Changeset 15973 for branches/2522_RefactorPluginInfrastructure/HeuristicLab.Algorithms.DataAnalysis/3.4/Linear

Timestamp:

06/28/18 11:13:37 (6 years ago)

Author:

gkronber

Message:

#2522: merged trunk changes from r13402:15972 to branch resolving conflicts where necessary

Location:

branches/2522_RefactorPluginInfrastructure

Files:

• . (modified) (2 props)
• HeuristicLab.Algorithms.DataAnalysis (modified) (1 prop)
• HeuristicLab.Algorithms.DataAnalysis/3.4 (modified) (1 prop)
• HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/AlglibUtil.cs (deleted)
• HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/LinearDiscriminantAnalysis.cs (modified) (7 diffs)
• HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/LinearRegression.cs (modified) (5 diffs)
• HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/MultinomialLogitClassification.cs (modified) (5 diffs)
• HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/MultinomialLogitClassificationSolution.cs (modified) (2 diffs)
• HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/MultinomialLogitModel.cs (modified) (7 diffs)
• HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/Scaling.cs (modified) (2 diffs)

branches/2522_RefactorPluginInfrastructure

@@ -24 +24 @@
 protoc.exe
 obj
+.vs

@@ -24 +24 @@
 protoc.exe
 obj
+.vs

branches/2522_RefactorPluginInfrastructure/HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/LinearDiscriminantAnalysis.cs

@@ -1 +1 @@
 #region License Information
 /* HeuristicLab
- * Copyright (C) 2002-2015 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
+ * Copyright (C) 2002-2018 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
  *
  * This file is part of HeuristicLab.
@@ -23 +23 @@
 using System.Collections.Generic;
 using System.Linq;
+using System.Threading;
 using HeuristicLab.Common;
 using HeuristicLab.Core;
@@ -36 +37 @@
   /// Linear discriminant analysis classification algorithm.
   /// </summary>
-  [Item("Linear Discriminant Analysis", "Linear discriminant analysis classification algorithm (wrapper for ALGLIB).")]
+  [Item("Linear Discriminant Analysis (LDA)", "Linear discriminant analysis classification algorithm (wrapper for ALGLIB).")]
   [Creatable(CreatableAttribute.Categories.DataAnalysisClassification, Priority = 100)]
   [StorableClass]
@@ -59 +60 @@
 
     #region Fisher LDA
-    protected override void Run() {
+    protected override void Run(CancellationToken cancellationToken) {
       var solution = CreateLinearDiscriminantAnalysisSolution(Problem.ProblemData);
       Results.Add(new Result(LinearDiscriminantAnalysisSolutionResultName, "The linear discriminant analysis.", solution));
@@ -70 +71 @@
       IEnumerable<int> rows = problemData.TrainingIndices;
       int nClasses = problemData.ClassNames.Count();
-      double[,] inputMatrix = AlglibUtil.PrepareInputMatrix(dataset, allowedInputVariables.Concat(new string[] { targetVariable }), rows);
-      if (inputMatrix.Cast<double>().Any(x => double.IsNaN(x) || double.IsInfinity(x)))
+      var doubleVariableNames = allowedInputVariables.Where(dataset.VariableHasType<double>).ToArray();
+      var factorVariableNames = allowedInputVariables.Where(dataset.VariableHasType<string>).ToArray();
+      double[,] inputMatrix = dataset.ToArray(doubleVariableNames.Concat(new string[] { targetVariable }), rows);
+
+      var factorVariables = dataset.GetFactorVariableValues(factorVariableNames, rows);
+      var factorMatrix = dataset.ToArray(factorVariables, rows);
+
+      inputMatrix = factorMatrix.HorzCat(inputMatrix);
+
+      if (inputMatrix.ContainsNanOrInfinity())
         throw new NotSupportedException("Linear discriminant analysis does not support NaN or infinity values in the input dataset.");
 
@@ -82 +91 @@
       int info;
       double[] w;
-      alglib.fisherlda(inputMatrix, inputMatrix.GetLength(0), allowedInputVariables.Count(), nClasses, out info, out w);
+      alglib.fisherlda(inputMatrix, inputMatrix.GetLength(0), inputMatrix.GetLength(1) - 1, nClasses, out info, out w);
       if (info < 1) throw new ArgumentException("Error in calculation of linear discriminant analysis solution");
 
-      ISymbolicExpressionTree tree = new SymbolicExpressionTree(new ProgramRootSymbol().CreateTreeNode());
-      ISymbolicExpressionTreeNode startNode = new StartSymbol().CreateTreeNode();
-      tree.Root.AddSubtree(startNode);
-      ISymbolicExpressionTreeNode addition = new Addition().CreateTreeNode();
-      startNode.AddSubtree(addition);
+      var nFactorCoeff = factorMatrix.GetLength(1);
+      var tree = LinearModelToTreeConverter.CreateTree(factorVariables, w.Take(nFactorCoeff).ToArray(),
+        doubleVariableNames, w.Skip(nFactorCoeff).Take(doubleVariableNames.Length).ToArray());
 
