From 1f66526f43127478ea3fc05c0cba994425d44755 Mon Sep 17 00:00:00 2001 From: verel Date: Thu, 6 May 2010 15:13:51 +0000 Subject: [PATCH] Ajout du neutral degree, et correction Royal Road git-svn-id: svn://scm.gforge.inria.fr/svnroot/paradiseo@1790 331e1502-861f-0410-8da2-ba01fb791d7f --- trunk/paradiseo-mo/src/algo/moRandomSearch.h | 4 +- .../src/continuator/moNeighborhoodStat.h | 20 ++ .../src/continuator/moVectorMonitor.h | 10 + trunk/paradiseo-mo/src/mo.h | 2 + .../src/problems/eval/moRoyalRoadIncrEval.h | 18 +- .../src/sampling/moAutocorrelationSampling.h | 2 + .../src/sampling/moNeutralDegreeSampling.h | 124 ++++++++++ trunk/paradiseo-mo/src/sampling/moSampling.h | 18 +- .../tutorial/Lesson6/CMakeLists.txt | 2 + .../tutorial/Lesson6/autocorrelation.cpp | 2 +- .../tutorial/Lesson6/neutralDegree.cpp | 215 ++++++++++++++++++ trunk/problems/eval/royalRoadEval.h | 10 +- 12 files changed, 409 insertions(+), 18 deletions(-) create mode 100644 trunk/paradiseo-mo/src/sampling/moNeutralDegreeSampling.h create mode 100644 trunk/paradiseo-mo/tutorial/Lesson6/neutralDegree.cpp diff --git a/trunk/paradiseo-mo/src/algo/moRandomSearch.h b/trunk/paradiseo-mo/src/algo/moRandomSearch.h index 693f728b6..ba5beff67 100644 --- a/trunk/paradiseo-mo/src/algo/moRandomSearch.h +++ b/trunk/paradiseo-mo/src/algo/moRandomSearch.h @@ -58,7 +58,7 @@ public: */ moRandomSearch(eoInit & _init, eoEvalFunc& _fullEval, unsigned _nbSolMax): moLocalSearch(explorer, trueCont, _fullEval), - explorer(_init, _fullEval, _nbSolMax - 1) + explorer(_init, _fullEval, _nbSolMax>0?_nbSolMax - 1:0) {} /** @@ -69,7 +69,7 @@ public: */ moRandomSearch(eoInit & _init, eoEvalFunc& _fullEval, unsigned _nbSolMax, moContinuator& _cont): moLocalSearch(explorer, _cont, _fullEval), - explorer(_init, _fullEval, _nbSolMax - 1) + explorer(_init, _fullEval, _nbSolMax>0?_nbSolMax - 1:0) {} private: diff --git a/trunk/paradiseo-mo/src/continuator/moNeighborhoodStat.h b/trunk/paradiseo-mo/src/continuator/moNeighborhoodStat.h index ab10174fb..3806b8551 100644 --- a/trunk/paradiseo-mo/src/continuator/moNeighborhoodStat.h +++ b/trunk/paradiseo-mo/src/continuator/moNeighborhoodStat.h @@ -70,6 +70,20 @@ public : solNeighborComparator(_solNeighborComparator) {} + /** + * Default Constructor + * where the comparators are basic, there only compare the fitness values + * + * @param _neighborhood a neighborhood + * @param _eval an evaluation function + */ + moNeighborhoodStat(Neighborhood& _neighborhood, moEval& _eval): + moStat(true, "neighborhood"), + neighborhood(_neighborhood), eval(_eval), + neighborComparator(defaultNeighborComp), + solNeighborComparator(defaultSolNeighborComp) + {} + /** * Compute classical statistics of the first solution's neighborhood * @param _solution the first solution @@ -229,6 +243,12 @@ private: moNeighborComparator& neighborComparator; moSolNeighborComparator& solNeighborComparator; + // default comparators + // compare the fitness values of neighbors: true is strictly greater + moNeighborComparator defaultNeighborComp; + // compare the fitness values of the solution and the neighbor: true if strictly greater + moSolNeighborComparator defaultSolNeighborComp; + // the stastics of the fitness Fitness max, min; //mean and standard deviation diff --git a/trunk/paradiseo-mo/src/continuator/moVectorMonitor.h b/trunk/paradiseo-mo/src/continuator/moVectorMonitor.h index 049b8a500..6114b4ed5 100644 --- a/trunk/paradiseo-mo/src/continuator/moVectorMonitor.h +++ b/trunk/paradiseo-mo/src/continuator/moVectorMonitor.h @@ -69,6 +69,16 @@ public: moVectorMonitor(eoValueParam & _param) : doubleParam(NULL), intParam(NULL), eotParam(&_param) { } + /** + * Default Constructor + * @param _param the parameter of type EOT to save in the vector + */ + template + moVectorMonitor(eoValueParam & _param) : doubleParam(NULL), intParam(NULL), eotParam(NULL) + { + std::cerr << "Sorry the type can not be in a vector of moVectorMonitor" << std::endl; + } + /** * To test if the value are basic type (double or unsigned int), or EOT type * diff --git a/trunk/paradiseo-mo/src/mo.h b/trunk/paradiseo-mo/src/mo.h index 2755178a2..dcc2ca12f 100755 --- a/trunk/paradiseo-mo/src/mo.h +++ b/trunk/paradiseo-mo/src/mo.h @@ -140,6 +140,8 @@ #include #include #include +#include +#include #include #include diff --git a/trunk/paradiseo-mo/src/problems/eval/moRoyalRoadIncrEval.h