diff --git a/trunk/paradiseo-mo/src/continuator/moAverageFitnessNeighborStat.h b/trunk/paradiseo-mo/src/continuator/moAverageFitnessNeighborStat.h new file mode 100644 index 000000000..c3de8e6f3 --- /dev/null +++ b/trunk/paradiseo-mo/src/continuator/moAverageFitnessNeighborStat.h @@ -0,0 +1,88 @@ +/* + + Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010 + + Sébastien Verel, Arnaud Liefooghe, Jérémie 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 moAverageFitnessNeighborStat_h +#define moAverageFitnessNeighborStat_h + +#include +#include + +/** + * From moNeighborhoodStat, to compute the average and the standard deviation of fitness in the neighborhood + */ +template< class Neighbor > +class moAverageFitnessNeighborStat : public moStat +{ +public : + typedef typename Neighbor::EOT EOT ; + typedef typename EOT::Fitness Fitness ; + + using moStat< EOT, double >::value; + + /** + * Default Constructor + * @param _nhStat a neighborhoodStat + */ + moAverageFitnessNeighborStat(moNeighborhoodStat & _nhStat): + moStat(0.0, "average"), nhStat(_nhStat) {} + + /** + * Set the average and the standard deviation of fitness in the neighborhood + * @param _sol the first solution + */ + virtual void init(EOT & _sol) { + value() = nhStat.getMean(); + } + + /** + * Set the average and the standard deviation of fitness in the neighborhood + * @param _sol the corresponding solution + */ + virtual void operator()(EOT & _sol) { + value() = nhStat.getMean(); + } + + /** + * @return the class name + */ + virtual std::string className(void) const { + return "moAverageFitnessNeighborStat"; + } + +private: + /** moNeighborhoodStat */ + moNeighborhoodStat & nhStat; +}; + +#endif diff --git a/trunk/paradiseo-mo/src/continuator/moStdFitnessNeighborStat.h b/trunk/paradiseo-mo/src/continuator/moStdFitnessNeighborStat.h new file mode 100644 index 000000000..5f9d9433d --- /dev/null +++ b/trunk/paradiseo-mo/src/continuator/moStdFitnessNeighborStat.h @@ -0,0 +1,88 @@ +/* + + Copyright (C) DOLPHIN Project-Team, INRIA Lille - Nord Europe, 2006-2010 + + Sébastien Verel, Arnaud Liefooghe, Jérémie 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 moStdFitnessNeighborStat_h +#define moStdFitnessNeighborStat_h + +#include +#include + +/** + * From moNeighborhoodStat, to compute the average and the standard deviation of fitness in the neighborhood + */ +template< class Neighbor > +class moStdFitnessNeighborStat : public moStat +{ +public : + typedef typename Neighbor::EOT EOT ; + typedef typename EOT::Fitness Fitness ; + + using moStat< EOT, double >::value; + + /** + * Default Constructor + * @param _nhStat a neighborhoodStat + */ + moStdFitnessNeighborStat(moNeighborhoodStat & _nhStat): + moStat(0.0, "stdev"), nhStat(_nhStat) {} + + /** + * Set the average and the standard deviation of fitness in the neighborhood + * @param _sol the first solution + */ + virtual void init(EOT & _sol) { + value() = nhStat.getSD(); + } + + /** + * Set the average and the standard deviation of fitness in the neighborhood + * @param _sol the corresponding solution + */ + virtual void operator()(EOT & _sol) { + value() = nhStat.getSD(); + } + + /** + * @return the class name + */ + virtual std::string className(void) const { + return "moStdFitnessNeighborStat"; + } + +private: + /** moNeighborhoodStat */ + moNeighborhoodStat & nhStat; +}; + +#endif diff --git a/trunk/paradiseo-mo/src/mo.h b/trunk/paradiseo-mo/src/mo.h index b25551b0b..4a5670006 100755 --- a/trunk/paradiseo-mo/src/mo.h +++ b/trunk/paradiseo-mo/src/mo.h @@ -45,6 +45,7 @@ #include #include #include +#include #include #include @@ -67,6 +68,8 @@ #include #include #include +#include +#include #include #include #include @@ -133,6 +136,7 @@ #include #include #include +#include #include #include @@ -152,6 +156,7 @@ #include #include #include +#include #include #include diff --git a/trunk/paradiseo-mo/src/perturb/moSolInit.h b/trunk/paradiseo-mo/src/perturb/moSolInit.h new file mode 100644 index 000000000..56af5c996 --- /dev/null +++ b/trunk/paradiseo-mo/src/perturb/moSolInit.h @@ -0,0 +1,60 @@ +/* + +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 ue, +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". + +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 _moSolInit_h +#define _moSolInit_h + +#include + +/** + * Initialization of the solution with the external solution + */ +template< class EOT > +class moSolInit : public eoInit { +public: + /** + * Default Constructor + * @param _extSol external solution of the intiialization + */ + moSolInit(EOT & _extSol) : extSol(_extSol) { + } + + /** + * Initialization on the externatl solution + * @param _solution to initialize + */ + void operator()(EOT& _solution){ + _solution = extSol; + } + +private: + EOT& extSol; +}; + +#endif diff --git a/trunk/paradiseo-mo/src/sampling/moMHRndFitnessCloudSampling.h b/trunk/paradiseo-mo/src/sampling/moMHRndFitnessCloudSampling.h index dec8e01cc..a06a39c05 100644 --- a/trunk/paradiseo-mo/src/sampling/moMHRndFitnessCloudSampling.h +++ b/trunk/paradiseo-mo/src/sampling/moMHRndFitnessCloudSampling.h @@ -52,7 +52,7 @@ * Sample the fitness of solutions from Metropolis-Hasting sampling * and the fitness of one random neighbor * - * The values are collected during the random search + * The values are collected during the Metropolis-Hasting walk * */ template diff --git a/trunk/paradiseo-mo/src/sampling/moNeutralWalkSampling.h b/trunk/paradiseo-mo/src/sampling/moNeutralWalkSampling.h new file mode 100644 index 000000000..03547593a --- /dev/null +++ b/trunk/paradiseo-mo/src/sampling/moNeutralWalkSampling.h @@ -0,0 +1,148 @@ +/* + + 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 moNeutralWalkSampling_h +#define moNeutralWalkSampling_h + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +/** + * To explore the evolvability of solutions in a neutral networks: + * Perform a random neutral walk based on the neighborhood, + * The measures of evolvability of solutions are collected during the random neutral walk + * The distribution and autocorrelation can be computed from the serie of values + * + * Informations collected: + * - the current solution of the walk + * - the distance from the starting solution + * - the minimal fitness in the neighborhood + * - the average fitness + * - the standard deviation of the fitness + * - the maximal fitness + * - the size of the neighborhood + * - the number of neighbors with lower fitness + * - the number of neighbors with equal fitness (neutral degree) + * - the number of neighbors with higher fitness + */ +template +class moNeutralWalkSampling : public moSampling +{ +public: + typedef typename Neighbor::EOT EOT ; + + using moSampling::localSearch; + + /** + * Default Constructor + * @param _initSol the first the solution of the walk + * @param _neighborhood neighborhood giving neighbor in random order + * @param _fullEval Fitness function, full evaluation function + * @param _eval neighbor evaluation, incremental evaluation function + * @param _distance the distance to measure the distance from the initial solution + * @param _nbStep Number of steps of the random walk + */ + moNeutralWalkSampling(EOT & _initSol, + moNeighborhood & _neighborhood, + eoEvalFunc& _fullEval, + moEval& _eval, + eoDistance & _distance, + unsigned int _nbStep) : + moSampling(init, * new moRandomNeutralWalk(_neighborhood, _fullEval, _eval, _nbStep), solutionStat), + init(_initSol), + distStat(_distance, _initSol), + neighborhoodStat(_neighborhood, _eval), + minStat(neighborhoodStat), + averageStat(neighborhoodStat), + stdStat(neighborhoodStat), + maxStat(neighborhoodStat), + nbSupStat(neighborhoodStat), + nbInfStat(neighborhoodStat), + sizeStat(neighborhoodStat), + ndStat(neighborhoodStat) + { + add(neighborhoodStat, false); + add(distStat); + add(minStat); + add(averageStat); + add(stdStat); + add(maxStat); + add(sizeStat); + add(nbInfStat); + add(ndStat); + add(nbSupStat); + } + + /** + * default destructor + */ + ~moNeutralWalkSampling() { + // delete the pointer on the local search which has been constructed in the constructor + delete localSearch; + } + +protected: + moSolInit init; + moSolutionStat