-      int col = 0;
-      foreach (string column in allowedInputVariables) {
-        VariableTreeNode vNode = (VariableTreeNode)new HeuristicLab.Problems.DataAnalysis.Symbolic.Variable().CreateTreeNode();
-        vNode.VariableName = column;
-        vNode.Weight = w[col];
-        addition.AddSubtree(vNode);
-        col++;
-      }
-
-      var model = LinearDiscriminantAnalysis.CreateDiscriminantFunctionModel(tree, new SymbolicDataAnalysisExpressionTreeInterpreter(), problemData, rows);
+      var model = CreateDiscriminantFunctionModel(tree, new SymbolicDataAnalysisExpressionTreeLinearInterpreter(), problemData, rows);
       SymbolicDiscriminantFunctionClassificationSolution solution = new SymbolicDiscriminantFunctionClassificationSolution(model, (IClassificationProblemData)problemData.Clone());
 
@@ -111 +109 @@
       IClassificationProblemData problemData,
       IEnumerable<int> rows) {
-      var model = new SymbolicDiscriminantFunctionClassificationModel(tree, interpreter, new AccuracyMaximizationThresholdCalculator());
+      var model = new SymbolicDiscriminantFunctionClassificationModel(problemData.TargetVariable, tree, interpreter, new AccuracyMaximizationThresholdCalculator());
       model.RecalculateModelParameters(problemData, rows);
       return model;

branches/2522_RefactorPluginInfrastructure/HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/LinearRegression.cs

@@ -1 +1 @@
 #region License Information
 /* HeuristicLab
- * Copyright (C) 2002-2015 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
+ * Copyright (C) 2002-2018 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
  *
  * This file is part of HeuristicLab.
@@ -23 +23 @@
 using System.Collections.Generic;
 using System.Linq;
+using System.Threading;
 using HeuristicLab.Common;
 using HeuristicLab.Core;
 using HeuristicLab.Data;
-using HeuristicLab.Encodings.SymbolicExpressionTreeEncoding;
 using HeuristicLab.Optimization;
 using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
@@ -60 +60 @@
 
     #region linear regression
-    protected override void Run() {
+    protected override void Run(CancellationToken cancellationToken) {
       double rmsError, cvRmsError;
       var solution = CreateLinearRegressionSolution(Problem.ProblemData, out rmsError, out cvRmsError);
@@ -73 +73 @@
       IEnumerable<string> allowedInputVariables = problemData.AllowedInputVariables;
       IEnumerable<int> rows = problemData.TrainingIndices;
-      double[,] inputMatrix = AlglibUtil.PrepareInputMatrix(dataset, allowedInputVariables.Concat(new string[] { targetVariable }), rows);
-      if (inputMatrix.Cast<double>().Any(x => double.IsNaN(x) || double.IsInfinity(x)))
+      var doubleVariables = allowedInputVariables.Where(dataset.VariableHasType<double>);
+      var factorVariableNames = allowedInputVariables.Where(dataset.VariableHasType<string>);
+      var factorVariables = dataset.GetFactorVariableValues(factorVariableNames, rows);
+      double[,] binaryMatrix = dataset.ToArray(factorVariables, rows);
+      double[,] doubleVarMatrix = dataset.ToArray(doubleVariables.Concat(new string[] { targetVariable }), rows);
+      var inputMatrix = binaryMatrix.HorzCat(doubleVarMatrix);
+
+      if (inputMatrix.ContainsNanOrInfinity())
         throw new NotSupportedException("Linear regression does not support NaN or infinity values in the input dataset.");
 
@@ -91 +97 @@
       alglib.lrunpack(lm, out coefficients, out nFeatures);
 
-      ISymbolicExpressionTree tree = new SymbolicExpressionTree(new ProgramRootSymbol().CreateTreeNode());
-      ISymbolicExpressionTreeNode startNode = new StartSymbol().CreateTreeNode();
-      tree.Root.AddSubtree(startNode);
-      ISymbolicExpressionTreeNode addition = new Addition().CreateTreeNode();
-      startNode.AddSubtree(addition);
+      int nFactorCoeff = binaryMatrix.GetLength(1);
+      int nVarCoeff = doubleVariables.Count();
+      var tree = LinearModelToTreeConverter.CreateTree(factorVariables, coefficients.Take(nFactorCoeff).ToArray(),
+        doubleVariables.ToArray(), coefficients.Skip(nFactorCoeff).Take(nVarCoeff).ToArray(),
+        @const: coefficients[nFeatures]);
 
