Strzelecki Łukasz > AI-Genetic-Pro-0.401 > AI::Genetic::Pro

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NAME ^

AI::Genetic::Pro - Efficient genetic algorithms for professional purpose.

SYNOPSIS ^

    use AI::Genetic::Pro;
    
    sub fitness {
        my ($ga, $chromosome) = @_;
        return oct('0b' . $ga->as_string($chromosome)); 
    }
    
    sub terminate {
        my ($ga) = @_;
        my $result = oct('0b' . $ga->as_string($ga->getFittest));
        return $result == 4294967295 ? 1 : 0;
    }
    
    my $ga = AI::Genetic::Pro->new(        
        -fitness         => \&fitness,        # fitness function
        -terminate       => \&terminate,      # terminate function
        -type            => 'bitvector',      # type of chromosomes
        -population      => 1000,             # population
        -crossover       => 0.9,              # probab. of crossover
        -mutation        => 0.01,             # probab. of mutation
        -parents         => 2,                # number  of parents
        -selection       => [ 'Roulette' ],   # selection strategy
        -strategy        => [ 'Points', 2 ],  # crossover strategy
        -cache           => 0,                # cache results
        -history         => 1,                # remember best results
        -preserve        => 3,                # remember the bests
        -variable_length => 1,                # turn variable length ON
    );
        
    # init population of 32-bit vectors
    $ga->init(32);
        
    # evolve 10 generations
    $ga->evolve(10);
    
    # best score
    print "SCORE: ", $ga->as_value($ga->getFittest), ".\n";
    
    # save evolution path as a chart
    $ga->chart(-filename => 'evolution.png');
     
    # save state of GA
    $ga->save('genetic.sga');
    
    # load state of GA
    $ga->load('genetic.sga');

DESCRIPTION ^

This module provides efficient implementation of a genetic algorithm for professional use. It was designed to operate as fast as possible even on very large populations and big individuals/chromosomes. AI::Genetic::Pro was inspired by AI::Genetic, so it is in most cases compatible (there are some changes). Additionally AI::Genetic::Pro isn't a pure Perl solution, so it doesn't have limitations of its ancestor (such as serious slow-down in the case of big populations ( >10000 ) or vectors with more than 33 fields).

If You are looking for a pure Perl solution, consider AI::Genetic.

Speed

To increase speed XS code is used, however with portability in mind. This distribution was tested on Windows and Linux platforms (and should work on any other).

Memory

This module was designed to use as little memory as possible. A population of size 10000 consisting of 92-bit vectors uses only ~24MB (AI::Genetic would use about 78MB!).

Advanced options

To provide more flexibility AI::Genetic::Pro supports many statistical distributions, such as uniform, natural, chi_square and others. This feature can be used in selection and/or crossover. See the documentation below.

METHODS ^

$ga->new( %options )

Constructor. It accepts options in hash-value style. See options and an example below.

-fitness

This defines a fitness function. It expects a reference to a subroutine.

-terminate

This defines a terminate function. It expects a reference to a subroutine.

-type

This defines the type of chromosomes. Currently, AI::Genetic::Pro supports four types:

bitvector

Individuals/chromosomes of this type have genes that are bits. Each gene can be in one of two possible states, on or off.

listvector

Each gene of a "listvector" individual/chromosome can assume one string value from a specified list of possible string values.

rangevector

Each gene of a "rangevector" individual/chromosome can assume one integer value from a range of possible integer values. Note that only integers are supported. The user can always transform any desired fractional values by multiplying and dividing by an appropriate power of 10.

combination

Each gene of a "combination" individual/chromosome can assume one string value from a specified list of possible string values. All genes are unique.

-population

This defines the size of the population, i.e. how many chromosomes simultaneously exist at each generation.

-crossover

This defines the crossover rate. The fairest results are achieved with crossover rate ~0.95.

-mutation

This defines the mutation rate. The fairest results are achieved with mutation rate ~0.01.

-preserve

This defines injection of the bests chromosomes into a next generation. It causes a little slow down, however (very often) much better results are achieved. You can specify, how many chromosomes will be preserved, i.e.

    -preserve => 1, # only one chromosome will be preserved
    # or
    -preserve => 9, # 9 chromosomes will be preserved
    # and so on...

