Added mathsym+tcc and boost against all advice
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maartenkeijzer
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58ae49dd99
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90702a435d
136 changed files with 14409 additions and 0 deletions
359
eo/contrib/mathsym/symreg.cpp
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359
eo/contrib/mathsym/symreg.cpp
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/*
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* Copyright (C) 2005 Maarten Keijzer
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*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of version 2 of the GNU General Public License as
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* published by the Free Software Foundation.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
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*/
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#include <LanguageTable.h>
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#include <TreeBuilder.h>
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#include <FunDef.h>
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#include <Dataset.h>
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#include <eoSymInit.h>
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#include <eoSym.h>
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#include <eoPop.h>
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#include <eoSymMutate.h>
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#include <eoSymCrossover.h>
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#include <eoSymEval.h>
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#include <eoOpContainer.h>
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#include <eoDetTournamentSelect.h>
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#include <eoMergeReduce.h>
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#include <eoGenContinue.h>
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#include <eoEasyEA.h>
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#include <eoGeneralBreeder.h>
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#include <utils/eoParser.h>
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#include <utils/eoCheckPoint.h>
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#include <utils/eoStat.h>
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#include <utils/eoStdoutMonitor.h>
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#include <utils/eoRNG.h>
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using namespace std;
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typedef EoSym<eoMinimizingFitness> EoType;
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static int functions_added = 0;
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void add_function(LanguageTable& table, eoParser& parser, string name, unsigned arity, token_t token, const FunDef& fun);
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void setup_language(LanguageTable& table, eoParser& parser);
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template <class T>
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T& select(bool check, T& a, T& b) { if (check) return a; return b; }
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class eoBestIndividualStat : public eoSortedStat<EoType, string> {
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public:
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eoBestIndividualStat() : eoSortedStat<EoType, string>("", "best individual") {}
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void operator()(const vector<const EoType*>& _pop) {
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ostringstream os;
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os << (Sym) *_pop[0];
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value() = os.str();
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}
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};
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class AverageSizeStat : public eoStat<EoType, double> {
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public:
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AverageSizeStat() : eoStat<EoType, double>(0.0, "Average size population") {}
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void operator()(const eoPop<EoType>& _pop) {
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double total = 0.0;
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for (unsigned i = 0; i < _pop.size(); ++i) {
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total += _pop[i].size();
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}
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value() = total/_pop.size();
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}
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};
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class SumSizeStat : public eoStat<EoType, unsigned> {
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public:
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SumSizeStat() : eoStat<EoType, unsigned>(0u, "Number of subtrees") {}
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void operator()(const eoPop<EoType>& _pop) {
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unsigned total = 0;
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for (unsigned i = 0; i < _pop.size(); ++i) {
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total += _pop[i].size();
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}
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value() = total;
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}
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};
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class DagSizeStat : public eoStat<EoType, unsigned> {
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public:
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DagSizeStat() : eoStat<EoType, unsigned>(0u, "Number of distinct subtrees") {}
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void operator()(const eoPop<EoType>& _pop) {
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value() = Sym::get_dag().size();
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}
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};
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int main(int argc, char* argv[]) {
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eoParser parser(argc, argv);
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/* Language */
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LanguageTable table;
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setup_language(table, parser);
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/* Data */
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eoValueParam<string> datafile = parser.createParam(string(""), "datafile", "Training data", 'd', string("Regression"), true); // mandatory
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double train_percentage = parser.createParam(1.0, "trainperc", "Percentage of data used for training", 0, string("Regression")).value();
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/* Population */
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unsigned pop_size = parser.createParam(1500u, "population-size", "Population Size", 'p', string("Population")).value();
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uint32_t seed = parser.createParam( uint32_t(time(0)), "random-seed", "Seed for rng", 'D').value();
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cout << "Seed " << seed << endl;
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rng.reseed(seed);
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double var_prob = parser.createParam(
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0.9,
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"var-prob",
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"Probability of selecting a var vs. const when creating a terminal",
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0,
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"Population").value();
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double grow_prob = parser.createParam(
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0.5,
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"grow-prob",
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"Probability of selecting 'grow' method instead of 'full' in initialization and mutation",
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0,
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"Population").value();
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unsigned max_depth = parser.createParam(
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8u,
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"max-depth",
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"Maximum depth used in initialization and mutation",
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0,
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"Population").value();
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bool use_uniform = parser.createParam(
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false,
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"use-uniform",
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"Use uniform node selection instead of bias towards internal nodes (functions)",
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0,
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"Population").value();
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double subtree_mut_prob = parser.createParam(
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0.2,
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"subtree-mut-rate",
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"Probability of performing subtree mutation",
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0,
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"Population").value();
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double node_mut_prob = parser.createParam(
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0.2,
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"node-mut-rate",
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"Probability of performing node mutation",
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0,
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"Population").value();
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double subtree_xover_prob = parser.createParam(
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0.4,
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"xover-rate",
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"Probability of performing subtree crossover",
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0,
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"Population").value();
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double homologous_prob = parser.createParam(
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0.4,
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"homologous-rate",
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"Probability of performing homologous crossover",
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0,
