From yi.zong at risoe.dk  Thu Oct  2 06:03:56 2008
From: yi.zong at risoe.dk (yi.zong@risoe.dk)
Date: Thu, 02 Oct 2008 12:03:56 +0200
Subject: [galib] Help: still about initializer?
Message-ID: <7F526FDC6908FB4AA1985F13F0AFAC1402CD682A@EXCHG-VS1.risoe.dk>

Dear all,

   Thank you for your help for my  question.

   I write my initializer. But the first generation's individuals are always zeros and they are not the real number, Like 19.2.

   Could you tell me why?

   Please, see my code snippet from my application as follows. 

   Looking forward to your answer.

   

   Yi

 

float Objective(GAGenome &);

void Myinitializer(GAGenome &);

 

int

main(int argc, char** argv)

{

 

/*

// See if we've been given a seed to use (for testing purposes).  When you

// specify a random seed, the evolution will be exactly the same each time

// you use that seed number.

 

  for(int jj=1; jj<argc; jj++) {

    if(strcmp(argv[jj++],"seed") == 0) {

      GARandomSeed((unsigned int)atoi(argv[jj]));

    }

  }*/

  int length=36;

 

  GARealAlleleSetArray alleles;

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  alleles.add(-21,-18);

  GARealGenome genome(alleles, Objective);

 

 

 GANoScaling scale;//GAScalingScheme::GANoScaling--the fitness scores = the objectivescores

 

  genome.crossover(GARealTwoPointCrossover);

  

  genome.initializer(Myinitializer); // Initial with given by manual, but all with values as 0 ??  

  

  GASimpleGA ga(genome);

  ga.minimize();             // by default we want to minimize the objective

  ga.scaling(scale);                    // set the scaling method to our sharing

  ga.populationSize(73); // how many individuals in the population

  ga.nGenerations(100); // number of generations to evolve

  ga.nBestGenomes(1);           // Specify how many 'best' genomes to record, the default is 1

  ga.pMutation(0.05);                  // likelihood of mutating new offspring

  ga.pCrossover(0.6);                 // likelihood of crossing over parents

  ga.scoreFilename("yinw13.dat"); // name of file for scores

  ga.scoreFrequency(1);                        // keep the scores of every generation

  ga.flushFrequency(1);          // specify how often to write the score to disk, if generation<10, then it only records once

  ga.selectScores(GAStatistics::AllScores);

  ga.parameters(argc, argv, gaTrue); // parse commands, complain if bogus args

   ...

 

}

 

 

void Myinitializer( GAGenome &g )

   {

      GARealGenome &genome = (GARealGenome &)g;

      double IC[]={-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2};

   

      for( int i = 0; i < 36; ++i )

        {

             genome.gene(i, IC[i]);

        }    

   }

 

 

Yi Zong
Post doc
Phone direct +45 4677 5045
Mobile 
yi.zong at risoe.dk
 

Wind Energy Department
Ris? National Laboratory for Sustainable Energy
Technical University of Denmark - DTU
Building 118, P.O. Box 49
DK-4000 Roskilde, Denmark
Tel +45 4677 4677
Fax +45 4677 5083
www.risoe.dtu.dk 







 

Yi Zong
Post doc
Phone direct +45 4677 5045
Mobile 
yi.zong at risoe.dk
 

Wind Energy Department
Ris? National Laboratory for Sustainable Energy
Technical University of Denmark - DTU
Building 118, P.O. Box 49
DK-4000 Roskilde, Denmark
Tel +45 4677 4677
Fax +45 4677 5083
www.risoe.dtu.dk 













 

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From Michael.Kupfer at nasa.gov  Wed Oct  1 12:38:03 2008
From: Michael.Kupfer at nasa.gov (Kupfer, Michael (ARC-AFA)[UC SANTA CRUZ])
Date: Wed, 1 Oct 2008 11:38:03 -0500
Subject: [galib] Antwort: GAlib: how to initialize my first generation's
	individuals in real numbers (not zeros) ?
In-Reply-To: <OF369E64FD.BDAFC989-ONC12574D4.00604C88-C12574D4.006050FD@ise.fhg.de>
References: <7F526FDC6908FB4AA1985F13F0AFAC1402CD64A3@EXCHG-VS1.risoe.dk>
	<OF369E64FD.BDAFC989-ONC12574D4.00604C88-C12574D4.006050FD@ise.fhg.de>
Message-ID: <87D67DA289F034488A9D7E4CDEFD28CC98C8BB@NDMSEVS34B.ndc.nasa.gov>

Hello Torsten, Hello Yi!

 

I am myself a GAlib beginner but what I'd suggest is to write your own initializer.

I believe there even should be some examples.

But here is a code snippet from my application.

What you have to do is basically replace what I did in the MyArrayInitializer with your desired real numbers.

Maybe this helps.

 

Best,

Michael.

 

--------------------------------------------------

Michael Kupfer

 

 

University Affiliated Research Center

UC Santa Cruz

NASA Ames Research Center

Building 210, Room 255, Mail Stop 210-6

Moffett Field, CA 94035

U.S.A.

 

Email: Michael.Kupfer -AT- nasa.gov <mailto:Michael.Kupfer at nasa.gov> 

Phone: (650)604-6424

-----------------------------------------------------

 

#include

#include

#include

...

 

#define

...