Attention! You cannot preserve more chromosomes than exist in your population.

-variable_length

This defines whether variable-length chromosomes are turned on (default off) and a which types of mutation are allowed. See below.

level 0

Feature is inactive (default). Example:

        -variable_length => 0
        
    # chromosomes (i.e. bitvectors)
    0 1 0 0 1 1 0 1 1 1 0 1 0 1
    0 0 1 1 0 1 1 1 1 0 0 1 1 0
    0 1 1 1 0 1 0 0 1 1 0 1 1 1
    0 1 0 0 1 1 0 1 1 1 1 0 1 0
    # ...and so on
level 1

Feature is active, but chromosomes can varies only on the right side, Example:

        -variable_length => 1
        
    # chromosomes (i.e. bitvectors)
    0 1 0 0 1 1 0 1 1 1 
    0 0 1 1 0 1 1 1 1
    0 1 1 1 0 1 0 0 1 1 0 1 1 1
    0 1 0 0 1 1 0 1 1 1
    # ...and so on
level 2

Feature is active and chromosomes can varies on the left side and on the right side; unwanted values/genes on the left side are replaced with undef, ie.

        -variable_length => 2
 
    # chromosomes (i.e. bitvectors)
    x x x 0 1 1 0 1 1 1 
    x x x x 0 1 1 1 1
    x 1 1 1 0 1 0 0 1 1 0 1 1 1
    0 1 0 0 1 1 0 1 1 1
    # where 'x' means 'undef'
    # ...and so on

In this situation returned chromosomes in an array context ($ga->as_array($chromosome)) can have undef values on the left side (only). In a scalar context each undefined value is replaced with a single space. If You don't want to see any undef or space, just use as_array_def_only and as_string_def_only instead of as_array and as_string.

-parents

This defines how many parents should be used in a crossover.

-selection

This defines how individuals/chromosomes are selected to crossover. It expects an array reference listed below:

    -selection => [ $type, @params ]

where type is one of:

RouletteBasic

Each individual/chromosome can be selected with probability proportional to its fitness.

Roulette

First the best individuals/chromosomes are selected. From this collection parents are selected with probability poportional to their fitness.

RouletteDistribution

Each individual/chromosome has a portion of roulette wheel proportional to its fitness. Selection is done with the specified distribution. Supported distributions and parameters are listed below.

-selection => [ 'RouletteDistribution', 'uniform' ]

Standard uniform distribution. No additional parameters are needed.

-selection => [ 'RouletteDistribution', 'normal', $av, $sd ]

Normal distribution, where $av is average (default: size of population /2) and $$sd is standard deviation (default: size of population).

-selection => [ 'RouletteDistribution', 'beta', $aa, $bb ]

Beta distribution. The density of the beta is:

    X^($aa - 1) * (1 - X)^($bb - 1) / B($aa , $bb) for 0 < X < 1.

$aa and $bb are set by default to number of parents.

Argument restrictions: Both $aa and $bb must not be less than 1.0E-37.

-selection => [ 'RouletteDistribution', 'binomial' ]

Binomial distribution. No additional parameters are needed.

-selection => [ 'RouletteDistribution', 'chi_square', $df ]

Chi-square distribution with $df degrees of freedom. $df by default is set to size of population.

-selection => [ 'RouletteDistribution', 'exponential', $av ]

Exponential distribution, where $av is average . $av by default is set to size of population.

-selection => [ 'RouletteDistribution', 'poisson', $mu ]

Poisson distribution, where $mu is mean. $mu by default is set to size of population.

Distribution

Chromosomes/individuals are selected with specified distribution. See below.

-selection => [ 'Distribution', 'uniform' ]

Standard uniform distribution. No additional parameters are needed.

-selection => [ 'Distribution', 'normal', $av, $sd ]

Normal distribution, where $av is average (default: size of population /2) and $$sd is standard deviation (default: size of population).

-selection => [ 'Distribution', 'beta', $aa, $bb ]

Beta distribution. The density of the beta is:

    X^($aa - 1) * (1 - X)^($bb - 1) / B($aa , $bb) for 0 < X < 1.

$aa and $bb are set by default to number of parents.

