| 1 | #region License Information
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| 2 | /* HeuristicLab
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| 3 | * Copyright (C) 2002-2008 Heuristic and Evolutionary Algorithms Laboratory (HEAL)
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| 4 | *
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| 5 | * This file is part of HeuristicLab.
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| 6 | *
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| 7 | * HeuristicLab is free software: you can redistribute it and/or modify
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| 8 | * it under the terms of the GNU General Public License as published by
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| 9 | * the Free Software Foundation, either version 3 of the License, or
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| 10 | * (at your option) any later version.
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| 11 | *
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| 12 | * HeuristicLab is distributed in the hope that it will be useful,
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| 13 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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| 14 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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| 15 | * GNU General Public License for more details.
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| 16 | *
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| 17 | * You should have received a copy of the GNU General Public License
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| 18 | * along with HeuristicLab. If not, see <http://www.gnu.org/licenses/>.
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| 19 | */
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| 20 | #endregion
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| 21 |
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| 22 | using System;
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| 23 | using System.Collections.Generic;
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| 24 | using System.Linq;
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| 25 | using System.Text;
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| 26 | using HeuristicLab.Core;
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| 27 | using System.Xml;
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| 28 | using System.Diagnostics;
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| 29 | using HeuristicLab.DataAnalysis;
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| 30 | using HeuristicLab.Operators;
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| 31 | using HeuristicLab.Random;
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| 32 | using HeuristicLab.Selection;
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| 33 | using HeuristicLab.Logging;
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| 34 | using HeuristicLab.Data;
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| 35 | using HeuristicLab.Operators.Programmable;
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| 36 | using HeuristicLab.Modeling;
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| 37 |
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| 38 | namespace HeuristicLab.GP.StructureIdentification {
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| 39 | public class StandardGP : AlgorithmBase, IEditable {
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| 40 |
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| 41 | public override string Name { get { return "StandardGP"; } }
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| 42 |
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| 43 | public override int TargetVariable {
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| 44 | get { return ProblemInjector.GetVariableValue<IntData>("TargetVariable", null, false).Data; }
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| 45 | set { ProblemInjector.GetVariableValue<IntData>("TargetVariable", null, false).Data = value; }
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| 46 | }
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| 47 |
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| 48 | public override Dataset Dataset {
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| 49 | get { return ProblemInjector.GetVariableValue<Dataset>("Dataset", null, false); }
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| 50 | set { ProblemInjector.GetVariable("Dataset").Value = value; }
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| 51 | }
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| 52 |
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| 53 | public virtual int MaxGenerations {
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| 54 | get { return GetVariableInjector().GetVariable("MaxGenerations").GetValue<IntData>().Data; }
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| 55 | set { GetVariableInjector().GetVariable("MaxGenerations").GetValue<IntData>().Data = value; }
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| 56 | }
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| 57 |
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| 58 | public virtual int TournamentSize {
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| 59 | get { return GetVariableInjector().GetVariable("TournamentSize").GetValue<IntData>().Data; }
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| 60 | set { GetVariableInjector().GetVariable("TournamentSize").GetValue<IntData>().Data = value; }
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| 61 | }
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| 62 |
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| 63 | public double FullTreeShakingFactor {
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| 64 | get { return GetVariableInjector().GetVariable("FullTreeShakingFactor").GetValue<DoubleData>().Data; }
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| 65 | set { GetVariableInjector().GetVariable("FullTreeShakingFactor").GetValue<DoubleData>().Data = value; }
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| 66 | }
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| 67 |