 

 

//------------------- own initializer ----------------------

void MyArrayInitializer(GAGenome & g)

{

      int sep_value;

      

      GARealGenome &genome = (GARealGenome &)g;

      

      // set first gene to the ETA_f

      genome.gene(0, unit[0].arr_f);

      

      //[SNIP ... ]

//check for some constraint violation

 

// set the other genes ...

      if(unit[i].arr_f > genome.gene(i-1) + SV)

      {

            genome.gene(i, unit[i].arr_f);

      }

      else

      {     

            genome.gene(i, genome.gene(i-1) + SV);

      }     

}

//---------------------end of own initializer--------------------------

 

//--------------begin of main------------------------------------------

 

int main(int argc, char* argv [])

{

      // declaration of the GAlib included random number generator      

      void GARandomSeed(unsigned s = 0);

      

      //[SNIP ... ]

 

      GARealGenome genome(alleles, Objective); 

 

      genome.initializer(MyArrayInitializer);

      genome.crossover(GARealGenome::OnePointCrossover);

 

      //[SNIP ... ]

}

 

 

 

________________________________

From: galib-bounces at mit.edu [mailto:galib-bounces at mit.edu] On Behalf Of Torsten.Gutjahr at ise.fraunhofer.de
Sent: Tuesday, September 30, 2008 10:32 AM
To: yi.zong at risoe.dk
Cc: galib-bounces at mit.edu; galib at mit.edu
Subject: [galib] Antwort: GAlib: how to initialize my first generation's individuals in real numbers (not zeros) ?

 


Dear all, 

I have the same problem like Yi Zong. Please, could somebody help us? 

Best Regards 

----------------------------------------------------------------------------------------

Torsten Gutjahr 
Dept. Materials Research and Applied Optics
Fraunhofer-Institut f?r Solare Energiesysteme ISE
Heidenhofstra?e 2, 79110 Freiburg, Germany
Phone: +49 (0) 7 61/ 4588-59 80  Fax: +49 (0) 7 61/ 4588-99 81
torsten.gutjahr at ise.fraunhofer.de
www.ise.fraunhofer.de 



yi.zong at risoe.dk 
Gesendet von: galib-bounces at mit.edu 

30.09.2008 16:30 

An

galib at mit.edu 

Kopie

 

Thema

[galib] GAlib: how to initialize my first generation's individuals in real numbers (not zeros) ?

 

 

 




Dear all, 
  When I use Galib to optimize, I want to initialize my first generation's individuals in some real numbers (not zeros), which I think they are in the best results range. That is to say, the first generation is specified as some numbers by myself and not gets diverse by random seed. 
  How can I realize it? 
  Thank you in advance, 
  
  

Yi Zong
Post doc
Phone direct +45 4677 5045
Mobile 
yi.zong at risoe.dk

Wind Energy Department
Ris? National Laboratory for Sustainable Energy
Technical University of Denmark - DTU
Building 118, P.O. Box 49
DK-4000 Roskilde, Denmark
Tel +45 4677 4677
Fax +45 4677 5083
www.risoe.dtu.dk 












 _______________________________________________
galib mailing list
galib at mit.edu
http://mailman.mit.edu/mailman/listinfo/galib

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From yi.zong at risoe.dk  Fri Oct  3 06:11:57 2008
From: yi.zong at risoe.dk (yi.zong@risoe.dk)
Date: Fri, 03 Oct 2008 12:11:57 +0200
Subject: [galib] Help: Initializer: first generation always are zeros,
 not a real number!
Message-ID: <7F526FDC6908FB4AA1985F13F0AFAC1402D3ED71@EXCHG-VS1.risoe.dk>

Dear Michael, Patrik and all,

I have tried your suggestion, but it still has the problem: the first generation's individuals always are zeros, not a real number that I expect!

Could you give me some other suggestion? 

 Thank you in advance,

 

Yi

 

 

 

Yi Zong
Post doc
Phone direct +45 4677 5045
Mobile 
yi.zong at risoe.dk
 

Wind Energy Department
Ris? National Laboratory for Sustainable Energy
Technical University of Denmark - DTU
Building 118, P.O. Box 49
DK-4000 Roskilde, Denmark
Tel +45 4677 4677
Fax +45 4677 5083
www.risoe.dtu.dk 













 

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From Michael.Kupfer at nasa.gov  Fri Oct  3 13:25:26 2008
From: Michael.Kupfer at nasa.gov (Kupfer, Michael (ARC-AFA)[UC SANTA CRUZ])
Date: Fri, 3 Oct 2008 12:25:26 -0500
Subject: [galib] Help: Initializer: first generation always are zeros,
	not a real number!
In-Reply-To: <7F526FDC6908FB4AA1985F13F0AFAC1402D3ED71@EXCHG-VS1.risoe.dk>
References: <7F526FDC6908FB4AA1985F13F0AFAC1402D3ED71@EXCHG-VS1.risoe.dk>
Message-ID: <87D67DA289F034488A9D7E4CDEFD28CC98CB08@NDMSEVS34B.ndc.nasa.gov>

Hello Yi!

 

I took GAlib example1 and added an own initializer.

With it (line 41) one now can set the first genes either to 0 or to 1.

Try to go from there.

 

Best,

Michael.

 

--------------------------------------------------

Michael Kupfer

 

 

University Affiliated Research Center

UC Santa Cruz

NASA Ames Research Center

Building 210, Room 255, Mail Stop 210-6

Moffett Field, CA 94035

U.S.A.