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"Population").value();
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unsigned max_gens = parser.createParam(
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50,
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"max-gens",
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"Maximum number of generations to run",
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'g',
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"Population").value();
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unsigned tournamentsize = parser.createParam(
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5,
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"tournament-size",
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"Tournament size used for selection",
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't',
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"Population").value();
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unsigned meas_param = parser.createParam(
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2u,
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"measure",
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"Error measure:\n\
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0 -> absolute error\n\
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1 -> mean squared error\n\
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2 -> mean squared error scaled (equivalent with correlation)\n\
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",
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'm',
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"Regression").value();
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ErrorMeasure::measure meas = ErrorMeasure::mean_squared_scaled;
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if (meas_param == 0) meas = ErrorMeasure::absolute;
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if (meas_param == 1) meas = ErrorMeasure::mean_squared;
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if (functions_added == 0) {
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cout << "ERROR: no functions defined" << endl;
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exit(1);
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}
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/* End parsing */
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if (parser.userNeedsHelp())
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{
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parser.printHelp(std::cout);
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return 1;
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}
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Dataset dataset;
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dataset.load_data(datafile.value());
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cout << "Data " << datafile.value() << " loaded " << endl;
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/* Add Variables */
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unsigned nvars = dataset.n_fields();
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for (unsigned i = 0; i < nvars; ++i) {
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table.add_function( SymVar(i).token(), 0);
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}
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TreeBuilder builder(table, var_prob);
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eoSymInit<EoType> init(builder, grow_prob, max_depth);
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eoPop<EoType> pop(pop_size, init);
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BiasedNodeSelector biased_sel;
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RandomNodeSelector random_sel;
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NodeSelector& node_selector = select<NodeSelector>(use_uniform, random_sel, biased_sel);
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eoProportionalOp<EoType> genetic_operator;
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eoSymSubtreeMutate<EoType> submutate(builder, node_selector);
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genetic_operator.add( submutate, subtree_mut_prob);
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eoSymNodeMutate<EoType> nodemutate(table);
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genetic_operator.add(nodemutate, node_mut_prob);
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//eoQuadSubtreeCrossover<EoType> quad(node_selector);
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eoBinSubtreeCrossover<EoType> bin(node_selector);
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genetic_operator.add(bin, subtree_xover_prob);
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eoBinHomologousCrossover<EoType> hom;
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genetic_operator.add(hom, homologous_prob);
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IntervalBoundsCheck check(dataset.input_minima(), dataset.input_maxima());
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ErrorMeasure measure(dataset, train_percentage, meas);
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eoSymPopEval<EoType> evaluator(check, measure);
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eoDetTournamentSelect<EoType> selectOne(tournamentsize);
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eoGeneralBreeder<EoType> breeder(selectOne, genetic_operator);
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eoPlusReplacement<EoType> replace;
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// Terminators
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eoGenContinue<EoType> term(max_gens);
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eoCheckPoint<EoType> checkpoint(term);
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eoBestFitnessStat<EoType> beststat;
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checkpoint.add(beststat);
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eoBestIndividualStat printer;
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AverageSizeStat avgSize;
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DagSizeStat dagSize;
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SumSizeStat sumSize;
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checkpoint.add(printer);
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checkpoint.add(avgSize);
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checkpoint.add(dagSize);
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checkpoint.add(sumSize);
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eoStdoutMonitor genmon;
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genmon.add(beststat);
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genmon.add(printer);
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genmon.add(avgSize);
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genmon.add(dagSize);
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genmon.add(sumSize);
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checkpoint.add(genmon);
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eoPop<EoType> dummy;
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evaluator(pop, dummy);
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eoEasyEA<EoType> ea(checkpoint, evaluator, breeder, replace);
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ea(pop); // run
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}
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void add_function(LanguageTable& table, eoParser& parser, string name, unsigned arity, token_t token, const FunDef& fun, bool all) {
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ostringstream desc;
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desc << "Enable function " << name << " arity = " << arity;
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bool enabled = parser.createParam(false, name, desc.str(), 0, "Language").value();
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if (enabled || all) {
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cout << "Func " << name << " enabled" << endl;
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table.add_function(token, arity);
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if (arity > 0) functions_added++;
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}
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}
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void setup_language(LanguageTable& table, eoParser& parser) {
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bool all = parser.createParam(false,"all", "Enable all functions").value();
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bool ratio = parser.createParam(false,"ratio","Enable rational functions (inv,min,sum,prod)").value();
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bool poly = parser.createParam(false,"poly","Enable polynomial functions (min,sum,prod)").value();
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// assumes that at this point all tokens are defined (none are zeroed out, which can happen with ERCs)
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vector<const FunDef*> lang = get_defined_functions();
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for (token_t i = 0; i < lang.size(); ++i) {
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if (lang[i] == 0) continue;
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bool is_poly = false;
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if (poly && (i == prod_token || i == sum_token || i == min_token) ) {
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is_poly = true;
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}
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bool is_ratio = false;
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if (ratio && (is_poly || i == inv_token)) {
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is_ratio = true;
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}
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const FunDef& fun = *lang[i];
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if (fun.has_varargs() ) {
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for (unsigned j = fun.min_arity(); j < fun.min_arity() + 8; ++j) {
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if (j==1) continue; // prod 1 and sum 1 are useless
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ostringstream nm;
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nm << fun.name() << j;
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bool addanyway = (all || is_ratio || is_poly) && j == 2;
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add_function(table, parser, nm.str(), j, i, fun, addanyway);
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}
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}
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else {
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add_function(table, parser, fun.name(), fun.min_arity(), i, fun, all || is_ratio || is_poly);
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}
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}
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}
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