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Added 'Viral' operators with test. Implements the Mobile Genetic Elements Technique

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jmerelo 2001-05-10 12:16:00 +00:00
commit 88f281b606
7 changed files with 500 additions and 26 deletions
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106
eo/src/MGE/VirusOp.h Normal file
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/*
ViruOp.h
(c) GeNeura Team 2001, Marc Schoenauer 2000
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
CVS Info: $Date: 2001-05-10 12:16:00 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/MGE/Attic/VirusOp.h,v 1.1 2001-05-10 12:16:00 jmerelo Exp $ $Author: jmerelo $
*/
#ifndef VirusOp_h
#define VirusOp_h
//-----------------------------------------------------------------------------
#include <iostream> // ostream, istream
#include <functional> // bind2nd
#include <string> // string
#include <utils/eoRNG.h>
#include <MGE/eoVirus.h>
/** eoBitFlip --> changes 1 bit
\class eoBitBitFlip eoBitOp.h ga/eoBitOp.h
\ingroup bitstring
*/
template<class FitT>
class VirusBitFlip: public eoMonOp<eoVirus<FitT> > {
public:
/// The class name.
virtual string className() const { return "VirusBitFlip"; };
/**
* Change one bit.
* @param chrom The cromosome which one bit is going to be changed.
*/
bool operator()(eoVirus<FitT>& _chrom) {
unsigned i = eo::rng.random(_chrom.size());
_chrom.virusBitSet(i, _chrom.virusBit(i) ? false : true );
return true;
}
};
template<class FitT>
class VirusMutation: public eoMonOp<eoVirus<FitT> > {
public:
/// The class name.
virtual string className() const { return "VirusMutation"; };
/**
* Change one bit.
* @param chrom The cromosome which one bit is going to be changed.
*/
bool operator()(eoVirus<FitT>& _chrom) {
// Search for virus bits
vector<unsigned> bitsSet;
for ( unsigned i = 0; i < _chrom.size(); i ++ ) {
if ( _chrom.virusBit(i) ) {
bitsSet.push_back( i );
}
}
if ( !bitsSet.size() ) {
return false;
}
unsigned flipSite = eo::rng.random(bitsSet.size());
unsigned flipValue = bitsSet[ flipSite ];
_chrom[flipValue] = _chrom[flipValue] ? false : true;
return true;
}
};
template<class FitT>
class VirusTransmission: public eoBinOp<eoVirus<FitT> > {
public:
/// The class name.
virtual string className() const { return "VirusTransmission"; };
/**
* Change one bit.
* @param _chrom The "receptor" chromosome
* @param _chrom2 The "donor" chromosome
*/
bool operator()(eoVirus<FitT>& _chrom,const eoVirus<FitT>& _chrom2) {
// Search for virus bits
for ( unsigned i = 0; i < _chrom.size(); i ++ ) {
_chrom.virusBitSet(i, _chrom2.virusBit(i) );
}
return true;
}
};
#endif //VirusOp_h

64
eo/src/MGE/eoInitVirus.h Normal file
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// -*- mode: c++; c-indent-level: 4; c++-member-init-indent: 8; comment-column: 35; -*-
//-----------------------------------------------------------------------------
// eoInit.h
// (c) Maarten Keijzer 2000, GeNeura Team, 2000
/*
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
mak@dhi.dk
*/
//-----------------------------------------------------------------------------
#ifndef _eoInitVirus_H
#define _eoInitVirus_H
#include <algorithm>
#include <eoOp.h>
#include <eoSTLFunctor.h>
#include <utils/eoRndGenerators.h>
#include <eoInit.h>
/**
Initializer for binary chromosome with MGE
*/
template <class FitT>
class eoInitVirus: public eoInit< eoVirus<FitT> > {
public:
eoInitVirus(unsigned _combien, eoRndGenerator<bool>& _generator)
: combien(_combien), generator(_generator) {}
virtual void operator()( eoVirus<FitT>& chrom)
{
chrom.resize(combien);
chrom.virResize(combien);
std::generate(chrom.begin(), chrom.end(), generator);
for ( unsigned i = 0; i < combien; i ++ ) {
chrom.virusBitSet(i, generator() );
}
chrom.invalidate();
}
private :
unsigned combien;
/// generic wrapper for eoFunctor (s), to make them have the function-pointer style copy semantics
eoSTLF<bool> generator;
};
#endif