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| 68 | public double OnePointShakingFactor {
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| 69 | get { return GetVariableInjector().GetVariable("OnePointShakingFactor").GetValue<DoubleData>().Data; }
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| 70 | set { GetVariableInjector().GetVariable("OnePointShakingFactor").GetValue<DoubleData>().Data = value; }
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| 71 | }
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| 72 |
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| 73 | public int MinInitialTreeSize {
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| 74 | get { return GetVariableInjector().GetVariable("MinInitialTreeSize").GetValue<IntData>().Data; }
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| 75 | set { GetVariableInjector().GetVariable("MinInitialTreeSize").GetValue<IntData>().Data = value; }
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| 76 | }
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| 77 |
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| 78 | public override int MaxTreeSize {
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| 79 | get {
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| 80 | return base.MaxTreeSize;
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| 81 | }
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| 82 | set {
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| 83 | base.MaxTreeSize = value;
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| 84 | MinInitialTreeSize = value / 2;
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| 85 | }
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| 86 | }
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| 87 |
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| 88 | public override int PopulationSize {
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| 89 | get {
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| 90 | return base.PopulationSize;
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| 91 | }
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| 92 | set {
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| 93 | base.PopulationSize = value;
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| 94 | Parents = 2 * value;
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| 95 | }
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| 96 | }
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| 97 |
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| 98 | public StandardGP()
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| 99 | : base() {
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| 100 | PopulationSize = 10000;
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| 101 | MaxGenerations = 100;
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| 102 | TournamentSize = 7;
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| 103 | MutationRate = 0.15;
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| 104 | Elites = 1;
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| 105 | MaxTreeSize = 100;
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| 106 | MaxTreeHeight = 10;
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| 107 | FullTreeShakingFactor = 0.1;
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| 108 | OnePointShakingFactor = 1.0;
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| 109 | PunishmentFactor = 10.0;
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| 110 | UseEstimatedTargetValue = false;
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| 111 | SetSeedRandomly = true;
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| 112 | }
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| 113 |
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| 114 | protected internal override IOperator CreateProblemInjector() {
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| 115 | return new ProblemInjector();
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| 116 | }
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| 117 |
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| 118 | protected internal override IOperator CreateSelector() {
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| 119 | TournamentSelector selector = new TournamentSelector();
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| 120 | selector.Name = "Selector";
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| 121 | selector.GetVariableInfo("Selected").ActualName = "Parents";
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| 122 | selector.GetVariableInfo("GroupSize").Local = false;
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| 123 | selector.RemoveVariable("GroupSize");
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| 124 | selector.GetVariableInfo("GroupSize").ActualName = "TournamentSize";
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| 125 | return selector;
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| 126 | }
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| 127 |
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| 128 | protected internal override IOperator CreateGlobalInjector() {
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| 129 | VariableInjector globalInjector = (VariableInjector)base.CreateGlobalInjector();
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| 130 | globalInjector.AddVariable(new HeuristicLab.Core.Variable("TournamentSize", new IntData()));
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| 131 | globalInjector.AddVariable(new HeuristicLab.Core.Variable("MaxGenerations", new IntData()));
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| 132 | globalInjector.AddVariable(new HeuristicLab.Core.Variable("FullTreeShakingFactor", new DoubleData()));
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| 133 | globalInjector.AddVariable(new HeuristicLab.Core.Variable("OnePointShakingFactor", new DoubleData()));
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| 134 | globalInjector.AddVariable(new HeuristicLab.Core.Variable("MinInitialTreeSize", new IntData()));
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| 135 | return globalInjector;
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| 136 | }
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| 137 |
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| 138 | protected internal override IOperator CreateCrossover() {