b/trunk/paradiseo-mo/src/problems/eval/moRoyalRoadIncrEval.h index a20965851..66a6bf4b9 100644 --- a/trunk/paradiseo-mo/src/problems/eval/moRoyalRoadIncrEval.h +++ b/trunk/paradiseo-mo/src/problems/eval/moRoyalRoadIncrEval.h @@ -31,6 +31,7 @@ Contact: paradiseo-help@lists.gforge.inria.fr #define _moRoyalRoadIncrEval_H #include +#include /** * Incremental evaluation Function for the Royal Road problem @@ -45,7 +46,7 @@ public: * Default constructor * @param _k size of a block */ - moRoyalRoadIncrEval(unsigned int _k) : k(_k) {} + moRoyalRoadIncrEval(RoyalRoadEval & _rr) : k(_rr.blockSize()) {} /* * incremental evaluation of the neighbor for the Royal Road problem @@ -53,13 +54,13 @@ public: * @param _neighbor the neighbor to consider (of type moBitNeigbor) */ virtual void operator()(EOT & _solution, Neighbor & _neighbor) { - // which block can change? + // which block can be changed? unsigned int n = _neighbor.index() / k; // complete block? - offset = n * k; + unsigned int offset = n * k; - j = 0; + unsigned int j = 0; while (_solution[offset + j] && j < k) j++; if (j == k) // the block is complete, so the fitness decreases from one @@ -71,9 +72,16 @@ public: if (j == k) // the block can be filled, so the fitness increases from one _neighbor.fitness(_solution.fitness() + 1); - } + else + _neighbor.fitness(_solution.fitness()); + } else + _neighbor.fitness(_solution.fitness()); } } + +protected: + // size of the blocks + unsigned int k; }; #endif diff --git a/trunk/paradiseo-mo/src/sampling/moAutocorrelationSampling.h b/trunk/paradiseo-mo/src/sampling/moAutocorrelationSampling.h index e667a0cd5..4061a8052 100644 --- a/trunk/paradiseo-mo/src/sampling/moAutocorrelationSampling.h +++ b/trunk/paradiseo-mo/src/sampling/moAutocorrelationSampling.h @@ -61,6 +61,8 @@ public: * Default Constructor * @param _init initialisation method of the solution * @param _neighborhood neighborhood giving neighbor in random order + * @param _fullEval Fitness function, full evaluation function + * @param _eval neighbor evaluation, incremental evaluation function * @param _nbStep Number of steps of the random walk */ moAutocorrelationSampling(eoInit & _init, diff --git a/trunk/paradiseo-mo/src/sampling/moNeutralDegreeSampling.h b/trunk/paradiseo-mo/src/sampling/moNeutralDegreeSampling.h new file mode 100644 index 000000000..6ea7d4ab0 --- /dev/null +++ b/trunk/paradiseo-mo/src/sampling/moNeutralDegreeSampling.h @@ -0,0 +1,124 @@ +/* + + Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010 + + Sebastien Verel, Arnaud Liefooghe, Jeremie Humeau + + This software is governed by the CeCILL license under French law and + abiding by the rules of distribution of free software. You can use, + modify and/ or redistribute the software under the terms of the CeCILL + license as circulated by CEA, CNRS and INRIA at the following URL + "http://www.cecill.info". + + As a counterpart to the access to the source code and rights to copy, + modify and redistribute granted by the license, users are provided only + with a limited warranty and the software's author, the holder of the + economic rights, and the successive licensors have only limited liability. + + In this respect, the user's attention is drawn to the risks associated + with loading, using, modifying and/or developing or reproducing the + software by the user in light of its specific status of free software, + that may mean that it is complicated to manipulate, and that also + therefore means that it is reserved for developers and experienced + professionals having in-depth computer knowledge. Users are therefore + encouraged to load and test the software's suitability as regards their + requirements in conditions enabling the security of their systems and/or + data to be ensured and, more generally, to use and operate it in the + same conditions as regards security. + The fact that you are presently reading this means that you have had + knowledge of the CeCILL license and that you accept its terms. + + ParadisEO WebSite : http://paradiseo.gforge.inria.fr + Contact: paradiseo-help@lists.gforge.inria.fr +*/ + +#ifndef moNeutralDegreeSampling_h +#define moNeutralDegreeSampling_h + +#include +#include +#include +#include +#include +#include +#include +#include +#include + +/** + * To compute the density of states: + * Sample the fitness of random solution