Argument restrictions: Both $aa and $bb must not be less than 1.0E-37.

-selection => [ 'Distribution', 'binomial' ]

Binomial distribution. No additional parameters are needed.

-selection => [ 'Distribution', 'chi_square', $df ]

Chi-square distribution with $df degrees of freedom. $df by default is set to size of population.

-selection => [ 'Distribution', 'exponential', $av ]

Exponential distribution, where $av is average . $av by default is set to size of population.

-selection => [ 'Distribution', 'poisson', $mu ]

Poisson distribution, where $mu is mean. $mu by default is set to size of population.

-strategy

This defines the astrategy of crossover operation. It expects an array reference listed below:

    -strategy => [ $type, @params ]

where type is one of:

PointsSimple

Simple crossover in one or many points. The best chromosomes/individuals are selected for the new generation. For example:

    -strategy => [ 'PointsSimple', $n ]

where $n is the number of points for crossing.

PointsBasic

Crossover in one or many points. In basic crossover selected parents are crossed and one (randomly-chosen) child is moved to the new generation. For example:

    -strategy => [ 'PointsBasic', $n ]

where $n is the number of points for crossing.

Points

Crossover in one or many points. In normal crossover selected parents are crossed and the best child is moved to the new generation. For example:

    -strategy => [ 'Points', $n ]

where $n is number of points for crossing.

PointsAdvenced

Crossover in one or many points. After crossover the best chromosomes/individuals from all parents and chidren are selected for the new generation. For example:

    -strategy => [ 'PointsAdvanced', $n ]

where $n is the number of points for crossing.

Distribution

In distribution crossover parents are crossed in points selected with the specified distribution. See below.

-strategy => [ 'Distribution', 'uniform' ]

Standard uniform distribution. No additional parameters are needed.

-strategy => [ 'Distribution', 'normal', $av, $sd ]

Normal distribution, where $av is average (default: number of parents/2) and $sd is standard deviation (default: number of parents).

-strategy => [ 'Distribution', 'beta', $aa, $bb ]

Beta distribution. The density of the beta is:

    X^($aa - 1) * (1 - X)^($bb - 1) / B($aa , $bb) for 0 < X < 1.

$aa and $bb are set by default to the number of parents.

Argument restrictions: Both $aa and $bb must not be less than 1.0E-37.

-strategy => [ 'Distribution', 'binomial' ]

Binomial distribution. No additional parameters are needed.

-strategy => [ 'Distribution', 'chi_square', $df ]

Chi-squared distribution with $df degrees of freedom. $df by default is set to the number of parents.

-strategy => [ 'Distribution', 'exponential', $av ]

Exponential distribution, where $av is average . $av by default is set to the number of parents.

-strategy => [ 'Distribution', 'poisson', $mu ]

Poisson distribution, where $mu is mean. $mu by default is set to the number of parents.

PMX

PMX method defined by Goldberg and Lingle in 1985. Parameters: none.

OX

OX method defined by Davis (?) in 1985. Parameters: none.

-cache

This defines whether a cache should be used. Allowed values are 1 or 0 (default: 0).

-history

This defines whether history should be collected. Allowed values are 1 or 0 (default: 0).

-strict

This defines if the check for modifying chromosomes in a user-defined fitness function is active. Directly modifying chromosomes is not allowed and it is a highway to big trouble. This mode should be used only for testing, because it is slow.

$ga->inject($chromosomes)

Inject new, user defined, chromosomes into the current population. See example below:

    # example for bitvector
    my $chromosomes = [
        [ 1, 1, 0, 1, 0, 1 ],
        [ 0, 0, 0, 1, 0, 1 ],
        [ 0, 1, 0, 1, 0, 0 ],
        ...
    ];
    
    # inject
    $ga->inject($chromosomes);

If You want to delete some chromosomes from population, just splice them:

    my @remove = qw(1 2 3 9 12);
        for my $idx (sort { $b <=> $a }  @remove){
        splice @{$ga->chromosomes}, $idx, 1;
    }
$ga->population($population)

Set/get size of the population. This defines the size of the population, i.e. how many chromosomes to simultaneously exist at each generation.