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| 139 | StandardCrossOver crossover = new StandardCrossOver();
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| 140 | crossover.Name = "Crossover";
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| 141 | crossover.GetVariableInfo("OperatorLibrary").ActualName = "FunctionLibrary";
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| 142 | return crossover;
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| 143 | }
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| 144 |
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| 145 | protected internal override IOperator CreateTreeCreator() {
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| 146 | ProbabilisticTreeCreator treeCreator = new ProbabilisticTreeCreator();
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| 147 | treeCreator.Name = "Tree generator";
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| 148 | treeCreator.GetVariableInfo("OperatorLibrary").ActualName = "FunctionLibrary";
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| 149 | treeCreator.GetVariableInfo("MinTreeSize").ActualName = "MinInitialTreeSize";
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| 150 | return treeCreator;
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| 151 | }
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| 152 |
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| 153 | protected internal override IOperator CreateFunctionLibraryInjector() {
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| 154 | FunctionLibraryInjector funLibInjector = new FunctionLibraryInjector();
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| 155 | funLibInjector.GetVariableValue<BoolData>("Xor", null, false).Data = false;
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| 156 | funLibInjector.GetVariableValue<BoolData>("Average", null, false).Data = false;
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| 157 | return funLibInjector;
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| 158 | }
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| 159 |
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| 160 | protected internal override IOperator CreateManipulator() {
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| 161 | CombinedOperator manipulator = new CombinedOperator();
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| 162 | manipulator.Name = "Manipulator";
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| 163 | StochasticMultiBranch multibranch = new StochasticMultiBranch();
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| 164 | FullTreeShaker fullTreeShaker = new FullTreeShaker();
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| 165 | fullTreeShaker.GetVariableInfo("OperatorLibrary").ActualName = "FunctionLibrary";
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| 166 | fullTreeShaker.GetVariableInfo("ShakingFactor").ActualName = "FullTreeShakingFactor";
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| 167 |
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| 168 | OnePointShaker onepointShaker = new OnePointShaker();
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| 169 | onepointShaker.GetVariableInfo("OperatorLibrary").ActualName = "FunctionLibrary";
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| 170 | onepointShaker.GetVariableInfo("ShakingFactor").ActualName = "OnePointShakingFactor";
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| 171 | ChangeNodeTypeManipulation changeNodeTypeManipulation = new ChangeNodeTypeManipulation();
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| 172 | changeNodeTypeManipulation.GetVariableInfo("OperatorLibrary").ActualName = "FunctionLibrary";
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| 173 | CutOutNodeManipulation cutOutNodeManipulation = new CutOutNodeManipulation();
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| 174 | cutOutNodeManipulation.GetVariableInfo("OperatorLibrary").ActualName = "FunctionLibrary";
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| 175 | DeleteSubTreeManipulation deleteSubTreeManipulation = new DeleteSubTreeManipulation();
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| 176 | deleteSubTreeManipulation.GetVariableInfo("OperatorLibrary").ActualName = "FunctionLibrary";
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| 177 | SubstituteSubTreeManipulation substituteSubTreeManipulation = new SubstituteSubTreeManipulation();
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| 178 | substituteSubTreeManipulation.GetVariableInfo("OperatorLibrary").ActualName = "FunctionLibrary";
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| 179 |
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| 180 | IOperator[] manipulators = new IOperator[] {
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| 181 | onepointShaker, fullTreeShaker,
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| 182 | changeNodeTypeManipulation,
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| 183 | cutOutNodeManipulation,
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| 184 | deleteSubTreeManipulation,
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| 185 | substituteSubTreeManipulation};
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| 186 |
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| 187 | DoubleArrayData probabilities = new DoubleArrayData(new double[manipulators.Length]);
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| 188 | for (int i = 0; i < manipulators.Length; i++) {
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| 189 | probabilities.Data[i] = 1.0;
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| 190 | multibranch.AddSubOperator(manipulators[i]);
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| 191 | }
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| 192 | multibranch.GetVariableInfo("Probabilities").Local = true;
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| 193 | multibranch.AddVariable(new HeuristicLab.Core.Variable("Probabilities", probabilities));
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| 194 |
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| 195 | manipulator.OperatorGraph.AddOperator(multibranch);
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| 196 | manipulator.OperatorGraph.InitialOperator = multibranch;