 

Email: Michael.Kupfer AT nasa.gov <mailto:Michael.Kupfer at nasa.gov> 

Phone: (650)604-6424

 

 

/* ----------------------------------------------------------------------------

  ex1.C

  mbwall 28jul94

  Copyright (c) 1995-1996  Massachusetts Institute of Technology

 

 DESCRIPTION:

   Example program for the SimpleGA class and 2DBinaryStringGenome class.

This program tries to fill the 2Dgenome with alternating 1s and 0s. 

  This example uses the default crossover (single point), default mutator

(uniform random bit flip), and default initializer (uniform random) for the

2D genome.

  Notice that one-point crossover is not necessarily the best kind of crossover

to use if you want to generate a 'good' genome with this kind of objective 

function.  But it does work.

---------------------------------------------------------------------------- */

#include <ga/GASimpleGA.h>    // we're going to use the simple GA

#include <ga/GA2DBinStrGenome.h> // and the 2D binary string genome

#include <ga/std_stream.h>

 

#define cout STD_COUT

 

void MyInitializer(GAGenome & g);

 

float Objective(GAGenome &);  // This is the declaration of our obj function.

                        // The definition comes later in the file.

 

int k = 0;

 

 

//------------------- own initializer---------------------

void MyInitializer(GAGenome & g)

{

      //cout << "Hello" <<endl;     

      

      GA2DBinaryStringGenome & genome = (GA2DBinaryStringGenome &)g;

 

            for(int j=0; j<genome.height(); j++)

            {

                  for(int i=0; i<genome.width(); i++)

                  {

                        genome.gene(i,j,1); // to set the genes with which the population gets initialized: either 1 or 0

                                                      // stupid example; I should have taken one where one can seed it also with non binary values

                  }

            }

}

//---------------------end of own initializer--------------------------

 

 

int

main(int argc, char **argv)

{

  cout << "Example 1\n\n";

  cout << "This program tries to fill a 2DBinaryStringGenome with\n";

  cout << "alternating 1s and 0s using a SimpleGA\n\n"; cout.flush();

 

// See if we've been given a seed to use (for testing purposes).  When you

// specify a random seed, the evolution will be exactly the same each time

// you use that seed number.

 

  for(int ii=1; ii<argc; ii++) {

    if(strcmp(argv[ii++],"seed") == 0) {

      GARandomSeed((unsigned int)atoi(argv[ii]));

    }

  }

 

// Declare variables for the GA parameters and set them to some default values.

 

  int width    = 10;

  int height   = 5;

  int popsize  = 10;

  int ngen     = 200;

  float pmut   = 0.001;

  float pcross = 0.9;

 

// Now create the GA and run it.  First we create a genome of the type that

// we want to use in the GA.  The ga doesn't operate on this genome in the

// optimization - it just uses it to clone a population of genomes.

 

  GA2DBinaryStringGenome genome(width, height, Objective);

  genome.initializer(MyInitializer);

 

// Now that we have the genome, we create the genetic algorithm and set

// its parameters - number of generations, mutation probability, and crossover

// probability.  And finally we tell it to evolve itself.

 

  GASimpleGA ga(genome);

  ga.populationSize(popsize);

  ga.nGenerations(ngen);

  ga.pMutation(pmut);

  ga.pCrossover(pcross);

    

  ga.evolve();

 

    

// Now we print out the best genome that the GA found.

 

  cout << "The GA found:\n" << ga.statistics().bestIndividual() << "\n";

 

// That's it!

  return 0;

}

 

 

// This is the objective function.  All it does is check for alternating 0s and

// 1s.  If the gene is odd and contains a 1, the fitness is incremented by 1.

// If the gene is even and contains a 0, the fitness is incremented by 1.  No

// penalties are assigned. 

//   We have to do the cast because a plain, generic GAGenome doesn't have 

// the members that a GA2DBinaryStringGenome has.  And it's ok to cast it

// because we know that we will only get GA2DBinaryStringGenomes and

// nothing else.

 

float

Objective(GAGenome& g) {

  GA2DBinaryStringGenome & genome = (GA2DBinaryStringGenome &)g;

  float score=0.0;

  int count=0;

  

  if(k < 40)            // print out the first few generations to see how the genome looks like

  {

      for(int j=0; j<genome.height(); j++)

      {

            for(int i=0; i<genome.width(); i++)

            {

                  cout << genome.gene(i,j);

            }

            cout << endl;

      }

      cout << endl;

  }

 

  for(int i=0; i<genome.width(); i++){

    for(int j=0; j<genome.height(); j++){

      if(genome.gene(i,j) == 0 && count%2 == 0)

      score += 1.0;

      if(genome.gene(i,j) == 1 && count%2 != 0)

      score += 1.0;

      count++;

    }

  }

  k++;

  return score;

  

}

 

 

________________________________

From: galib-bounces at mit.edu [mailto:galib-bounces at mit.edu] On Behalf Of yi.zong at risoe.dk
Sent: Friday, October 03, 2008 3:12 AM
To: galib at mit.edu
Subject: [galib] Help: Initializer: first generation always are zeros, not a real number!

 

Dear Michael, Patrik and all,

I have tried your suggestion, but it still has the problem: the first generation's individuals always are zeros, not a real number that I expect!

Could you give me some other suggestion? 