112
eo/src/MGE/eoVirus.h Normal file
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/*
eoVirus.h
(c) GeNeura Team 2001, Marc Schoenauer 2000
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
CVS Info: $Date: 2001-05-10 12:16:00 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/MGE/Attic/eoVirus.h,v 1.1 2001-05-10 12:16:00 jmerelo Exp $ $Author: jmerelo $
*/
#ifndef eoVirus_h
#define eoVirus_h
//-----------------------------------------------------------------------------
#include <iostream> // ostream, istream
#include <functional> // bind2nd
#include <string> // string
#include <ga/eoBit.h>
/**
\defgroup bitstring
Various functions for a bitstring representation
*/
/** eoBit: implementation of bitstring chromosome.
\class eoBit eoBit.h ga/eoBit.h
\ingroup bitstring
* based on STL's vector<bool> specialization.
*/
template <class FitT> class eoVirus: public eoBit<FitT>
{
public:
/**
* (Default) Constructor.
* @param size Size of the binary string.
*/
eoVirus(unsigned _size = 0, bool _value = false, bool _virValue = false):
eoBit<FitT>(_size, _value), virus( _size, _virValue) {}
/// My class name.
virtual string className() const {
return "eoVirus";
}
/// Access to virus features
void virResize( unsigned _i ) {
virus.resize(_i );
}
/// Access to virus features
bool virusBit( unsigned _i ) const {
return virus[_i];
}
/// Change virus features
void virusBitSet( unsigned _i, bool _bit ) {
virus[_i ] = _bit;
}
/**
* To print me on a stream.
* @param os The ostream.
*/
virtual void printOn(ostream& os) const {
EO<FitT>::printOn(os);
os << ' ';
os << size() << ' ';
copy(begin(), end(), ostream_iterator<bool>(os));
cout << endl;
copy(virus.begin(), virus.end(), ostream_iterator<bool>(os));
}
/**
* To read me from a stream.
* @param is The istream.
*/
virtual void readFrom(istream& is){
eoBit<FitT>::readFrom(is);
unsigned s;
is >> s;
string bits;
is >> bits;
if (is) {
virus.resize(bits.size());
transform(bits.begin(), bits.end(), virus.begin(),
bind2nd(equal_to<char>(), '1'));
}
}
private:
vector<bool> virus;
};
//-----------------------------------------------------------------------------
#endif //eoBit_h

26
eo/src/ga/eoBitOp.h
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@ -21,33 +21,9 @@
Contact: todos@geneura.ugr.es, http://geneura.ugr.es
Marc.Schoenauer@polytechnique.fr
mak@dhi.dk
CVS Info: $Date: 2001-05-10 12:16:00 $ $Header: /home/nojhan/dev/eodev/eodev_cvs/eo/src/ga/eoBitOp.h,v 1.13 2001-05-10 12:16:00 jmerelo Exp $ $Author: jmerelo $
*/
//-----------------------------------------------------------------------------
// MS 17/10/2000
// Added the uniform crossover - which, for some reasons, had dissapeared!
// Added the eoDetBitFlip, which flips exactly num_bit bits
// Aslo added the above standard header
// I also want to start the discussion about the "gene" crossover.
// I think the word "gene" is not appropriate: if real numbers are coded in
// binary format, then a "gene" is a bit, and that's it
// if you want to exchange real number per se, then use real coding
//
// Because all crossover operators here except that Gene crossover
// ARE generic, i.e. appky to any vertor of something.
// Note that for mutations, if instead of
// chrom[i] = (chrom[i]) ? false : true;
// we were calling something like
// specific_mutate(chrom[i])
// all mutation would also be generic ... except those eoBitNext and eoBitPrev
// If anybody reads this and want to change that (I'm also testing to see
// if someone ever reads the headers :-), drop me a mail
// Marc (Marc.Schoenauer@polytechnique.fr)
//-----------------------------------------------------------------------------
// eoBitOp.h
//-----------------------------------------------------------------------------
#ifndef eoBitOp_h
#define eoBitOp_h