solutionStat; + moDistanceStat distStat; + moNeighborhoodStat< Neighbor > neighborhoodStat; + moMinNeighborStat< Neighbor > minStat; + moAverageFitnessNeighborStat< Neighbor > averageStat; + moStdFitnessNeighborStat< Neighbor > stdStat; + moMaxNeighborStat< Neighbor > maxStat; + moNbSupNeighborStat< Neighbor > nbSupStat; + moNbInfNeighborStat< Neighbor > nbInfStat; + moSizeNeighborStat< Neighbor > sizeStat; + moNeutralDegreeNeighborStat< Neighbor > ndStat; + +}; + + +#endif diff --git a/trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt b/trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt index 91e3d33d6..07d187e28 100644 --- a/trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt +++ b/trunk/paradiseo-mo/tutorial/Lesson6/CMakeLists.txt @@ -16,6 +16,7 @@ ADD_EXECUTABLE(adaptiveWalks adaptiveWalks.cpp) ADD_EXECUTABLE(fdc fdc.cpp) ADD_EXECUTABLE(neutralDegree neutralDegree.cpp) ADD_EXECUTABLE(fitnessCloud fitnessCloud.cpp) +ADD_EXECUTABLE(neutralWalk neutralWalk.cpp) TARGET_LINK_LIBRARIES(testRandomWalk eoutils ga eo) TARGET_LINK_LIBRARIES(testMetropolisHasting eoutils ga eo) @@ -27,3 +28,4 @@ TARGET_LINK_LIBRARIES(adaptiveWalks eoutils ga eo) TARGET_LINK_LIBRARIES(fdc eoutils ga eo) TARGET_LINK_LIBRARIES(neutralDegree eoutils ga eo) TARGET_LINK_LIBRARIES(fitnessCloud eoutils ga eo) +TARGET_LINK_LIBRARIES(neutralWalk eoutils ga eo) diff --git a/trunk/paradiseo-mo/tutorial/Lesson6/neutralWalk.cpp b/trunk/paradiseo-mo/tutorial/Lesson6/neutralWalk.cpp new file mode 100644 index 000000000..1e8964dea --- /dev/null +++ b/trunk/paradiseo-mo/tutorial/Lesson6/neutralWalk.cpp @@ -0,0 +1,222 @@ +//----------------------------------------------------------------------------- +/** neutralWalk.cpp + * + * SV - 07/05/10 + * + */ +//----------------------------------------------------------------------------- + +// 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 one random neighbor possibly the same one several times + +//----------------------------------------------------------------------------- +// the sampling class +#include +#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 steps of the random walk + eoValueParam stepParam(100, "nbStep", "Number of steps of the random walk", 'n'); + parser.processParam( stepParam, "Representation" ); + unsigned nbStep = stepParam.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); + + /* ========================================================= + * + * 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 random order + // at each step one bit is randomly generated + moRndWithoutReplNeighborhood neighborhood(vecSize); + + /* ========================================================= + * + * The sampling of the search space + * + * ========================================================= */ + + // Initial Solution of the random neutral walk + Indi initialSol(vecSize, false); + + // Hamming distance + eoHammingDistance distance; + + // sampling object : + // - random initialization + // - neighborhood to compute the next step + // - fitness function + // - neighbor evaluation + // - number of steps of the walk + moNeutralWalkSampling sampling(initialSol, neighborhood, fullEval, neighborEval, distance, nbStep); + + /* ========================================================= + * + * execute the sampling + * + * ========================================================= */ + + // nearly 2 blocks are complete + for(unsigned i = 0; i < blockSize - 1; i++) { + initialSol[i] = true; + initialSol[blockSize + i] = true; + initialSol[2 * blockSize + i] = true; + } + // first block is complete + initialSol[blockSize - 1] = true; + + fullEval(initialSol); + + std::cout << "Initial Solution: " << initialSol << std::endl; + + // 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 & solutions = sampling.getSolutions(0); + + std::cout << "First values:" << std::endl; + std::cout << "Solution " << solutions[0] << std::endl; + + std::cout << "Last values:" << std::endl; + std::cout << "Solution " << solutions[solutions.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; +}