 Thank you in advance,

 

Yi

 

 

 

Yi Zong
Post doc
Phone direct +45 4677 5045
Mobile 
yi.zong at risoe.dk
 

Wind Energy Department
Ris? National Laboratory for Sustainable Energy
Technical University of Denmark - DTU
Building 118, P.O. Box 49
DK-4000 Roskilde, Denmark
Tel +45 4677 4677
Fax +45 4677 5083
www.risoe.dtu.dk 












 

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From yi.zong at risoe.dk  Tue Oct  7 09:33:19 2008
From: yi.zong at risoe.dk (yi.zong@risoe.dk)
Date: Tue, 07 Oct 2008 15:33:19 +0200
Subject: [galib] galib Digest, Vol 63, Issue 5
In-Reply-To: <mailman.273740.1223140073.6365.galib@mit.edu>
References: <mailman.273740.1223140073.6365.galib@mit.edu>
Message-ID: <7F526FDC6908FB4AA1985F13F0AFAC1402D3F321@EXCHG-VS1.risoe.dk>



Dear all,
   I still can not solve my problem. (Initializer: first generation
always are zeros,	not a real number!)
   Could you give me any idea?
   
   Thank you for your help!

   	Yi

-----Original Message-----
From: galib-bounces at mit.edu [mailto:galib-bounces at mit.edu] On Behalf Of
galib-request at mit.edu
Sent: Saturday, October 04, 2008 7:08 PM
To: galib at mit.edu
Subject: galib Digest, Vol 63, Issue 5

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Today's Topics:

   1. Re: Help: Initializer: first generation always are zeros,	not
      a real number! (Kupfer, Michael (ARC-AFA)[UC SANTA CRUZ])


----------------------------------------------------------------------

Message: 1
Date: Fri, 3 Oct 2008 12:25:26 -0500
From: "Kupfer, Michael (ARC-AFA)[UC SANTA CRUZ]"
	<Michael.Kupfer at nasa.gov>
Subject: Re: [galib] Help: Initializer: first generation always are
	zeros,	not a real number!
To: <yi.zong at risoe.dk>, <galib at mit.edu>
Message-ID:
	<87D67DA289F034488A9D7E4CDEFD28CC98CB08 at NDMSEVS34B.ndc.nasa.gov>
Content-Type: text/plain; charset="iso-8859-1"

Hello Yi!

 

I took GAlib example1 and added an own initializer.

With it (line 41) one now can set the first genes either to 0 or to 1.

Try to go from there.

 

Best,

Michael.

 

--------------------------------------------------

Michael Kupfer

 

 

University Affiliated Research Center

UC Santa Cruz

NASA Ames Research Center

Building 210, Room 255, Mail Stop 210-6

Moffett Field, CA 94035

U.S.A.

 

Email: Michael.Kupfer AT nasa.gov <mailto:Michael.Kupfer at nasa.gov> 

Phone: (650)604-6424

 

 

/*
------------------------------------------------------------------------
----

  ex1.C

  mbwall 28jul94

  Copyright (c) 1995-1996  Massachusetts Institute of Technology

 

 DESCRIPTION:

   Example program for the SimpleGA class and 2DBinaryStringGenome
class.

This program tries to fill the 2Dgenome with alternating 1s and 0s. 

  This example uses the default crossover (single point), default
mutator

(uniform random bit flip), and default initializer (uniform random) for
the

2D genome.

  Notice that one-point crossover is not necessarily the best kind of
crossover

to use if you want to generate a 'good' genome with this kind of
objective 

function.  But it does work.

------------------------------------------------------------------------
---- */

#include <ga/GASimpleGA.h>    // we're going to use the simple GA

#include <ga/GA2DBinStrGenome.h> // and the 2D binary string genome

#include <ga/std_stream.h>

 

#define cout STD_COUT

 

void MyInitializer(GAGenome & g);

 

float Objective(GAGenome &);  // This is the declaration of our obj
function.

                        // The definition comes later in the file.

 

int k = 0;

 

 

//------------------- own initializer---------------------

void MyInitializer(GAGenome & g)

{

      //cout << "Hello" <<endl;     

      

      GA2DBinaryStringGenome & genome = (GA2DBinaryStringGenome &)g;

 

            for(int j=0; j<genome.height(); j++)

            {

                  for(int i=0; i<genome.width(); i++)

                  {

                        genome.gene(i,j,1); // to set the genes with
which the population gets initialized: either 1 or 0

                                                      // stupid example;
I should have taken one where one can seed it also with non binary
values

                  }

            }

}

//---------------------end of own initializer--------------------------

 

 

int

main(int argc, char **argv)

{

  cout << "Example 1\n\n";

  cout << "This program tries to fill a 2DBinaryStringGenome with\n";

  cout << "alternating 1s and 0s using a SimpleGA\n\n"; cout.flush();

 

// See if we've been given a seed to use (for testing purposes).  When
you

// specify a random seed, the evolution will be exactly the same each
time

// you use that seed number.

 

  for(int ii=1; ii<argc; ii++) {

    if(strcmp(argv[ii++],"seed") == 0) {

      GARandomSeed((unsigned int)atoi(argv[ii]));

    }

  }

 

// Declare variables for the GA parameters and set them to some default
values.

 

  int width    = 10;

  int height   = 5;

  int popsize  = 10;

  int ngen     = 200;

  float pmut   = 0.001;

  float pcross = 0.9;

 

// Now create the GA and run it.  First we create a genome of the type
that

// we want to use in the GA.  The ga doesn't operate on this genome in
the

// optimization - it just uses it to clone a population of genomes.

 

  GA2DBinaryStringGenome genome(width, height, Objective);

  genome.initializer(MyInitializer);

 

// Now that we have the genome, we create the genetic algorithm and set

// its parameters - number of generations, mutation probability, and
crossover

// probability.  And finally we tell it to evolve itself.

