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.Collections.Generic;
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24 | using System.Linq;
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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.Parameters;
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31 | using HeuristicLab.Persistence.Default.CompositeSerializers.Storable;
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32 |
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33 | namespace HeuristicLab.Problems.DataAnalysis.Symbolic {
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34 | [Item("SchemaCreator", "An operator that builds schemas based on the heredity relationship in the genealogy graph.")]
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35 | [StorableClass]
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36 | public class SchemaCreator : EvolutionTrackingOperator<ISymbolicExpressionTree> {
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37 | #region parameter names
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38 | private const string MinimumSchemaLengthParameterName = "MinimumSchemaLength";
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39 | private const string MinimumSchemaFrequencyParameterName = "MinimumSchemaFrequency";
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40 | private const string MinimumPhenotypicSimilarityParameterName = "MinimumPhenotypicSimilarity";
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41 | private const string ReplacementRatioParameterName = "ReplacementRatio";
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42 | private const string RandomReplacementParameterName = "RandomReplacement";
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43 | private const string ExecuteInParallelParameterName = "ExecuteInParallel";
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44 | private const string MaxDegreeOfParalellismParameterName = "MaxDegreeOfParallelism";
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45 | private const string PercentageOfPopulationParameterName = "PercentageOfPopulationToDiversify";
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46 | private const string ScaleEstimatedValuesParameterName = "ScaleEstimatedValues";
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47 | private const string ExclusiveMatchingParameterName = "ExclusiveMatching";
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48 | private const string NumberOfChangedTreesParameterName = "NumberOfChangedTrees";
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49 | private const string NumberOfSchemasParameterName = "NumberOfSchemas";
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50 | private const string AverageSchemaLengthParameterName = "AverageSchemaLength";
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51 | private const string UseAdaptiveReplacementRatioParameterName = "UseAdaptiveReplacementRatio";
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52 | private const string ReplacementRatioUpdateRuleParameterName = "ReplacementRatioUpdateRule";
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53 | #endregion
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54 |
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55 | #region parameters
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56 |
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57 | public IConstrainedValueParameter<StringValue> ReplacementRatioUpdateRuleParameter {
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58 | get { return (IConstrainedValueParameter<StringValue>)Parameters[ReplacementRatioUpdateRuleParameterName]; }
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59 | }
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60 | public IFixedValueParameter<BoolValue> UseAdaptiveReplacementRatioParameter {
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61 | get { return (IFixedValueParameter<BoolValue>)Parameters[UseAdaptiveReplacementRatioParameterName]; }
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62 | }
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63 | public IFixedValueParameter<BoolValue> ExclusiveMatchingParameter {
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64 | get { return (IFixedValueParameter<BoolValue>)Parameters[ExclusiveMatchingParameterName]; }
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65 | }
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66 | public IFixedValueParameter<BoolValue> ScaleEstimatedValuesParameter {
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67 | get { return (IFixedValueParameter<BoolValue>)Parameters[ScaleEstimatedValuesParameterName]; }
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68 | }
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69 | public IFixedValueParameter<PercentValue> PercentageOfPopulationParameter {
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70 | get { return (IFixedValueParameter<PercentValue>)Parameters[PercentageOfPopulationParameterName]; }
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71 | }
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72 | public IFixedValueParameter<IntValue> MinimumSchemaLengthParameter {
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73 | get { return (IFixedValueParameter<IntValue>)Parameters[MinimumSchemaLengthParameterName]; }
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74 | }
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75 | public IFixedValueParameter<BoolValue> ExecuteInParallelParameter {
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76 | get { return (IFixedValueParameter<BoolValue>)Parameters[ExecuteInParallelParameterName]; }
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77 | }
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78 | public IFixedValueParameter<IntValue> MaxDegreeOfParallelismParameter {
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79 | get { return (IFixedValueParameter<IntValue>)Parameters[MaxDegreeOfParalellismParameterName]; }
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80 | }
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81 | public IFixedValueParameter<PercentValue> MinimumSchemaFrequencyParameter {
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82 | get { return (IFixedValueParameter<PercentValue>)Parameters[MinimumSchemaFrequencyParameterName]; }
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83 | }
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84 | public IFixedValueParameter<PercentValue> MinimumPhenotypicSimilarityParameter {