-      int col = 0;
-      foreach (string column in allowedInputVariables) {
-        VariableTreeNode vNode = (VariableTreeNode)new HeuristicLab.Problems.DataAnalysis.Symbolic.Variable().CreateTreeNode();
-        vNode.VariableName = column;
-        vNode.Weight = coefficients[col];
-        addition.AddSubtree(vNode);
-        col++;
-      }
-
-      ConstantTreeNode cNode = (ConstantTreeNode)new Constant().CreateTreeNode();
-      cNode.Value = coefficients[coefficients.Length - 1];
-      addition.AddSubtree(cNode);
-
-      SymbolicRegressionSolution solution = new SymbolicRegressionSolution(new SymbolicRegressionModel(tree, new SymbolicDataAnalysisExpressionTreeInterpreter()), (IRegressionProblemData)problemData.Clone());
+      SymbolicRegressionSolution solution = new SymbolicRegressionSolution(new SymbolicRegressionModel(problemData.TargetVariable, tree, new SymbolicDataAnalysisExpressionTreeLinearInterpreter()), (IRegressionProblemData)problemData.Clone());
       solution.Model.Name = "Linear Regression Model";
       solution.Name = "Linear Regression Solution";

branches/2522_RefactorPluginInfrastructure/HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/MultinomialLogitClassification.cs

@@ -1 +1 @@
 #region License Information
 /* HeuristicLab
- * Copyright (C) 2002-2015 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
+ * Copyright (C) 2002-2018 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
  *
  * This file is part of HeuristicLab.
@@ -23 +23 @@
 using System.Collections.Generic;
 using System.Linq;
+using System.Threading;
 using HeuristicLab.Common;
 using HeuristicLab.Core;
@@ -57 +58 @@
 
     #region logit classification
-    protected override void Run() {
+    protected override void Run(CancellationToken cancellationToken) {
       double rmsError, relClassError;
       var solution = CreateLogitClassificationSolution(Problem.ProblemData, out rmsError, out relClassError);
@@ -68 +69 @@
       var dataset = problemData.Dataset;
       string targetVariable = problemData.TargetVariable;
-      IEnumerable<string> allowedInputVariables = problemData.AllowedInputVariables;
+      var doubleVariableNames = problemData.AllowedInputVariables.Where(dataset.VariableHasType<double>);
+      var factorVariableNames = problemData.AllowedInputVariables.Where(dataset.VariableHasType<string>);
       IEnumerable<int> rows = problemData.TrainingIndices;
-      double[,] inputMatrix = AlglibUtil.PrepareInputMatrix(dataset, allowedInputVariables.Concat(new string[] { targetVariable }), rows);
-      if (inputMatrix.Cast<double>().Any(x => double.IsNaN(x) || double.IsInfinity(x)))
+      double[,] inputMatrix = dataset.ToArray(doubleVariableNames.Concat(new string[] { targetVariable }), rows);
+
+      var factorVariableValues = dataset.GetFactorVariableValues(factorVariableNames, rows);
+      var factorMatrix = dataset.ToArray(factorVariableValues, rows);
+      inputMatrix = factorMatrix.HorzCat(inputMatrix);
+
+      if (inputMatrix.ContainsNanOrInfinity())
         throw new NotSupportedException("Multinomial logit classification does not support NaN or infinity values in the input dataset.");
 
@@ -95 +102 @@
       relClassError = alglib.mnlrelclserror(lm, inputMatrix, nRows);
 
-      MultinomialLogitClassificationSolution solution = new MultinomialLogitClassificationSolution((IClassificationProblemData)problemData.Clone(), new MultinomialLogitModel(lm, targetVariable, allowedInputVariables, classValues));
+      MultinomialLogitClassificationSolution solution = new MultinomialLogitClassificationSolution(new MultinomialLogitModel(lm, targetVariable, doubleVariableNames, factorVariableValues, classValues), (IClassificationProblemData)problemData.Clone());
       return solution;
     }

branches/2522_RefactorPluginInfrastructure/HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/MultinomialLogitClassificationSolution.cs

@@ -1 +1 @@
 #region License Information
 /* HeuristicLab
- * Copyright (C) 2002-2015 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
+ * Copyright (C) 2002-2018 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
  *
  * This file is part of HeuristicLab.
@@ -43 +43 @@
       : base(original, cloner) {
     }
-    public MultinomialLogitClassificationSolution(IClassificationProblemData problemData, MultinomialLogitModel logitModel)
+    public MultinomialLogitClassificationSolution(MultinomialLogitModel logitModel, IClassificationProblemData problemData)
       : base(logitModel, problemData) {
     }

branches/2522_RefactorPluginInfrastructure/HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/MultinomialLogitModel.cs