 

  GASimpleGA ga(genome);

  ga.populationSize(popsize);

  ga.nGenerations(ngen);

  ga.pMutation(pmut);

  ga.pCrossover(pcross);

    

  ga.evolve();

 

    

// Now we print out the best genome that the GA found.

 

  cout << "The GA found:\n" << ga.statistics().bestIndividual() << "\n";

 

// That's it!

  return 0;

}

 

 

// This is the objective function.  All it does is check for alternating
0s and

// 1s.  If the gene is odd and contains a 1, the fitness is incremented
by 1.

// If the gene is even and contains a 0, the fitness is incremented by
1.  No

// penalties are assigned. 

//   We have to do the cast because a plain, generic GAGenome doesn't
have 

// the members that a GA2DBinaryStringGenome has.  And it's ok to cast
it

// because we know that we will only get GA2DBinaryStringGenomes and

// nothing else.

 

float

Objective(GAGenome& g) {

  GA2DBinaryStringGenome & genome = (GA2DBinaryStringGenome &)g;

  float score=0.0;

  int count=0;

  

  if(k < 40)            // print out the first few generations to see
how the genome looks like

  {

      for(int j=0; j<genome.height(); j++)

      {

            for(int i=0; i<genome.width(); i++)

            {

                  cout << genome.gene(i,j);

            }

            cout << endl;

      }

      cout << endl;

  }

 

  for(int i=0; i<genome.width(); i++){

    for(int j=0; j<genome.height(); j++){

      if(genome.gene(i,j) == 0 && count%2 == 0)

      score += 1.0;

      if(genome.gene(i,j) == 1 && count%2 != 0)

      score += 1.0;

      count++;

    }

  }

  k++;

  return score;

  

}

 

 

________________________________

From: galib-bounces at mit.edu [mailto:galib-bounces at mit.edu] On Behalf Of
yi.zong at risoe.dk
Sent: Friday, October 03, 2008 3:12 AM
To: galib at mit.edu
Subject: [galib] Help: Initializer: first generation always are zeros,
not a real number!

 

Dear Michael, Patrik and all,

I have tried your suggestion, but it still has the problem: the first
generation's individuals always are zeros, not a real number that I
expect!

Could you give me some other suggestion? 

 Thank you in advance,

 

Yi

 

 

 

Yi Zong
Post doc
Phone direct +45 4677 5045
Mobile 
yi.zong at risoe.dk
 

Wind Energy Department
Ris? National Laboratory for Sustainable Energy
Technical University of Denmark - DTU
Building 118, P.O. Box 49
DK-4000 Roskilde, Denmark
Tel +45 4677 4677
Fax +45 4677 5083
www.risoe.dtu.dk 












 

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http://mailman.mit.edu/mailman/listinfo/galib


End of galib Digest, Vol 63, Issue 5
************************************




From yi.zong at risoe.dk  Wed Oct  8 06:48:55 2008
From: yi.zong at risoe.dk (yi.zong@risoe.dk)
Date: Wed, 08 Oct 2008 12:48:55 +0200
Subject: [galib] galib Digest, Vol 63, Issue 5
In-Reply-To: <48EC8A35.9000003@unice.fr>
References: <mailman.273740.1223140073.6365.galib@mit.edu>
	<7F526FDC6908FB4AA1985F13F0AFAC1402D3F321@EXCHG-VS1.risoe.dk>
	<48EC8A35.9000003@unice.fr>
Message-ID: <7F526FDC6908FB4AA1985F13F0AFAC1402D3F472@EXCHG-VS1.risoe.dk>

Dear Patrick,

   Thank you for your help.

   I had changed double to float in Myinitializer. But it is still not working.

It seems that the Program never calls Myinitializer and without ga.initialize(), so it specified the first generation's individuals as 0.

 

Anybody has solution?

 

Thanks 

   

 

Yi Zong
Post doc
Phone direct +45 4677 5045
Mobile 
yi.zong at risoe.dk
 

Wind Energy Department
Ris? National Laboratory for Sustainable Energy
Technical University of Denmark - DTU
Building 118, P.O. Box 49
DK-4000 Roskilde, Denmark
Tel +45 4677 4677
Fax +45 4677 5083
www.risoe.dtu.dk 













________________________________

From: Patrick Coquillard [mailto:patrick.coquillard at unice.fr] 
Sent: Wednesday, October 08, 2008 12:24 PM
To: yi.zong at risoe.dk
Subject: Re: [galib] galib Digest, Vol 63, Issue 5

 

Dera Yi,

Here is your initializer :

void Myinitializer( GAGenome &g )

   {

      GARealGenome &genome = (GARealGenome &)g;

      double IC[]={-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2};

         for( int i = 0; i < 36; ++i )

        {

             genome.gene(i, IC[i]);

        }    

   }

But, the declaration of  GAAlleleSetArray is :

typedef GAAlleleSetArray<float> GARealAlleleSetArray;

Try to initialize your genome with float instead of double ?

regards, P.




yi.zong at risoe.dk a ?crit : 

 
Dear all,
   I still can not solve my problem. (Initializer: first generation
always are zeros,      not a real number!)
   Could you give me any idea?
   
   Thank you for your help!
 
