parameters.Add(new ValueLookupParameter<IntRange>(ValidationPartitionParameterName, "Thes validation partition."));
+      Parameters.Add(new ValueLookupParameter<IntRange>(ValidationPartitionParameterName, "The validation partition."));
       Parameters.Add(new ValueLookupParameter<PercentValue>(RelativeNumberOfEvaluatedSamplesParameterName, "The relative number of samples of the dataset partition, which should be randomly chosen for evaluation between the start and end index."));
       Parameters.Add(new ValueLookupParameter<PercentValue>(PercentageOfBestSolutionsParameterName,

branches/Sliding Window GP/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisSingleObjectiveValidationParetoBestSolutionAnalyzer.cs

@@ -20 +20 @@
 #endregion
 
+using System;
 using System.Collections.Generic;
 using System.Linq;
@@ -26 +27 @@
 using HeuristicLab.Data;
 using HeuristicLab.Encodings.SymbolicExpressionTreeEncoding;
-using HeuristicLab.Operators;
 using HeuristicLab.Optimization;
 using HeuristicLab.Parameters;
 using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
-using System;
 
 namespace HeuristicLab.Problems.DataAnalysis.Symbolic {
@@ -38 +37 @@
   [Item("SymbolicDataAnalysisSingleObjectiveValidationParetoBestSolutionAnalyzer", "An operator that analyzes the Pareto-best symbolic data analysis solution for single objective symbolic data analysis problems.")]
   [StorableClass]
-  public abstract class SymbolicDataAnalysisSingleObjectiveValidationParetoBestSolutionAnalyzer<S, T, U> : SymbolicDataAnalysisSingleObjectiveValidationAnalyzer<T, U>
+  public abstract class SymbolicDataAnalysisSingleObjectiveValidationParetoBestSolutionAnalyzer<S, T, U> : SymbolicDataAnalysisSingleObjectiveValidationAnalyzer<T, U>, ISymbolicDataAnalysisBoundedOperator
     where S : class, ISymbolicDataAnalysisSolution
     where T : class, ISymbolicDataAnalysisSingleObjectiveEvaluator<U>
@@ -45 +44 @@
     private const string ValidationBestSolutionQualitiesParameterName = "Best validation solution qualities";
     private const string ComplexityParameterName = "Complexity";
+    private const string EstimationLimitsParameterName = "EstimationLimits";
 
     public override bool EnabledByDefault {
@@ -60 +60 @@
       get { return (IScopeTreeLookupParameter<DoubleValue>)Parameters[ComplexityParameterName]; }
     }
+    public IValueLookupParameter<DoubleLimit> EstimationLimitsParameter {
+      get { return (IValueLookupParameter<DoubleLimit>)Parameters[EstimationLimitsParameterName]; }
+    }
+
     #endregion
     #region properties
@@ -80 +84 @@
       Parameters.Add(new LookupParameter<ItemList<DoubleArray>>(ValidationBestSolutionQualitiesParameterName, "The qualities of the validation best (Pareto-optimal) solutions."));
       Parameters.Add(new ScopeTreeLookupParameter<DoubleValue>(ComplexityParameterName, "The complexity of each tree."));
+      Parameters.Add(new ValueLookupParameter<DoubleLimit>(EstimationLimitsParameterName, "The lower and upper limit for the estimated values produced by the symbolic classification model."));
     }
 
@@ -137 +142 @@
 
       List<double> complexities;
-      if (ComplexityParameter.ActualValue != null) {
+      if (ComplexityParameter.ActualValue != null && ComplexityParameter.ActualValue.Length == trainingQuality.Length) {
         complexities = ComplexityParameter.ActualValue.Select(x => x.Value).ToList();
       } else {

branches/Sliding Window GP/HeuristicLab.Problems.DataAnalysis.Symbolic/3.4/Analyzers/SymbolicDataAnalysisVariableFrequencyAnalyzer.cs

@@ -109 +109 @@
       // update variable impacts matrix
       var orderedImpacts = (from row in datatable.Rows
-                            select new { Name = row.Name, Impact = datatable.Rows[row.Name].Values.Average() })
+                            select new { Name = row.Name, Impact = Math.Round(datatable.Rows[row.Name].Values.Average(), 3) })
                            .OrderByDescending(p => p.Impact)
                            .ToList();

@@ +1 @@
+*.user
+Plugin.cs
 bin
-*.user
-HeuristicLabProblemsDataAnalysisSymbolicPlugin.cs
 obj
-*.vs10x
-Plugin.cs