20
eo/test/Makefile.am
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@ -13,7 +13,7 @@ LDADDS = $(top_builddir)/src/utils/libeoutils.a $(top_builddir)/src/libeo.a
CXXFLAGS = -g -Wall
###############################################################################
check_PROGRAMS = t-eoParetoFitness t-eoPareto t-eofitness t-eoRandom t-eobin t-eoStateAndParser t-eoCheckpointing t-eoSSGA \
check_PROGRAMS = t-eoParetoFitness t-eoPareto t-eofitness t-eoRandom t-eobin t-eoVirus t-MGE t-MGE-control t-eoStateAndParser t-eoCheckpointing t-eoSSGA \
t-eoExternalEO t-eoSymreg t-eo t-eoReplacement t-eoSelect t-eoGenOp t-eoGA t-eoReal t-eoVector t-eoESAll
TESTS=run_tests t-eoVector t-eoRandom t-eoSSGA t-eoPareto t-eoParetoFitness
# removing temporarily t-eoESFull
@ -39,6 +39,24 @@ t_eobin_LDADD = $(LDADDS)
###############################################################################
t_eoVirus_SOURCES = t-eoVirus.cpp binary_value.h
t_eoVirus_DEPENDENCIES = $(DEPS)
t_eoVirus_LDADD = $(LDADDS)
###############################################################################
t_MGE_SOURCES = t-MGE.cpp binary_value.h
t_MGE_DEPENDENCIES = $(DEPS)
t_MGE_LDADD = $(LDADDS)
###############################################################################
t_MGE_control_SOURCES = t-MGE-control.cpp binary_value.h
t_MGE_control_DEPENDENCIES = $(DEPS)
t_MGE_control_LDADD = $(LDADDS)
###############################################################################
t_eoStateAndParser_SOURCES = t-eoStateAndParser.cpp
t_eoStateAndParser_DEPENDENCIES = $(DEPS)
t_eoStateAndParser_LDFLAGS = -lm

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eo/test/t-MGE-control.cpp Normal file
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//-----------------------------------------------------------------------------
// t-eoMGE.cpp
//-----------------------------------------------------------------------------
#ifndef __GNUG__
// to avoid long name warnings
#pragma warning(disable:4786)
#endif // __GNUG__
#include <eo>
#include <ga/eoBitOp.h>
#include "binary_value.h"
// Viri
#include <MGE/VirusOp.h>
#include <MGE/eoVirus.h>
#include <MGE/eoInitVirus.h>
//-----------------------------------------------------------------------------
typedef eoVirus<float> Chrom;
//-----------------------------------------------------------------------------
int main()
{
const unsigned POP_SIZE = 100, CHROM_SIZE = 16;
unsigned i;
eoBooleanGenerator gen;
// the populations:
eoPop<Chrom> pop;
// Evaluation
eoEvalFuncPtr<Chrom> eval( binary_value );
eoInitVirus<float> random(CHROM_SIZE, gen);
for (i = 0; i < POP_SIZE; ++i) {
Chrom chrom;
random(chrom);
eval(chrom);
pop.push_back(chrom);
}
cout << "population:" << endl;
for (i = 0; i < pop.size(); ++i)
cout << "\t" << pop[i] << " " << pop[i].fitness() << endl;
// selection
eoDetTournamentSelect<Chrom> lottery( 3) ;
// breeder
eoOneBitFlip<Chrom> bf;
eoUBitXover<Chrom> xover;
eoProportionalOp<Chrom> propSel;
eoGeneralBreeder<Chrom> breeder( lottery, propSel );
propSel.add(bf, 0.75);
propSel.add(xover, 0.25);
// Replace a single one
eoPlusReplacement<Chrom> replace;
// Terminators
eoGenContinue<Chrom> continuator1(50);
eoFitContinue<Chrom> continuator2(65535.f);
eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
eoCheckPoint<Chrom> checkpoint(continuator);
eoStdoutMonitor monitor;
checkpoint.add(monitor);
eoSecondMomentStats<Chrom> stats;
monitor.add(stats);
checkpoint.add(stats);
// GA generation
eoEasyEA<Chrom> ea(checkpoint, eval, breeder, replace );
// evolution
try
{
ea(pop);
}
catch (exception& e)
{
cout << "exception: " << e.what() << endl;;
exit(EXIT_FAILURE);
}
cout << "pop" << endl;
for (i = 0; i < pop.size(); ++i)
cout << "\t" << pop[i] << " " << pop[i].fitness() << endl;
return 0;
}
//-----------------------------------------------------------------------------