        Yi
 
-----Original Message-----
From: galib-bounces at mit.edu [mailto:galib-bounces at mit.edu] On Behalf Of
galib-request at mit.edu
Sent: Saturday, October 04, 2008 7:08 PM
To: galib at mit.edu
Subject: galib Digest, Vol 63, Issue 5
 
Send galib mailing list submissions to
        galib at mit.edu
 
To subscribe or unsubscribe via the World Wide Web, visit
        http://mailman.mit.edu/mailman/listinfo/galib
or, via email, send a message with subject or body 'help' to
        galib-request at mit.edu
 
You can reach the person managing the list at
        galib-owner at mit.edu
 
When replying, please edit your Subject line so it is more specific
than "Re: Contents of galib digest..."
 
 
Today's Topics:
 
   1. Re: Help: Initializer: first generation always are zeros,      not
      a real number! (Kupfer, Michael (ARC-AFA)[UC SANTA CRUZ])
 
 
----------------------------------------------------------------------
 
Message: 1
Date: Fri, 3 Oct 2008 12:25:26 -0500
From: "Kupfer, Michael (ARC-AFA)[UC SANTA CRUZ]"
        <Michael.Kupfer at nasa.gov> <mailto:Michael.Kupfer at nasa.gov> 
Subject: Re: [galib] Help: Initializer: first generation always are
        zeros,  not a real number!
To: <yi.zong at risoe.dk> <mailto:yi.zong at risoe.dk> , <galib at mit.edu> <mailto:galib at mit.edu> 
Message-ID:
        <87D67DA289F034488A9D7E4CDEFD28CC98CB08 at NDMSEVS34B.ndc.nasa.gov> <mailto:87D67DA289F034488A9D7E4CDEFD28CC98CB08 at NDMSEVS34B.ndc.nasa.gov> 
Content-Type: text/plain; charset="iso-8859-1"
 
Hello Yi!
 
 
 
I took GAlib example1 and added an own initializer.
 
With it (line 41) one now can set the first genes either to 0 or to 1.
 
Try to go from there.
 
 
 
Best,
 
Michael.
 
 
 
--------------------------------------------------
 
Michael Kupfer
 
 
 
 
 
University Affiliated Research Center
 
UC Santa Cruz
 
NASA Ames Research Center
 
Building 210, Room 255, Mail Stop 210-6
 
Moffett Field, CA 94035
 
U.S.A.
 
 
 
Email: Michael.Kupfer AT nasa.gov <mailto:Michael.Kupfer at nasa.gov> <mailto:Michael.Kupfer at nasa.gov>  
 
Phone: (650)604-6424
 
 
 
 
 
/*
------------------------------------------------------------------------
----
 
  ex1.C
 
  mbwall 28jul94
 
  Copyright (c) 1995-1996  Massachusetts Institute of Technology
 
 
 
 DESCRIPTION:
 
   Example program for the SimpleGA class and 2DBinaryStringGenome
class.
 
This program tries to fill the 2Dgenome with alternating 1s and 0s. 
 
  This example uses the default crossover (single point), default
mutator
 
(uniform random bit flip), and default initializer (uniform random) for
the
 
2D genome.
 
  Notice that one-point crossover is not necessarily the best kind of
crossover
 
to use if you want to generate a 'good' genome with this kind of
objective 
 
function.  But it does work.
 
------------------------------------------------------------------------
---- */
 
#include <ga/GASimpleGA.h>    // we're going to use the simple GA
 
#include <ga/GA2DBinStrGenome.h> // and the 2D binary string genome
 
#include <ga/std_stream.h>
 
 
 
#define cout STD_COUT
 
 
 
void MyInitializer(GAGenome & g);
 
 
 
float Objective(GAGenome &);  // This is the declaration of our obj
function.
 
                        // The definition comes later in the file.
 
 
 
int k = 0;
 
 
 
 
 
//------------------- own initializer---------------------
 
void MyInitializer(GAGenome & g)
 
{
 
      //cout << "Hello" <<endl;     
 
      
 
      GA2DBinaryStringGenome & genome = (GA2DBinaryStringGenome &)g;
 
 
 
            for(int j=0; j<genome.height(); j++)
 
            {
 
                  for(int i=0; i<genome.width(); i++)
 
                  {
 
                        genome.gene(i,j,1); // to set the genes with
which the population gets initialized: either 1 or 0
 
                                                      // stupid example;
I should have taken one where one can seed it also with non binary
values
 
                  }
 
            }
 
}
 
//---------------------end of own initializer--------------------------
 
 
 
 
 
int
 
main(int argc, char **argv)
 
{
 
  cout << "Example 1\n\n";
 
  cout << "This program tries to fill a 2DBinaryStringGenome with\n";
 
  cout << "alternating 1s and 0s using a SimpleGA\n\n"; cout.flush();
 
 
 
// See if we've been given a seed to use (for testing purposes).  When
you
 
// specify a random seed, the evolution will be exactly the same each
time
 
// you use that seed number.
 
 
 
  for(int ii=1; ii<argc; ii++) {
 
    if(strcmp(argv[ii++],"seed") == 0) {
 
      GARandomSeed((unsigned int)atoi(argv[ii]));
 
    }
 
  }
 
 
 
// Declare variables for the GA parameters and set them to some default
values.
 
 
 
  int width    = 10;
 
  int height   = 5;
 
  int popsize  = 10;
 
  int ngen     = 200;
 
  float pmut   = 0.001;
 
  float pcross = 0.9;
 
 
 
// Now create the GA and run it.  First we create a genome of the type
that
 
// we want to use in the GA.  The ga doesn't operate on this genome in
the
 
// optimization - it just uses it to clone a population of genomes.
 