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85 | get { return (IFixedValueParameter<PercentValue>)Parameters[MinimumPhenotypicSimilarityParameterName]; }
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86 | }
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87 | public IFixedValueParameter<PercentValue> ReplacementRatioParameter {
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88 | get { return (IFixedValueParameter<PercentValue>)Parameters[ReplacementRatioParameterName]; }
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89 | }
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90 | public IValueParameter<IntValue> NumberOfSchemasParameter {
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91 | get { return (IValueParameter<IntValue>)Parameters[NumberOfSchemasParameterName]; }
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92 | }
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93 | public IValueParameter<DoubleValue> AverageSchemaLengthParameter {
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94 | get { return (IValueParameter<DoubleValue>)Parameters[AverageSchemaLengthParameterName]; }
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95 | }
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96 | public IValueParameter<IntValue> NumberOfChangedTreesParameter {
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97 | get { return (IValueParameter<IntValue>)Parameters[NumberOfChangedTreesParameterName]; }
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98 | }
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99 | #endregion
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100 |
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101 | #region parameter properties
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102 | public int MinimumSchemaLength { get { return MinimumSchemaLengthParameter.Value.Value; } }
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103 | public int MaxDegreeOfParallelism { get { return MaxDegreeOfParallelismParameter.Value.Value; } }
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104 | public bool ExecuteInParallel { get { return ExecuteInParallelParameter.Value.Value; } }
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105 | public double PercentageOfPopulation { get { return PercentageOfPopulationParameter.Value.Value; } }
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106 | #endregion
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107 |
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108 | private UpdateEstimatedValuesOperator updateEstimatedValuesOperator;
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109 | private DiversificationStatisticsOperator diversificationStatisticsOperator;
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110 |
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111 | public SchemaCreator() {
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112 | #region add parameters
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113 | Parameters.Add(new FixedValueParameter<IntValue>(MinimumSchemaLengthParameterName, new IntValue(10)));
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114 | Parameters.Add(new FixedValueParameter<PercentValue>(MinimumSchemaFrequencyParameterName, new PercentValue(0.01)));
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115 | Parameters.Add(new FixedValueParameter<PercentValue>(MinimumPhenotypicSimilarityParameterName, new PercentValue(0.9)));
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116 | Parameters.Add(new FixedValueParameter<PercentValue>(ReplacementRatioParameterName, new PercentValue(0.9)));
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117 | Parameters.Add(new FixedValueParameter<PercentValue>(PercentageOfPopulationParameterName, new PercentValue(1)));
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118 | Parameters.Add(new FixedValueParameter<BoolValue>(RandomReplacementParameterName, new BoolValue(false)));
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119 | Parameters.Add(new FixedValueParameter<BoolValue>(ExecuteInParallelParameterName, new BoolValue(false)));
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120 | Parameters.Add(new FixedValueParameter<IntValue>(MaxDegreeOfParalellismParameterName, new IntValue(-1)));
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121 | Parameters.Add(new FixedValueParameter<BoolValue>(ScaleEstimatedValuesParameterName, new BoolValue(true)));
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122 | Parameters.Add(new FixedValueParameter<BoolValue>(ExclusiveMatchingParameterName, new BoolValue(false)));
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123 | Parameters.Add(new ValueParameter<IntValue>(NumberOfChangedTreesParameterName, new IntValue(0)));
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124 | Parameters.Add(new ValueParameter<IntValue>(NumberOfSchemasParameterName, new IntValue(0)));
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125 | Parameters.Add(new ValueParameter<DoubleValue>(AverageSchemaLengthParameterName, new DoubleValue(0)));
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126 | Parameters.Add(new FixedValueParameter<BoolValue>(UseAdaptiveReplacementRatioParameterName, new BoolValue(true)));
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127 |
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128 | var replacementRatioUpdateRules = new ItemSet<StringValue>(new[] { new StringValue("f(x) = x"), new StringValue("f(x) = tanh(x)"), new StringValue("f(x) = tanh(2x)"), new StringValue("f(x) = tanh(3x)") });
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129 | Parameters.Add(new ConstrainedValueParameter<StringValue>(ReplacementRatioUpdateRuleParameterName, replacementRatioUpdateRules));
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130 | #endregion
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131 | NumberOfChangedTreesParameter.Hidden = true;
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132 | NumberOfSchemasParameter.Hidden = true;
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133 | AverageSchemaLengthParameter.Hidden = true;
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134 |
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135 | ExecuteInParallelParameter.Hidden = true;
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136 | MaxDegreeOfParallelismParameter.Hidden = true;
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137 | }
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138 |
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139 | protected SchemaCreator(SchemaCreator original, Cloner cloner) : base(original, cloner) { }
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140 |
