1 | #region License Information
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2 | /* HeuristicLab
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3 | * Copyright (C) 2002-2015 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.Linq;
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24 | using HeuristicLab.Analysis;
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25 | using HeuristicLab.Common;
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26 | using HeuristicLab.Core;
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27 | using HeuristicLab.Data;
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28 | using HeuristicLab.Encodings.SymbolicExpressionTreeEncoding;
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29 | using HeuristicLab.EvolutionTracking;
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30 | using HeuristicLab.Operators;
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31 | using HeuristicLab.Optimization.Operators;
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32 | using HeuristicLab.Parameters;
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33 | using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
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34 |
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35 | namespace HeuristicLab.Problems.DataAnalysis.Symbolic {
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36 | [Item("SchemaCreator", "An operator that builds schemas based on the heredity relationship in the genealogy graph.")]
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37 | [StorableClass]
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38 | public class SchemaCreator : EvolutionTrackingOperator<ISymbolicExpressionTree> {
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39 | private const string MinimumSchemaLengthParameterName = "MinimumSchemaLength";
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40 | private const string MinimumSchemaFrequencyParameterName = "MinimumSchemaFrequency";
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41 | private const string MinimumPhenotypicSimilarityParameterName = "MinimumPhenotypicSimilarity";
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42 | private const string ReplacementRatioParameterName = "ReplacementRatio";
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43 | private const string RandomReplacementParameterName = "RandomReplacement";
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44 |
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45 | #region parameters
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46 | public IFixedValueParameter<IntValue> MinimumSchemaLengthParameter {
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47 | get { return (IFixedValueParameter<IntValue>)Parameters[MinimumSchemaLengthParameterName]; }
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48 | }
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49 |
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50 | public IFixedValueParameter<PercentValue> MinimumSchemaFrequencyParameter {
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51 | get { return (IFixedValueParameter<PercentValue>)Parameters[MinimumSchemaFrequencyParameterName]; }
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52 | }
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53 |
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54 | public IFixedValueParameter<PercentValue> MinimumPhenotypicSimilarityParameter {
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55 | get { return (IFixedValueParameter<PercentValue>)Parameters[MinimumPhenotypicSimilarityParameterName]; }
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56 | }
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57 |
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58 | public IFixedValueParameter<PercentValue> ReplacementRatioParameter {
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59 | get { return (IFixedValueParameter<PercentValue>)Parameters[ReplacementRatioParameterName]; }
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60 | }
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61 | #endregion
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62 |
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63 | #region parameter properties
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64 | public int MinimumSchemaLength {
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65 | get { return MinimumSchemaLengthParameter.Value.Value; }
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66 | }
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67 | #endregion
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68 |
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69 | private SchemaEvaluator schemaEvaluator;
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70 | private SchemaCleanupOperator schemaCleanupOperator;
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71 | private DataReducer changedTreesReducer;
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72 | private DataTableValuesCollector valuesCollector;
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73 | private ResultsCollector resultsCollector;
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74 |
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75 | private void ParameterizeOperators() {
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76 | schemaEvaluator = new SchemaEvaluator();
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77 | schemaCleanupOperator = new SchemaCleanupOperator();
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78 |
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79 | changedTreesReducer = new DataReducer();
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80 | changedTreesReducer.ParameterToReduce.ActualName = schemaEvaluator.ChangedTreesParameter.ActualName;
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81 | changedTreesReducer.ReductionOperation.Value = new ReductionOperation(ReductionOperations.Sum);
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82 | changedTreesReducer.TargetOperation.Value = new ReductionOperation(ReductionOperations.Assign); // asign the sum to the target parameter
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83 | changedTreesReducer.TargetParameter.ActualName = "NumberOfChangedTrees";
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84 |
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85 | valuesCollector = new DataTableValuesCollector();
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86 | valuesCollector.CollectedValues.Add(new LookupParameter<IntValue>("NumberOfChangedTrees"));
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87 | valuesCollector.DataTableParameter.ActualName = "Diversification";
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88 |
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89 | resultsCollector = new ResultsCollector();
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90 | resultsCollector.CollectedValues.Add(new LookupParameter<DataTable>("Diversification"));
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91 | }
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92 |
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93 | public SchemaCreator() {
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94 | Parameters.Add(new FixedValueParameter<IntValue>(MinimumSchemaLengthParameterName, new IntValue(10)));
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95 | Parameters.Add(new FixedValueParameter<PercentValue>(MinimumSchemaFrequencyParameterName, new PercentValue(0.05)));
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96 | Parameters.Add(new FixedValueParameter<PercentValue>(MinimumPhenotypicSimilarityParameterName, new PercentValue(0.8)));
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97 | Parameters.Add(new FixedValueParameter<PercentValue>(ReplacementRatioParameterName, new PercentValue(0.2)));
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98 | Parameters.Add(new FixedValueParameter<BoolValue>(RandomReplacementParameterName, new BoolValue(false)));
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99 |
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100 | ParameterizeOperators();
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101 | }
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102 |
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103 | protected SchemaCreator(SchemaCreator original, Cloner cloner) : base(original, cloner) { }
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104 |
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105 | public override IDeepCloneable Clone(Cloner cloner) {
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106 | return new SchemaCreator(this, cloner);
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107 | }
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108 |
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109 | [StorableConstructor]