 
 
  GA2DBinaryStringGenome genome(width, height, Objective);
 
  genome.initializer(MyInitializer);
 
 
 
// Now that we have the genome, we create the genetic algorithm and set
 
// its parameters - number of generations, mutation probability, and
crossover
 
// probability.  And finally we tell it to evolve itself.
 
 
 
  GASimpleGA ga(genome);
 
  ga.populationSize(popsize);
 
  ga.nGenerations(ngen);
 
  ga.pMutation(pmut);
 
  ga.pCrossover(pcross);
 
    
 
  ga.evolve();
 
 
 
    
 
// Now we print out the best genome that the GA found.
 
 
 
  cout << "The GA found:\n" << ga.statistics().bestIndividual() << "\n";
 
 
 
// That's it!
 
  return 0;
 
}
 
 
 
 
 
// This is the objective function.  All it does is check for alternating
0s and
 
// 1s.  If the gene is odd and contains a 1, the fitness is incremented
by 1.
 
// If the gene is even and contains a 0, the fitness is incremented by
1.  No
 
// penalties are assigned. 
 
//   We have to do the cast because a plain, generic GAGenome doesn't
have 
 
// the members that a GA2DBinaryStringGenome has.  And it's ok to cast
it
 
// because we know that we will only get GA2DBinaryStringGenomes and
 
// nothing else.
 
 
 
float
 
Objective(GAGenome& g) {
 
  GA2DBinaryStringGenome & genome = (GA2DBinaryStringGenome &)g;
 
  float score=0.0;
 
  int count=0;
 
  
 
  if(k < 40)            // print out the first few generations to see
how the genome looks like
 
  {
 
      for(int j=0; j<genome.height(); j++)
 
      {
 
            for(int i=0; i<genome.width(); i++)
 
            {
 
                  cout << genome.gene(i,j);
 
            }
 
            cout << endl;
 
      }
 
      cout << endl;
 
  }
 
 
 
  for(int i=0; i<genome.width(); i++){
 
    for(int j=0; j<genome.height(); j++){
 
      if(genome.gene(i,j) == 0 && count%2 == 0)
 
      score += 1.0;
 
      if(genome.gene(i,j) == 1 && count%2 != 0)
 
      score += 1.0;
 
      count++;
 
    }
 
  }
 
  k++;
 
  return score;
 
  
 
}
 
 
 
 
 
________________________________
 
From: galib-bounces at mit.edu [mailto:galib-bounces at mit.edu] On Behalf Of
yi.zong at risoe.dk
Sent: Friday, October 03, 2008 3:12 AM
To: galib at mit.edu
Subject: [galib] Help: Initializer: first generation always are zeros,
not a real number!
 
 
 
Dear Michael, Patrik and all,
 
I have tried your suggestion, but it still has the problem: the first
generation's individuals always are zeros, not a real number that I
expect!
 
Could you give me some other suggestion? 
 
 Thank you in advance,
 
 
 
Yi
 
 
 
 
 
 
 
Yi Zong
Post doc
Phone direct +45 4677 5045
Mobile 
yi.zong at risoe.dk
 
 
Wind Energy Department
Ris? National Laboratory for Sustainable Energy
Technical University of Denmark - DTU
Building 118, P.O. Box 49
DK-4000 Roskilde, Denmark
Tel +45 4677 4677
Fax +45 4677 5083
www.risoe.dtu.dk 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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_______________________________________________
galib mailing list
galib at mit.edu
http://mailman.mit.edu/mailman/listinfo/galib
 
 
End of galib Digest, Vol 63, Issue 5
************************************
 
 
_______________________________________________
galib mailing list
galib at mit.edu
http://mailman.mit.edu/mailman/listinfo/galib
 
 
  

 

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From yi.zong at risoe.dk  Thu Oct  9 08:25:27 2008
From: yi.zong at risoe.dk (yi.zong@risoe.dk)
Date: Thu, 09 Oct 2008 14:25:27 +0200
Subject: [galib] galib Digest, Vol 63, Issue 5
In-Reply-To: <48ECE4D6.2060908@unice.fr>
References: <mailman.273740.1223140073.6365.galib@mit.edu>
	<7F526FDC6908FB4AA1985F13F0AFAC1402D3F321@EXCHG-VS1.risoe.dk>
	<48EC8A35.9000003@unice.fr>
	<7F526FDC6908FB4AA1985F13F0AFAC1402D3F472@EXCHG-VS1.risoe.dk>
	<48ECE4D6.2060908@unice.fr>
Message-ID: <7F526FDC6908FB4AA1985F13F0AFAC1402D3F6EE@EXCHG-VS1.risoe.dk>

Dear all,

   Thanks a lot. 

Specially, many thanks to Patrick.

I have solved the problem.