$ga->indType()

Get type of individuals/chromosomes. Currently supported types are:

bitvector

Chromosomes will be just bitvectors. See documentation of new method.

listvector

Chromosomes will be lists of specified values. See documentation of new method.

rangevector

Chromosomes will be lists of values from specified range. See documentation of new method.

combination

Chromosomes will be unique lists of specified values. This is used for example in the Traveling Salesman Problem. See the documentation of the new method.

In example:

    my $type = $ga->type();
$ga->type()

Alias for indType.

$ga->crossProb()

This method is used to query and set the crossover rate.

$ga->crossover()

Alias for crossProb.

$ga->mutProb()

This method is used to query and set the mutation rate.

$ga->mutation()

Alias for mutProb.

$ga->parents($parents)

Set/get number of parents in a crossover.

$ga->init($args)

This method initializes the population with random individuals/chromosomes. It MUST be called before any call to evolve(). It expects one argument, which depends on the type of individuals/chromosomes:

bitvector

For bitvectors, the argument is simply the length of the bitvector.

    $ga->init(10);

This initializes a population where each individual/chromosome has 10 genes.

listvector

For listvectors, the argument is an anonymous list of lists. The number of sub-lists is equal to the number of genes of each individual/chromosome. Each sub-list defines the possible string values that the corresponding gene can assume.

    $ga->init([
               [qw/red blue green/],
               [qw/big medium small/],
               [qw/very_fat fat fit thin very_thin/],
              ]);

This initializes a population where each individual/chromosome has 3 genes and each gene can assume one of the given values.

rangevector

For rangevectors, the argument is an anonymous list of lists. The number of sub-lists is equal to the number of genes of each individual/chromosome. Each sub-list defines the minimum and maximum integer values that the corresponding gene can assume.

    $ga->init([
               [1, 5],
               [0, 20],
               [4, 9],
              ]);

This initializes a population where each individual/chromosome has 3 genes and each gene can assume an integer within the corresponding range.

combination

For combination, the argument is an anonymous list of possible values of gene.

    $ga->init( [ 'a', 'b', 'c' ] );

This initializes a population where each chromosome has 3 genes and each gene is a unique combination of 'a', 'b' and 'c'. For example genes looks something like that:

    [ 'a', 'b', 'c' ]    # gene 1
    [ 'c', 'a', 'b' ]    # gene 2
    [ 'b', 'c', 'a' ]    # gene 3
    # ...and so on...
$ga->evolve($n)

This method causes the GA to evolve the population for the specified number of generations. If its argument is 0 or undef GA will evolve the population to infinity unless a terminate function is specified.

$ga->getHistory()

Get history of the evolution. It is in a format listed below:

        [
                # gen0   gen1   gen2   ...          # generations
                [ max0,  max1,  max2,  ... ],       # max values
                [ mean,  mean1, mean2, ... ],       # mean values
                [ min0,  min1,  min2,  ... ],       # min values
        ]
$ga->getAvgFitness()

Get max, mean and min score of the current generation. In example:

    my ($max, $mean, $min) = $ga->getAvgFitness();
$ga->getFittest($n, $unique)

This function returns a list of the fittest chromosomes from the current population. You can specify how many chromosomes should be returned and if the returned chromosomes should be unique. See example below.

    # only one - the best
    my ($best) = $ga->getFittest;

    # or 5 bests chromosomes, NOT unique
    my @bests = $ga->getFittest(5);

    # or 7 bests and UNIQUE chromosomes
    my @bests = $ga->getFittest(7, 1);

If you want to get a large number of chromosomes, try to use the getFittest_as_arrayref function instead (for efficiency).

$ga->getFittest_as_arrayref($n, $unique)

This function is very similar to getFittest, but it returns a reference to an array instead of a list.

$ga->generation()

Get the number of the current generation.

$ga->people()

Returns an anonymous list of individuals/chromosomes of the current population.

IMPORTANT: the actual array reference used by the AI::Genetic::Pro object is returned, so any changes to it will be reflected in $ga.

$ga->chromosomes()

Alias for people.

$ga->chart(%options)

Generate a chart describing changes of min, mean, and max scores in your population. To satisfy your needs, you can pass the following options:

-filename

File to save a chart in (obligatory).