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| 197 | return manipulator;
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| 198 | }
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| 199 |
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| 200 | protected internal override IOperator CreateBestSolutionProcessor() {
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| 201 | SequentialProcessor bestSolutionProcessor = new SequentialProcessor();
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| 202 | MeanSquaredErrorEvaluator testMseEvaluator = new MeanSquaredErrorEvaluator();
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| 203 | testMseEvaluator.Name = "TestMeanSquaredErrorEvaluator";
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| 204 | testMseEvaluator.GetVariableInfo("MSE").ActualName = "TestQuality";
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| 205 | testMseEvaluator.GetVariableInfo("SamplesStart").ActualName = "TestSamplesStart";
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| 206 | testMseEvaluator.GetVariableInfo("SamplesEnd").ActualName = "TestSamplesEnd";
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| 207 | MeanAbsolutePercentageErrorEvaluator trainingMapeEvaluator = new MeanAbsolutePercentageErrorEvaluator();
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| 208 | trainingMapeEvaluator.Name = "TrainingMapeEvaluator";
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| 209 | trainingMapeEvaluator.GetVariableInfo("MAPE").ActualName = "TrainingMAPE";
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| 210 | trainingMapeEvaluator.GetVariableInfo("SamplesStart").ActualName = "TrainingSamplesStart";
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| 211 | trainingMapeEvaluator.GetVariableInfo("SamplesEnd").ActualName = "TrainingSamplesEnd";
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| 212 | MeanAbsolutePercentageErrorEvaluator validationMapeEvaluator = new MeanAbsolutePercentageErrorEvaluator();
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| 213 | validationMapeEvaluator.Name = "ValidationMapeEvaluator";
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| 214 | validationMapeEvaluator.GetVariableInfo("MAPE").ActualName = "ValidationMAPE";
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| 215 | validationMapeEvaluator.GetVariableInfo("SamplesStart").ActualName = "ValidationSamplesStart";
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| 216 | validationMapeEvaluator.GetVariableInfo("SamplesEnd").ActualName = "ValidationSamplesEnd";
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| 217 | MeanAbsolutePercentageErrorEvaluator testMapeEvaluator = new MeanAbsolutePercentageErrorEvaluator();
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| 218 | testMapeEvaluator.Name = "TestMapeEvaluator";
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| 219 | testMapeEvaluator.GetVariableInfo("MAPE").ActualName = "TestMAPE";
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| 220 | testMapeEvaluator.GetVariableInfo("SamplesStart").ActualName = "TestSamplesStart";
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| 221 | testMapeEvaluator.GetVariableInfo("SamplesEnd").ActualName = "TestSamplesEnd";
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| 222 | MeanAbsolutePercentageOfRangeErrorEvaluator trainingMapreEvaluator = new MeanAbsolutePercentageOfRangeErrorEvaluator();
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| 223 | trainingMapreEvaluator.Name = "TrainingMapreEvaluator";
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| 224 | trainingMapreEvaluator.GetVariableInfo("MAPRE").ActualName = "TrainingMAPRE";
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| 225 | trainingMapreEvaluator.GetVariableInfo("SamplesStart").ActualName = "TrainingSamplesStart";
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| 226 | trainingMapreEvaluator.GetVariableInfo("SamplesEnd").ActualName = "TrainingSamplesEnd";
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| 227 | MeanAbsolutePercentageOfRangeErrorEvaluator validationMapreEvaluator = new MeanAbsolutePercentageOfRangeErrorEvaluator();
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| 228 | validationMapreEvaluator.Name = "ValidationMapreEvaluator";
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| 229 | validationMapreEvaluator.GetVariableInfo("MAPRE").ActualName = "ValidationMAPRE";
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| 230 | validationMapreEvaluator.GetVariableInfo("SamplesStart").ActualName = "ValidationSamplesStart";
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| 231 | validationMapreEvaluator.GetVariableInfo("SamplesEnd").ActualName = "ValidationSamplesEnd";
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| 232 | MeanAbsolutePercentageOfRangeErrorEvaluator testMapreEvaluator = new MeanAbsolutePercentageOfRangeErrorEvaluator();
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| 233 | testMapreEvaluator.Name = "TestMapreEvaluator";
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| 234 | testMapreEvaluator.GetVariableInfo("MAPRE").ActualName = "TestMAPRE";
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| 235 | testMapreEvaluator.GetVariableInfo("SamplesStart").ActualName = "TestSamplesStart";
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| 236 | testMapreEvaluator.GetVariableInfo("SamplesEnd").ActualName = "TestSamplesEnd";
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| 237 | CoefficientOfDeterminationEvaluator trainingR2Evaluator = new CoefficientOfDeterminationEvaluator();
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| 238 | trainingR2Evaluator.Name = "TrainingR2Evaluator";
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| 239 | trainingR2Evaluator.GetVariableInfo("R2").ActualName = "TrainingR2";
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| 240 | trainingR2Evaluator.GetVariableInfo("SamplesStart").ActualName = "TrainingSamplesStart";
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| 241 | trainingR2Evaluator.GetVariableInfo("SamplesEnd").ActualName = "TrainingSamplesEnd";
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| 242 | CoefficientOfDeterminationEvaluator validationR2Evaluator = new CoefficientOfDeterminationEvaluator();
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| 243 | validationR2Evaluator.Name = "ValidationR2Evaluator";