in the search space + * The fitness values of solutions are collected during the random search + * + */ +template +class moNeutralDegreeSampling : public moSampling +{ +public: + typedef typename Neighbor::EOT EOT ; + + using moSampling::localSearch; + + /** + * Default Constructor + * @param _init initialisation method of the solution + * @param _neighborhood neighborhood to compute the neutral degree + * @param _fullEval Fitness function, full evaluation function + * @param _eval neighbor evaluation, incremental evaluation function + * @param _nbSol Number of solutions in the sample + */ + moNeutralDegreeSampling(eoInit & _init, + moNeighborhood & _neighborhood, + eoEvalFunc& _fullEval, + moEval& _eval, + unsigned int _nbSol) : + moSampling(_init, * new moRandomSearch(_init, _fullEval, _nbSol), fitnessStat), + neighborhoodStat(_neighborhood, _eval), + ndStat(neighborhoodStat) + { + add(neighborhoodStat, false); + add(ndStat); + } + + /** + * Constructor with comparators + * @param _init initialisation method of the solution + * @param _neighborhood neighborhood to compute the neutral degree + * @param _fullEval Fitness function, full evaluation function + * @param _eval neighbor evaluation, incremental evaluation function + * @param _neighborComparator a neighbor Comparator + * @param _solNeighborComparator a comparator between a solution and a neighbor + * @param _nbSol Number of solutions in the sample + */ + moNeutralDegreeSampling(eoInit & _init, + moNeighborhood & _neighborhood, + eoEvalFunc& _fullEval, + moEval& _eval, + moNeighborComparator& _neighborComparator, + moSolNeighborComparator& _solNeighborComparator, + unsigned int _nbSol) : + moSampling(_init, * new moRandomSearch(_init, _fullEval, _nbSol), fitnessStat), + neighborhoodStat(_neighborhood, _eval, _neighborComparator, _solNeighborComparator), + ndStat(neighborhoodStat) + { + add(neighborhoodStat, false); + add(ndStat); + } + + /** + * default destructor + */ + ~moNeutralDegreeSampling() { + // delete the pointer on the local search which has been constructed in the constructor + delete &localSearch; + } + +protected: + moFitnessStat fitnessStat; + moNeighborhoodStat< Neighbor > neighborhoodStat; + moNeutralDegreeNeighborStat< Neighbor > ndStat; + +}; + + +#endif diff --git a/trunk/paradiseo-mo/src/sampling/moSampling.h b/trunk/paradiseo-mo/src/sampling/moSampling.h index 75f46d09a..847e65b42 100644 --- a/trunk/paradiseo-mo/src/sampling/moSampling.h +++ b/trunk/paradiseo-mo/src/sampling/moSampling.h @@ -64,10 +64,10 @@ public: * @param _stat statistic to compute during the search */ template - moSampling(eoInit & _init, moLocalSearch & _localSearch, moStat & _stat) : init(_init), localSearch(_localSearch), continuator(_localSearch.getContinuator()) + moSampling(eoInit & _init, moLocalSearch & _localSearch, moStat & _stat, bool _monitoring = true) : init(_init), localSearch(_localSearch), continuator(_localSearch.getContinuator()) { checkpoint = new moCheckpoint(*continuator); - add(_stat); + add(_stat, _monitoring); } /** @@ -87,14 +87,14 @@ public: * @param _stat another statistic to compute during the search */ template< class ValueType > - void add(moStat & _stat) { - // statVec.push_back(&_stat); - - moVectorMonitor * monitor = new moVectorMonitor(_stat); - monitorVec.push_back(monitor); - + void add(moStat & _stat, bool _monitoring = true) { checkpoint->add(_stat); - checkpoint->add(*monitor); + + if (_monitoring) { + moVectorMonitor * monitor = new moVectorMonitor(_stat); + monitorVec.push_back(monitor); + checkpoint->add(*monitor); + } } /** diff --git a/trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt b/trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt index 77b365fb7..7dde0b881 100644 --- a/trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt +++ b/trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt @@ -14,6 +14,7 @@ ADD_EXECUTABLE(densityOfStates densityOfStates.cpp) ADD_EXECUTABLE(autocorrelation autocorrelation.cpp) ADD_EXECUTABLE(adaptiveWalks adaptiveWalks.cpp) ADD_EXECUTABLE(fdc fdc.cpp) +ADD_EXECUTABLE(neutralDegree neutralDegree.cpp) TARGET_LINK_LIBRARIES(testRandomWalk eoutils ga eo) TARGET_LINK_LIBRARIES(testMetropolisHasting eoutils ga eo) @@ -23,3 +24,4 @@ TARGET_LINK_LIBRARIES(densityOfStates eoutils ga eo) TARGET_LINK_LIBRARIES(autocorrelation eoutils ga