-title

Title of a chart (default: Evolution).

-x_label

X label (default: Generations).

-y_label

Y label (default: Value).

-format

Format of values, like sprintf (default: '%.2f').

-legend1

Description of min line (default: Min value).

-legend2

Description of min line (default: Mean value).

-legend3

Description of min line (default: Max value).

-width

Width of a chart (default: 640).

-height

Height of a chart (default: 480).

-font

Path to font (in *.ttf format) to be used (default: none).

-logo

Path to logo (png/jpg image) to embed in a chart (default: none).

For example:
        $ga->chart(-width => 480, height => 320, -filename => 'chart.png');
$ga->save($file)

Save the current state of the genetic algorithm to the specified file.

$ga->load($file)

Load a state of the genetic algorithm from the specified file.

$ga->as_array($chromosome)

In list context return an array representing the specified chromosome. In scalar context return an reference to an array representing the specified chromosome. If variable_length is turned on and is set to level 2, an array can have some undef values. To get only not undef values use as_array_def_only instead of as_array.

$ga->as_array_def_only($chromosome)

In list context return an array representing the specified chromosome. In scalar context return an reference to an array representing the specified chromosome. If variable_length is turned off, this function is just an alias for as_array. If variable_length is turned on and is set to level 2, this function will return only not undef values from chromosome. See example below:

    # -variable_length => 2, -type => 'bitvector'
        
    my @chromosome = $ga->as_array($chromosome)
    # @chromosome looks something like that
    # ( undef, undef, undef, 1, 0, 1, 1, 1, 0 )
        
    @chromosome = $ga->as_array_def_only($chromosome)
    # @chromosome looks something like that
    # ( 1, 0, 1, 1, 1, 0 )
$ga->as_string($chromosome)

Return a string representation of the specified chromosome. See example below:

        # -type => 'bitvector'
        
        my $string = $ga->as_string($chromosome);
        # $string looks something like that
        # 1___0___1___1___1___0 
        
        # or 
        
        # -type => 'listvector'
        
        $string = $ga->as_string($chromosome);
        # $string looks something like that
        # element0___element1___element2___element3...

Attention! If variable_length is turned on and is set to level 2, it is possible to get undef values on the left side of the vector. In the returned string undef values will be replaced with spaces. If you don't want to see any spaces, use as_string_def_only instead of as_string.

$ga->as_string_def_only($chromosome)

Return a string representation of specified chromosome. If variable_length is turned off, this function is just alias for as_string. If variable_length is turned on and is set to level 2, this function will return a string without undef values. See example below:

        # -variable_length => 2, -type => 'bitvector'
        
        my $string = $ga->as_string($chromosome);
        # $string looks something like that
        #  ___ ___ ___1___1___0 
        
        $string = $ga->as_string_def_only($chromosome);
        # $string looks something like that
        # 1___1___0 
$ga->as_value($chromosome)

Return the score of the specified chromosome. The value of chromosome is calculated by the fitness function.

SUPPORT ^

AI::Genetic::Pro is still under development; however, it is used in many production environments.

TODO ^

Examples.
More tests.
More warnings about incorrect parameters.

REPORTING BUGS ^

When reporting bugs/problems please include as much information as possible. It may be difficult for me to reproduce the problem as almost every setup is different.

A small script which yields the problem will probably be of help.

THANKS ^

Miles Gould for suggestions and some fixes (even in this documentation! :-).

Alun Jones for fixing memory leaks.

Tod Hagan for reporting a bug (rangevector values truncated to signed 8-bit quantities) and supplying a patch.

Randal L. Schwartz for reporting a bug in this documentation.

Maciej Misiak for reporting problems with combination (and a bug in a PMX strategy).

LEONID ZAMDBORG for recommending the addition of variable-length chromosomes as well as supplying relevant code samples, for testing and at the end reporting some bugs.

Christoph Meissner for reporting a bug.

Alec Chen for reporting some bugs.

AUTHOR ^

Strzelecki Lukasz <lukasz@strzeleccy.eu>

SEE ALSO ^

AI::Genetic Algorithm::Evolutionary

COPYRIGHT ^

Copyright (c) Strzelecki Lukasz. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

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