1. We need to use:  

    ga.initialize() in

 int main(int argc, char** argv)

{

 }

2. Addition: put Myinitializer 

              Before Objective

Like this:

 

void Myinitializer(GAGenome &);

float Objective(GAGenome &);

 

int

main(int argc, char** argv)

{

   for(int jj=1; jj<argc; jj++) {

    if(strcmp(argv[jj++],"seed") == 0) {

      GARandomSeed((unsigned int)atoi(argv[jj]));

     }

    }

 

  ofstream outfile;

 

  GARealGenome genome(length, alleles, Objective);

//  GASharing scale;//using GAScalingScheme::GASharing-default

  GANoScaling scale;//GAScalingScheme::GANoScaling--the fitness scores = the objectivescores

 

  genome.crossover(GARealTwoPointCrossover);

  genome.initializer(Myinitializer); // Initial with Myinitializer  

  

  GASimpleGA ga(genome);

  ga.minimize();                     // by default we want to minimize the objective

  ga.scaling(scale);                // set the scaling method to our sharing

  ga.populationSize(73);         // how many individuals in the population

  ga.nGenerations(100);         // number of generations to evolve

  ga.nBestGenomes(1);           // Specify how many 'best' genomes to record, the default is 1

  ga.pMutation(0.05);              // likelihood of mutating new offspring

  ga.pCrossover(0.6);             // likelihood of crossing over parents

  ga.scoreFilename("yinw25.dat"); // name of file for scores

  ga.scoreFrequency(1);                    // keep the scores of every generation

  ga.flushFrequency(1);          // specify how often to write the score to disk, if generation<10, then it only records once

  ga.selectScores(GAStatistics::AllScores);

  ga.parameters(argc, argv, gaTrue); // parse commands, complain if bogus args

  //unsigned int seed=0;

//ga.initialize(seed)

  ga.initialize();

 

....

}

 

void Myinitializer( GAGenome &g )

   {

      GARealGenome &genome = (GARealGenome &)g;

      float IC[]={-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2,-19.2};

   

      for( int i = 0; i < 36; ++i )

        {

             genome.gene(i, IC[i]);

        }    

   }

Yi Zong
Post doc
Phone direct +45 4677 5045
Mobile 
yi.zong at risoe.dk
 

Wind Energy Department
Ris? National Laboratory for Sustainable Energy
Technical University of Denmark - DTU
Building 118, P.O. Box 49
DK-4000 Roskilde, Denmark
Tel +45 4677 4677
Fax +45 4677 5083
www.risoe.dtu.dk 













________________________________

From: Patrick Coquillard [mailto:patrick.coquillard at unice.fr] 
Sent: Wednesday, October 08, 2008 6:51 PM
To: yi.zong at risoe.dk
Subject: Re: [galib] galib Digest, Vol 63, Issue 5

 

Hi Yi,

I embedded your code in a simple source...that did nothing. Compilation and execution. Really, I do not understand why your initializer is never called. May be you found a bug of galib. I suggest you could try to use an other kind of  genome ? I don't know.
I attach the stupid example I build from your code.
Sorry,
regards, P.





________________________________






 
 
 
 
 
 
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From parnurzeal at gmail.com  Sun Oct 19 06:49:43 2008
From: parnurzeal at gmail.com (Theeraphol Wattanavekin)
Date: Sun, 19 Oct 2008 17:49:43 +0700
Subject: [galib] What is flushfrequency?
Message-ID: <c31608d10810190349v2277ea38jfcd1172ef42bdbcb@mail.gmail.com>

Hello,
My name is Theeraphol. Now,I am doing homework in AI subject.
And I have a question.
What is flushfrequency?
I read pdf but I don't understand.
What will happen when flush score?

Thank you very much,
Theeraphol Wattanavekin


From jeedward at yahoo.com  Sun Oct 19 12:02:00 2008
From: jeedward at yahoo.com (John Edward)
Date: Sun, 19 Oct 2008 09:02:00 -0700 (PDT)
Subject: [galib] AIPR-09 call for papers
Message-ID: <535804.78164.qm@web45915.mail.sp1.yahoo.com>

AIPR-09 call for papers
?
The 2009 International Conference on Artificial Intelligence and Pattern Recognition (AIPR-09) (website: www.PromoteResearch.org ) will be held during July 13-16 2009 in Orlando, FL, USA. We invite draft paper submissions. The conference will take place at the same time and venue where several other international conferences are taking place. The other conferences include:
????????? International Conference on Automation, Robotics and Control Systems (ARCS-09)
????????? International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-09)
????????? International Conference on Enterprise Information Systems and Web Technologies (EISWT-09)
????????? International Conference on High Performance Computing, Networking and Communication Systems (HPCNCS-09) 
????????? International Conference on Information Security and Privacy (ISP-09)
????????? International Conference on Recent Advances in Information Technology and Applications (RAITA-09)
????????? International Conference on Software Engineering Theory and Practice (SETP-09) 
????????? International Conference on Theory and Applications of Computational Science (TACS-09)
????????? International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-09)
?
The website www.PromoteResearch.org contains more details.
?
Sincerely
John Edward
Publicity committee
?
?

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
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From sbahri at rocketmail.com  Thu Oct 30 06:43:28 2008
From: sbahri at rocketmail.com (Sjaiful Bahri)
Date: Thu, 30 Oct 2008 03:43:28 -0700 (PDT)
Subject: [galib] Search Engine for News
Message-ID: <372340.35046.qm@web30204.mail.mud.yahoo.com>

Hi Folks,

FYI, I am running a crawl algorithm on zipclue.com

Zipclue is a prototype of News Search Engine (abbreviated NSE), which makes extensive use of the structure present in hypertext. Zipclue NSE is designed to crawl news information on the web effectively and efficiently.

Zipclue stores and produces historical electronic news around the world depends upon limiting parameters which we as the authors can set up, in this particular instance, we rank them based upon news release time (NRT) which practically try to grab the latest news out there. The prototype with a full text and hyperlink database of electronic news is available here:
http://zipclue.com

Regards,
Sjaiful Bahri