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141 | public override IDeepCloneable Clone(Cloner cloner) {
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142 | return new SchemaCreator(this, cloner);
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143 | }
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144 |
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145 | [StorableConstructor]
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146 | protected SchemaCreator(bool deserializing) : base(deserializing) { }
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147 |
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148 | public override IOperation Apply() {
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149 | // apply only when at least one generation has passed
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150 | var gen = Generations.Value;
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151 | if (gen < 1 || GenealogyGraph == null)
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152 | return base.Apply();
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153 |
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154 | var n = (int)Math.Round(ExecutionContext.Scope.SubScopes.Count * PercentageOfPopulation);
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155 | var scopes = new ScopeList(ExecutionContext.Scope.SubScopes.Take(n));
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156 |
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157 | var updateEstimatedValues = new OperationCollection { Parallel = true };
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158 | if (updateEstimatedValuesOperator == null)
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159 | updateEstimatedValuesOperator = new UpdateEstimatedValuesOperator();
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160 |
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161 | foreach (var s in scopes) {
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162 | if (!s.Variables.ContainsKey("EstimatedValues"))
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163 | s.Variables.Add(new Core.Variable("EstimatedValues"));
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164 | updateEstimatedValues.Add(ExecutionContext.CreateChildOperation(updateEstimatedValuesOperator, s));
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165 | }
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166 |
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167 | Func<double, double> rule;
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168 | var replacementRule = ReplacementRatioUpdateRuleParameter.Value.Value;
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169 |
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170 | switch (replacementRule) {
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171 | case "f(x) = x": {
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172 | rule = x => x;
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173 | break;
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174 | }
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175 | case "f(x) = tanh(x)": {
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176 | rule = x => Math.Tanh(x);
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177 | break;
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178 | }
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179 | case "f(x) = tanh(2x)": {
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180 | rule = x => Math.Tanh(2 * x);
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181 | break;
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182 | }
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183 | case "f(x) = tanh(3x)": {
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184 | rule = x => Math.Tanh(3 * x);
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185 | break;
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186 | }
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187 | default:
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188 | throw new ArgumentException("Unknown replacement rule");
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189 | }
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190 |
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191 | var evaluateSchemas = new OperationCollection();
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192 |
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193 | // for now, only consider crossover offspring
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194 | var vertices = from s in scopes
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195 | let t = (ISymbolicExpressionTree)s.Variables["SymbolicExpressionTree"].Value
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196 | let v = GenealogyGraph.GetByContent(t)
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197 | where v.InDegree == 2
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198 | select v;
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199 |
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200 | var schemas = new List<ISymbolicExpressionTree>(GenerateSchemas(vertices, MinimumSchemaLength));
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201 |
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202 | #region create schemas and add subscopes representing the individuals
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203 | foreach (var schema in schemas) {
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204 | evaluateSchemas.Add(ExecutionContext.CreateChildOperation(new SchemaEvaluator { Schema = schema, ReplacementRule = rule }, ExecutionContext.Scope));
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205 | }
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206 | #endregion
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207 |
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208 | if (diversificationStatisticsOperator == null)
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209 | diversificationStatisticsOperator = new DiversificationStatisticsOperator();
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210 |
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211 | var calculateStatistics = ExecutionContext.CreateChildOperation(diversificationStatisticsOperator);
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212 |
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213 | // set parameters for statistics
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214 | AverageSchemaLengthParameter.Value = new DoubleValue(schemas.Average(x => x.Length));