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110 | protected SchemaCreator(bool deserializing) : base(deserializing) { }
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111 |
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112 | public override IOperation Apply() {
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113 | // apply only when at least one generation has passed
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114 | var gen = Generations.Value;
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115 | if (gen < 1 || GenealogyGraph == null)
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116 | return base.Apply();
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117 | // for now, only consider crossover offspring
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118 | var vertices = GenealogyGraph.GetByRank(gen).Where(x => x.InDegree == 2).Cast<IGenealogyGraphNode<ISymbolicExpressionTree>>();
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119 | var groups = vertices.GroupBy(x => x.Parents.First()).OrderByDescending(g => g.Count()).ToList();
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120 | var anySubtreeSymbol = new AnySubtreeSymbol();
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121 |
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122 | var scopes = new ScopeList(this.ExecutionContext.Scope.SubScopes);
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123 |
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124 | if (schemaEvaluator == null || schemaCleanupOperator == null || changedTreesReducer == null || valuesCollector == null || resultsCollector == null)
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125 | ParameterizeOperators();
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126 |
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127 | var reduceChangedTrees = ExecutionContext.CreateChildOperation(changedTreesReducer);
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128 | var collectValues = ExecutionContext.CreateChildOperation(valuesCollector);
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129 | var collectResults = ExecutionContext.CreateChildOperation(resultsCollector);
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130 |
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131 | var oc = new OperationCollection();
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132 |
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133 | #region create schemas and add subscopes representing the individuals
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134 | foreach (var g in groups) {
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135 | var parent = g.Key;
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136 | if (parent.Data.Length < MinimumSchemaLength)
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137 | continue;
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138 | bool replaced = false;
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139 | var schema = (ISymbolicExpressionTree)parent.Data.Clone();
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140 | var nodes = schema.IterateNodesPrefix().ToList();
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141 | var arcs = g.Select(x => x.InArcs.Last()).Where(x => x.Data != null);
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142 | var indices = arcs.Select(x => ((IFragment<ISymbolicExpressionTreeNode>)x.Data).Index1).Distinct().ToArray();
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143 | Array.Sort(indices);
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144 | var nodesToReplace = indices.Select(x => nodes[x]).ToList();
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145 | for (int i = nodesToReplace.Count - 1; i >= 0; --i) {
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146 | var node = nodesToReplace[i];
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147 |
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148 | // do not replace the node with a wildcard if it would result in a length < MinimumSchemaLength
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149 | if ((schema.Length - node.GetLength() + 1) < MinimumSchemaLength)
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150 | continue;
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151 |
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152 | var replacement = anySubtreeSymbol.CreateTreeNode();
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153 | ReplaceSubtree(node, replacement, false);
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154 | replaced = true;
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155 | }
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156 | if (replaced) {
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157 | var scope = new Scope("Schema");
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158 | scope.Variables.Add(new Core.Variable("Schema", schema));
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159 | scope.SubScopes.AddRange(ShallowCopy(scopes));
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160 |
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161 | oc.Add(ExecutionContext.CreateChildOperation(schemaEvaluator, scope));
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162 | ExecutionContext.Scope.SubScopes.Add(scope);
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163 | }
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164 | }
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165 | #endregion
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166 |
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167 | var cleanup = ExecutionContext.CreateChildOperation(schemaCleanupOperator);
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168 | // return an operation collection containing all the scope operations + base.Apply()
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169 | return new OperationCollection { oc, reduceChangedTrees, collectValues, collectResults, cleanup, base.Apply() };
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170 | }
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171 |
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172 | private static ScopeList ShallowCopy(ScopeList scopes) {
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173 | var scopeList = new ScopeList();
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174 | // shallow-copy means that we create a new scope but reuse the variables
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175 | foreach (var scope in scopes) {
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176 | var s = new Scope(scope.Name);
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177 | foreach (var v in scope.Variables)
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178 | s.Variables.Add(v);
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179 | scopeList.Add(s);
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180 | }
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181 | return scopeList;
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182 | }
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183 |
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184 | private static void ReplaceSubtree(ISymbolicExpressionTreeNode original, ISymbolicExpressionTreeNode replacement,
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185 | bool preserveChildren = true) {
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186 | var parent = original.Parent;
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187 | if (parent == null)
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188 | throw new ArgumentException("Parent cannot be null for node " + original);
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189 | var index = parent.IndexOfSubtree(original);
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190 | parent.RemoveSubtree(index);
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191 | parent.InsertSubtree(index, replacement);
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192 |
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193 | if (preserveChildren) {
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194 | var subtrees = original.Subtrees.ToList();
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195 |
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196 | for (int i = subtrees.Count - 1; i >= 0; --i)
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197 | original.RemoveSubtree(i);
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198 |
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199 | for (int i = 0; i < subtrees.Count; ++i) {
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200 | replacement.AddSubtree(subtrees[i]);
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201 | }
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202 | }
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203 | }
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204 | }
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205 | }
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