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| 244 | validationR2Evaluator.GetVariableInfo("R2").ActualName = "ValidationR2";
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| 245 | validationR2Evaluator.GetVariableInfo("SamplesStart").ActualName = "ValidationSamplesStart";
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| 246 | validationR2Evaluator.GetVariableInfo("SamplesEnd").ActualName = "ValidationSamplesEnd";
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| 247 | CoefficientOfDeterminationEvaluator testR2Evaluator = new CoefficientOfDeterminationEvaluator();
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| 248 | testR2Evaluator.Name = "TestR2Evaluator";
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| 249 | testR2Evaluator.GetVariableInfo("R2").ActualName = "TestR2";
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| 250 | testR2Evaluator.GetVariableInfo("SamplesStart").ActualName = "TestSamplesStart";
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| 251 | testR2Evaluator.GetVariableInfo("SamplesEnd").ActualName = "TestSamplesEnd";
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| 252 | VarianceAccountedForEvaluator trainingVAFEvaluator = new VarianceAccountedForEvaluator();
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| 253 | trainingVAFEvaluator.Name = "TrainingVAFEvaluator";
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| 254 | trainingVAFEvaluator.GetVariableInfo("VAF").ActualName = "TrainingVAF";
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| 255 | trainingVAFEvaluator.GetVariableInfo("SamplesStart").ActualName = "TrainingSamplesStart";
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| 256 | trainingVAFEvaluator.GetVariableInfo("SamplesEnd").ActualName = "TrainingSamplesEnd";
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| 257 | VarianceAccountedForEvaluator validationVAFEvaluator = new VarianceAccountedForEvaluator();
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| 258 | validationVAFEvaluator.Name = "ValidationVAFEvaluator";
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| 259 | validationVAFEvaluator.GetVariableInfo("VAF").ActualName = "ValidationVAF";
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| 260 | validationVAFEvaluator.GetVariableInfo("SamplesStart").ActualName = "ValidationSamplesStart";
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| 261 | validationVAFEvaluator.GetVariableInfo("SamplesEnd").ActualName = "ValidationSamplesEnd";
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| 262 | VarianceAccountedForEvaluator testVAFEvaluator = new VarianceAccountedForEvaluator();
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| 263 | testVAFEvaluator.Name = "TestVAFEvaluator";
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| 264 | testVAFEvaluator.GetVariableInfo("VAF").ActualName = "TestVAF";
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| 265 | testVAFEvaluator.GetVariableInfo("SamplesStart").ActualName = "TestSamplesStart";
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| 266 | testVAFEvaluator.GetVariableInfo("SamplesEnd").ActualName = "TestSamplesEnd";
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| 267 |
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| 268 | ProgrammableOperator progOperator = new ProgrammableOperator();
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| 269 | progOperator.RemoveVariableInfo("Result");
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| 270 | progOperator.AddVariableInfo(new HeuristicLab.Core.VariableInfo("EvaluatedSolutions", "", typeof(IntData), VariableKind.In));
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| 271 | progOperator.Code = @"
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| 272 | int evalSolutions = EvaluatedSolutions.Data;
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| 273 | scope.AddVariable(new Variable(""EvaluatedSolutions"", new IntData(evalSolutions)));
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| 274 | ";
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| 275 | bestSolutionProcessor.AddSubOperator(testMseEvaluator);
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| 276 | bestSolutionProcessor.AddSubOperator(trainingMapeEvaluator);
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| 277 | bestSolutionProcessor.AddSubOperator(validationMapeEvaluator);
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| 278 | bestSolutionProcessor.AddSubOperator(testMapeEvaluator);
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| 279 | bestSolutionProcessor.AddSubOperator(trainingMapreEvaluator);
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| 280 | bestSolutionProcessor.AddSubOperator(validationMapreEvaluator);
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| 281 | bestSolutionProcessor.AddSubOperator(testMapreEvaluator);
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| 282 | bestSolutionProcessor.AddSubOperator(trainingR2Evaluator);
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| 283 | bestSolutionProcessor.AddSubOperator(validationR2Evaluator);
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| 284 | bestSolutionProcessor.AddSubOperator(testR2Evaluator);
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| 285 | bestSolutionProcessor.AddSubOperator(trainingVAFEvaluator);
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| 286 | bestSolutionProcessor.AddSubOperator(validationVAFEvaluator);
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| 287 | bestSolutionProcessor.AddSubOperator(testVAFEvaluator);
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| 288 | bestSolutionProcessor.AddSubOperator(progOperator);
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| 289 | return bestSolutionProcessor;
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| 290 | }
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| 291 |
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| 292 | protected internal override IOperator CreateLoggingOperator() {
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| 293 | CombinedOperator loggingOperator = new CombinedOperator();
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| 294 | loggingOperator.Name = "Logging";
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| 295 | SequentialProcessor seq = new SequentialProcessor();
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| 296 |