eo) TARGET_LINK_LIBRARIES(adaptiveWalks eoutils ga eo) TARGET_LINK_LIBRARIES(fdc eoutils ga eo) +TARGET_LINK_LIBRARIES(neutralDegree eoutils ga eo) diff --git a/trunk/paradiseo-mo/tutorial/Lesson6/autocorrelation.cpp b/trunk/paradiseo-mo/tutorial/Lesson6/autocorrelation.cpp index 78dff0e87..42cca81e2 100644 --- a/trunk/paradiseo-mo/tutorial/Lesson6/autocorrelation.cpp +++ b/trunk/paradiseo-mo/tutorial/Lesson6/autocorrelation.cpp @@ -1,5 +1,5 @@ //----------------------------------------------------------------------------- -/** sampling.cpp +/** autocorrelation.cpp * * SV - 03/05/10 * diff --git a/trunk/paradiseo-mo/tutorial/Lesson6/neutralDegree.cpp b/trunk/paradiseo-mo/tutorial/Lesson6/neutralDegree.cpp new file mode 100644 index 000000000..2443c3ad0 --- /dev/null +++ b/trunk/paradiseo-mo/tutorial/Lesson6/neutralDegree.cpp @@ -0,0 +1,215 @@ +//----------------------------------------------------------------------------- +/** neutralDegree.cpp + * + * SV - 03/05/10 + * + */ +//----------------------------------------------------------------------------- + +// standard includes +#define HAVE_SSTREAM + +#include // runtime_error +#include // cout +#include // ostrstream, istrstream +#include +#include + +// the general include for eo +#include + +// declaration of the namespace +using namespace std; + +//----------------------------------------------------------------------------- +// representation of solutions, and neighbors +#include // bit string : see also EO tutorial lesson 1: FirstBitGA.cpp +#include // neighbor of bit string + +//----------------------------------------------------------------------------- +// fitness function, and evaluation of neighbors +#include +#include + +//----------------------------------------------------------------------------- +// neighborhood description +#include // visit all neighbor in order of their bit-flip + +//----------------------------------------------------------------------------- +// the sampling class +#include + +// Declaration of types +//----------------------------------------------------------------------------- +// Indi is the typedef of the solution type like in paradisEO-eo +typedef eoBit Indi; // bit string with unsigned fitness type +// Neighbor is the typedef of the neighbor type, +// Neighbor = How to compute the neighbor from the solution + information on it (i.e. fitness) +// all classes from paradisEO-mo use this template type +typedef moBitNeighbor Neighbor ; // bit string neighbor with unsigned fitness type + + +void main_function(int argc, char **argv) +{ + /* ========================================================= + * + * Parameters + * + * ========================================================= */ + // more information on the input parameters: see EO tutorial lesson 3 + // but don't care at first it just read the parameters of the bit string size and the random seed. + + // First define a parser from the command-line arguments + eoParser parser(argc, argv); + + // For each parameter, define Parameter, read it through the parser, + // and assign the value to the variable + + // random seed parameter + eoValueParam seedParam(time(0), "seed", "Random number seed", 'S'); + parser.processParam( seedParam ); + unsigned seed = seedParam.value(); + + // length of the bit string + eoValueParam vecSizeParam(20, "vecSize", "Genotype size", 'V'); + parser.processParam( vecSizeParam, "Representation" ); + unsigned vecSize = vecSizeParam.value(); + + // size of the block + eoValueParam blockSizeParam(4, "blockSize", "Block size of the Royal Road", 'k'); + parser.processParam( blockSizeParam, "Representation" ); + unsigned blockSize = blockSizeParam.value(); + + // the number of solution sampled + eoValueParam solParam(100, "nbSol", "Number of random solution", 'n'); + parser.processParam( solParam, "Representation" ); + unsigned nbSol = solParam.value(); + + // the name of the output file + string str_out = "out.dat"; // default value + eoValueParam outParam(str_out.c_str(), "out", "Output file of the sampling", 'o'); + parser.processParam(outParam, "Persistence" ); + + // the name of the "status" file where all actual parameter values will be saved + string str_status = parser.ProgramName() + ".status"; // default value + eoValueParam statusParam(str_status.c_str(), "status", "Status file"); + parser.processParam( statusParam, "Persistence" ); + + // do