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215 | NumberOfSchemasParameter.Value = new IntValue(schemas.Count);
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216 | NumberOfChangedTreesParameter.Value = new IntValue(0);
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217 |
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218 | // return an operation collection containing all the scope operations + base.Apply()
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219 | return new OperationCollection { updateEstimatedValues, evaluateSchemas, calculateStatistics, base.Apply() };
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220 | }
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221 |
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222 | public static IEnumerable<ISymbolicExpressionTree> GenerateSchemas(IEnumerable<IGenealogyGraphNode<ISymbolicExpressionTree>> vertices, int minimumSchemaLength) {
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223 | var anySubtreeSymbol = new AnySubtreeSymbol();
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224 | // var anyNodeSymbol = new AnyNodeSymbol();
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225 | var groups = vertices.GroupBy(x => x.Parents.First()).OrderByDescending(g => g.Count()).ToList();
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226 | var hash = new HashSet<string>();
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227 | var formatter = new SymbolicExpressionTreeStringFormatter { Indent = false, AppendNewLines = false };
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228 | foreach (var g in groups) {
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229 | var parent = g.Key;
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230 | if (parent.Data.Length < minimumSchemaLength)
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231 | continue;
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232 | bool replaced = false;
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233 | var schema = (ISymbolicExpressionTree)parent.Data.Clone();
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234 | var nodes = schema.IterateNodesPrefix().ToList();
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235 | var arcs = g.Select(x => x.InArcs.Last()).Where(x => x.Data != null);
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236 | var indices = (from arc in arcs
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237 | let fragment = (IFragment<ISymbolicExpressionTreeNode>)arc.Data
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238 | select fragment.Index1).Distinct().ToArray();
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239 | Array.Sort(indices);
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240 | var nodesToReplace = indices.Select(x => nodes[x]).ToList();
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241 | for (int i = nodesToReplace.Count - 1; i >= 0; --i) {
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242 | var node = nodesToReplace[i];
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243 |
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244 | // do not replace the node with a wildcard if it would result in a length < MinimumSchemaLength
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245 | if (schema.Length - node.GetLength() + 1 < minimumSchemaLength)
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246 | continue;
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247 |
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248 | // var replacement = anySubtreeSymbol.CreateTreeNode();
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249 | // ReplaceSubtree(node, replacement, false);
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250 | var replacement = new AnyNodeSymbol(node.Symbol.MinimumArity, node.Symbol.MinimumArity).CreateTreeNode();
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251 | ReplaceSubtree(node, replacement, true);
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252 | replaced = true;
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253 | }
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254 | if (replaced) {
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255 | var str = formatter.Format(schema.Root.GetSubtree(0).GetSubtree(0));
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256 | if (hash.Contains(str)) continue;
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257 | yield return schema;
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258 | hash.Add(str);
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259 | }
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260 | }
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261 | }
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262 |
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263 | private static void ReplaceSubtree(ISymbolicExpressionTreeNode original, ISymbolicExpressionTreeNode replacement, bool preserveChildren = true) {
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264 | var parent = original.Parent;
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265 | if (parent == null)
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266 | throw new ArgumentException("Parent cannot be null for node " + original);
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267 | var index = parent.IndexOfSubtree(original);
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268 | parent.RemoveSubtree(index);
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269 | parent.InsertSubtree(index, replacement);
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270 |
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271 | if (preserveChildren) {
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272 | var subtrees = original.Subtrees.ToList();
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273 |
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274 | for (int i = subtrees.Count - 1; i >= 0; --i)
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275 | original.RemoveSubtree(i);
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276 |
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277 | for (int i = 0; i < subtrees.Count; ++i) {
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278 | replacement.AddSubtree(subtrees[i]);
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279 | }
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280 | }
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281 | }
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282 | }
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283 | }
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