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| 297 | DataCollector collector = new DataCollector();
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| 298 | ItemList<StringData> names = collector.GetVariable("VariableNames").GetValue<ItemList<StringData>>();
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| 299 | names.Add(new StringData("BestQuality"));
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| 300 | names.Add(new StringData("AverageQuality"));
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| 301 | names.Add(new StringData("WorstQuality"));
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| 302 | names.Add(new StringData("BestValidationQuality"));
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| 303 | names.Add(new StringData("AverageValidationQuality"));
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| 304 | names.Add(new StringData("WorstValidationQuality"));
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| 305 | LinechartInjector lineChartInjector = new LinechartInjector();
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| 306 | lineChartInjector.GetVariableInfo("Linechart").ActualName = "Quality Linechart";
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| 307 | lineChartInjector.GetVariable("NumberOfLines").GetValue<IntData>().Data = 6;
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| 308 | QualityLogger qualityLogger = new QualityLogger();
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| 309 | QualityLogger validationQualityLogger = new QualityLogger();
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| 310 | validationQualityLogger.Name = "ValidationQualityLogger";
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| 311 | validationQualityLogger.GetVariableInfo("Quality").ActualName = "ValidationQuality";
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| 312 | validationQualityLogger.GetVariableInfo("QualityLog").ActualName = "ValidationQualityLog";
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| 313 |
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| 314 | seq.AddSubOperator(collector);
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| 315 | seq.AddSubOperator(lineChartInjector);
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| 316 | seq.AddSubOperator(qualityLogger);
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| 317 | seq.AddSubOperator(validationQualityLogger);
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| 318 |
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| 319 | loggingOperator.OperatorGraph.AddOperator(seq);
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| 320 | loggingOperator.OperatorGraph.InitialOperator = seq;
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| 321 | return loggingOperator;
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| 322 | }
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| 323 |
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| 324 | protected internal override Model CreateGPModel(IScope bestModelScope) {
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| 325 | Model model = base.CreateGPModel(bestModelScope);
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| 326 | model.TestMeanSquaredError = bestModelScope.GetVariableValue<DoubleData>("TestQuality", false).Data;
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| 327 | model.TrainingCoefficientOfDetermination = bestModelScope.GetVariableValue<DoubleData>("TrainingR2", false).Data;
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| 328 | model.ValidationCoefficientOfDetermination = bestModelScope.GetVariableValue<DoubleData>("ValidationR2", false).Data;
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| 329 | model.TestCoefficientOfDetermination = bestModelScope.GetVariableValue<DoubleData>("TestR2", false).Data;
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| 330 | model.TrainingMeanAbsolutePercentageError = bestModelScope.GetVariableValue<DoubleData>("TrainingMAPE", false).Data;
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| 331 | model.ValidationMeanAbsolutePercentageError = bestModelScope.GetVariableValue<DoubleData>("ValidationMAPE", false).Data;
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| 332 | model.TestMeanAbsolutePercentageError = bestModelScope.GetVariableValue<DoubleData>("TestMAPE", false).Data;
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| 333 | model.TrainingMeanAbsolutePercentageOfRangeError = bestModelScope.GetVariableValue<DoubleData>("TrainingMAPRE", false).Data;
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| 334 | model.ValidationMeanAbsolutePercentageOfRangeError = bestModelScope.GetVariableValue<DoubleData>("ValidationMAPRE", false).Data;
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| 335 | model.TestMeanAbsolutePercentageOfRangeError = bestModelScope.GetVariableValue<DoubleData>("TestMAPRE", false).Data;
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| 336 | model.TrainingVarianceAccountedFor = bestModelScope.GetVariableValue<DoubleData>("TrainingVAF", false).Data;
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| 337 | model.ValidationVarianceAccountedFor = bestModelScope.GetVariableValue<DoubleData>("ValidationVAF", false).Data;
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| 338 | model.TestVarianceAccountedFor = bestModelScope.GetVariableValue<DoubleData>("TestVAF", false).Data;
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| 339 |
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| 340 | return model;
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| 341 | }
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| 342 |
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| 343 | public virtual IEditor CreateEditor() {
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| 344 | return new StandardGpEditor(this);
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| 345 | }
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| 346 |
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| 347 | public override IView CreateView() {
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| 348 | return new StandardGpEditor(this);
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| 349 | }
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| 350 | }
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| 351 | }
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