the following AFTER ALL PARAMETERS HAVE BEEN PROCESSED + // i.e. in case you need parameters somewhere else, postpone these + if (parser.userNeedsHelp()) { + parser.printHelp(cout); + exit(1); + } + if (statusParam.value() != "") { + ofstream os(statusParam.value().c_str()); + os << parser;// and you can use that file as parameter file + } + + /* ========================================================= + * + * Random seed + * + * ========================================================= */ + + // reproducible random seed: if you don't change SEED above, + // you'll aways get the same result, NOT a random run + // more information: see EO tutorial lesson 1 (FirstBitGA.cpp) + rng.reseed(seed); + + /* ========================================================= + * + * Initialization of the solution + * + * ========================================================= */ + + // a Indi random initializer: each bit is random + // more information: see EO tutorial lesson 1 (FirstBitGA.cpp) + eoUniformGenerator uGen; + eoInitFixedLength random(vecSize, uGen); + + /* ========================================================= + * + * Eval fitness function (full evaluation) + * + * ========================================================= */ + + // the fitness function is the royal function (oneMax is a Royal Road with block of 1) + RoyalRoadEval fullEval(blockSize); + + /* ========================================================= + * + * evaluation of a neighbor solution + * + * ========================================================= */ + + // Incremental evaluation of the neighbor: fitness is modified by +1 , 0 or -1 + moRoyalRoadIncrEval neighborEval(fullEval); + + /* ========================================================= + * + * the neighborhood of a solution + * + * ========================================================= */ + + // Exploration of the neighborhood in increasing order of the neigbor's index: + // bit-flip from bit 0 to bit (vecSize - 1) + moOrderNeighborhood neighborhood(vecSize); + + /* ========================================================= + * + * The sampling of the search space + * + * ========================================================= */ + + // sampling object : + // - random initialization + // - neighborhood to compute the neutral degree + // - fitness function + // - neighbor evaluation + // - number of solutions to sample + moNeutralDegreeSampling sampling(random, neighborhood, fullEval, neighborEval, nbSol); + + /* ========================================================= + * + * execute the sampling + * + * ========================================================= */ + + sampling(); + + /* ========================================================= + * + * export the sampling + * + * ========================================================= */ + + // to export the statistics into file + sampling.fileExport(str_out); + + // to get the values of statistics + // so, you can compute some statistics in c++ from the data + const std::vector & fitnessValues = sampling.getValues(0); + const std::vector & ndValues = sampling.getValues(1); + + std::cout << "First values:" << std::endl; + std::cout << "Fitness " << fitnessValues[0] << std::endl; + std::cout << "N. Degree " << ndValues[0] << std::endl; + + std::cout << "Last values:" << std::endl; + std::cout << "Fitness " << fitnessValues[fitnessValues.size() - 1] << std::endl; + std::cout << "N. Degree " << ndValues[fitnessValues.size() - 1] << std::endl; +} + +// A main that catches the exceptions + +int main(int argc, char **argv) +{ + try { + main_function(argc, argv); + } + catch (exception& e) { + cout << "Exception: " << e.what() << '\n'; + } + return 1; +} diff --git a/trunk/problems/eval/royalRoadEval.h b/trunk/problems/eval/royalRoadEval.h index 5081868b9..2a3df8495 100644 --- a/trunk/problems/eval/royalRoadEval.h +++ b/trunk/problems/eval/royalRoadEval.h @@ -43,7 +43,7 @@ public: * Default constructor * @param _k size of a block */ - RoyalRoad(unsigned int _k) : k(_k) {} + RoyalRoadEval(unsigned int _k) : k(_k) {} /** * Count the number of complete blocks in the bit string @@ -70,6 +70,14 @@ public: _solution.fitness(sum); } + /** + * get the size of a block + * @return block size + */ + unsigned int blockSize() { + return k; + } + private: // size of a block unsigned int k;