@@ -1 +1 @@
 #region License Information
 /* HeuristicLab
- * Copyright (C) 2002-2015 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
+ * Copyright (C) 2002-2018 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
  *
  * This file is part of HeuristicLab.
@@ -34 +34 @@
   [StorableClass]
   [Item("Multinomial Logit Model", "Represents a multinomial logit model for classification.")]
-  public sealed class MultinomialLogitModel : NamedItem, IClassificationModel {
+  public sealed class MultinomialLogitModel : ClassificationModel {
 
     private alglib.logitmodel logitModel;
@@ -48 +48 @@
     }
 
-    [Storable]
-    private string targetVariable;
+    public override IEnumerable<string> VariablesUsedForPrediction {
+      get { return allowedInputVariables; }
+    }
+
     [Storable]
     private string[] allowedInputVariables;
     [Storable]
     private double[] classValues;
+    [Storable]
+    private List<KeyValuePair<string, IEnumerable<string>>> factorVariables;
+
     [StorableConstructor]
     private MultinomialLogitModel(bool deserializing)
@@ -64 +69 @@
       logitModel = new alglib.logitmodel();
       logitModel.innerobj.w = (double[])original.logitModel.innerobj.w.Clone();
-      targetVariable = original.targetVariable;
       allowedInputVariables = (string[])original.allowedInputVariables.Clone();
       classValues = (double[])original.classValues.Clone();
+      this.factorVariables = original.factorVariables.Select(kvp => new KeyValuePair<string, IEnumerable<string>>(kvp.Key, new List<string>(kvp.Value))).ToList();
     }
-    public MultinomialLogitModel(alglib.logitmodel logitModel, string targetVariable, IEnumerable<string> allowedInputVariables, double[] classValues)
-      : base() {
+    public MultinomialLogitModel(alglib.logitmodel logitModel, string targetVariable, IEnumerable<string> doubleInputVariables, IEnumerable<KeyValuePair<string, IEnumerable<string>>> factorVariables, double[] classValues)
+      : base(targetVariable) {
       this.name = ItemName;
       this.description = ItemDescription;
       this.logitModel = logitModel;
-      this.targetVariable = targetVariable;
-      this.allowedInputVariables = allowedInputVariables.ToArray();
+      this.allowedInputVariables = doubleInputVariables.ToArray();
+      this.factorVariables = factorVariables.Select(kvp => new KeyValuePair<string, IEnumerable<string>>(kvp.Key, new List<string>(kvp.Value))).ToList();
       this.classValues = (double[])classValues.Clone();
+    }
+
+    [StorableHook(HookType.AfterDeserialization)]
+    private void AfterDeserialization() {
+      // BackwardsCompatibility3.3
+      #region Backwards compatible code, remove with 3.4
+      factorVariables = new List<KeyValuePair<string, IEnumerable<string>>>();
+      #endregion
     }
 
@@ -82 +95 @@
     }
 
-    public IEnumerable<double> GetEstimatedClassValues(IDataset dataset, IEnumerable<int> rows) {
-      double[,] inputData = AlglibUtil.PrepareInputMatrix(dataset, allowedInputVariables, rows);
+    public override IEnumerable<double> GetEstimatedClassValues(IDataset dataset, IEnumerable<int> rows) {
+
+      double[,] inputData = dataset.ToArray(allowedInputVariables, rows);
+      double[,] factorData = dataset.ToArray(factorVariables, rows);
+
+      inputData = factorData.HorzCat(inputData);
 
       int n = inputData.GetLength(0);
@@ -108 +125 @@
     }
 
-    public MultinomialLogitClassificationSolution CreateClassificationSolution(IClassificationProblemData problemData) {
-      return new MultinomialLogitClassificationSolution(new ClassificationProblemData(problemData), this);
-    }
-    IClassificationSolution IClassificationModel.CreateClassificationSolution(IClassificationProblemData problemData) {
-      return CreateClassificationSolution(problemData);
+    public override IClassificationSolution CreateClassificationSolution(IClassificationProblemData problemData) {
+      return new MultinomialLogitClassificationSolution(this, new ClassificationProblemData(problemData));
     }
 
@@ -135 +149 @@
     }
     #endregion
+
   }
 }

branches/2522_RefactorPluginInfrastructure/HeuristicLab.Algorithms.DataAnalysis/3.4/Linear/Scaling.cs

@@ -1 +1 @@
 #region License Information
 /* HeuristicLab
- * Copyright (C) 2002-2015 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
+ * Copyright (C) 2002-2018 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
  *
  * This file is part of HeuristicLab.
@@ -29 +29 @@
 
 namespace HeuristicLab.Algorithms.DataAnalysis {
+  [Obsolete("Use transformation classes in Problems.DataAnalysis instead")]
   [StorableClass]
   [Item(Name = "Scaling", Description = "Contains information about scaling of variables for data-analysis algorithms.")]

@@ -24 +24 @@
 protoc.exe
 obj
+.vs