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eo/test/t-MGE.cpp Normal file
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//-----------------------------------------------------------------------------
// t-eoMGE.cpp
//-----------------------------------------------------------------------------
#ifndef __GNUG__
// to avoid long name warnings
#pragma warning(disable:4786)
#endif // __GNUG__
#include <eo>
#include <ga/eoBitOp.h>
#include "binary_value.h"
// Viri
#include <MGE/VirusOp.h>
#include <MGE/eoVirus.h>
#include <MGE/eoInitVirus.h>
//-----------------------------------------------------------------------------
typedef eoVirus<float> Chrom;
//-----------------------------------------------------------------------------
int main()
{
const unsigned POP_SIZE = 100, CHROM_SIZE = 16;
unsigned i;
eoBooleanGenerator gen;
// the populations:
eoPop<Chrom> pop;
// Evaluation
eoEvalFuncPtr<Chrom> eval( binary_value );
eoInitVirus<float> random(CHROM_SIZE, gen);
for (i = 0; i < POP_SIZE; ++i) {
Chrom chrom;
random(chrom);
eval(chrom);
pop.push_back(chrom);
}
cout << "population:" << endl;
for (i = 0; i < pop.size(); ++i)
cout << "\t" << pop[i] << " " << pop[i].fitness() << endl;
// selection
eoDetTournamentSelect<Chrom> lottery( 3) ;
// breeder
VirusMutation<float> vm;
VirusTransmission<float> vt;
VirusBitFlip<float> vf;
eoUBitXover<Chrom> xover;
eoProportionalOp<Chrom> propSel;
eoGeneralBreeder<Chrom> breeder( lottery, propSel );
propSel.add(vm, 0.25);
propSel.add(vf, 0.25);
propSel.add(vt, 0.25);
propSel.add(xover, 0.25);
// Replace a single one
eoPlusReplacement<Chrom> replace;
// Terminators
eoGenContinue<Chrom> continuator1(50);
eoFitContinue<Chrom> continuator2(65535.f);
eoCombinedContinue<Chrom> continuator(continuator1, continuator2);
eoCheckPoint<Chrom> checkpoint(continuator);
eoStdoutMonitor monitor;
checkpoint.add(monitor);
eoSecondMomentStats<Chrom> stats;
monitor.add(stats);
checkpoint.add(stats);
// GA generation
eoEasyEA<Chrom> ea(checkpoint, eval, breeder, replace );
// evolution
try
{
ea(pop);
}
catch (exception& e)
{
cout << "exception: " << e.what() << endl;;
exit(EXIT_FAILURE);
}
cout << "pop" << endl;
for (i = 0; i < pop.size(); ++i)
cout << "\t" << pop[i] << " " << pop[i].fitness() << endl;
return 0;
}
//-----------------------------------------------------------------------------