gegene 1.0.0 → 1.1.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/LICENSE.txt

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2013 Alexandre Ignjatovic
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/lib/chromosome.rb

@@ -1,26 +1,70 @@
 require 'gene'
 require 'allele'
+
+# This class represent a chromosome, which contains several allele (gene's values)
+# and is able to mutate, and to cross over.
 class Chromosome
   
+  # Construct a chromosome from an array of alleles
   def initialize(alleles)
+    raise "this constructor expect an array of alleles as input" unless
+      alleles.is_a?(Array)
     @alleles = alleles
   end
   
+  # Copy the current chromosome and all its alleles
   def copy
     Chromosome.new(@alleles.map{|allele| allele.copy })
   end
   
+  # Create a random chromosome from a description
   def Chromosome.create_random_from(description)
     Chromosome.new(description.map{|gene| gene.create_random() })
   end
   
+  # Returns the allele at a specific position
   def [](gene_position)
     @alleles[gene_position]
   end
   
+  # Number of underlying alleles
+  def size
+    @alleles.size
+  end
+  
+  # Mutate a randomly selected allele of the current chromosome
   def mutate
     allele_index = rand @alleles.size
     @alleles[allele_index].mutate()
   end
   
+  # Aggregate all alleles values
+  def aggregated_alleles()
+    @alleles.map {|a| a.value}.join(";")
+  end
+  
+  # Cross over two chromosomes to provide a new one
+  def Chromosome.cross_over(chromosome_a, chromosome_b)
+    if rand(2) == 0 then
+      chromosome_a, chromosome_b =
+        [chromosome_b, chromosome_a]
+    end
+    size = chromosome_a.size
+    if size < 2 then
+      return chromosome_a.copy
+    elsif size == 2 then
+      return Chromosome.new([chromosome_a[0],chromosome_b[1]])
+    else
+      swap_index = rand(size-1)
+      index = 0
+      new_alleles = []
+      while (index < size) do
+        new_alleles.push(
+          (index <= swap_index ? chromosome_a : chromosome_b)[index].copy)
+        index += 1
+      end
+      return Chromosome.new(new_alleles)
+    end
+  end
+  
 end

data/lib/genome.rb

@@ -1,7 +1,11 @@
 require 'Karyotype'
 
+# This class stands for the genome. It is a description of all
+# the gene describing a specific population.
 class Genome
   
+  DEFAULT_CROSS_OVER_RATE = 0.01
+  
   def initialize(genome_description)
     raise "Genome description MUST be an Array" unless genome_description.is_a? Array
     @chromosomes_description = []
@@ -14,8 +18,15 @@ class Genome
       end
       @chromosomes_description << gene_array
     end
+    @cross_over_rate = DEFAULT_CROSS_OVER_RATE
   end
   attr_accessor :gene_positions
+  attr_reader :cross_over_rate
+  def cross_over_rate=(rate)
+    raise "cross_over_rate must be included in [0,1]" unless rate.between?(0,1)
+    @cross_over_rate = rate
+  end
+  
   def get_gene_position(gene_name)
     @gene_positions[gene_name]
   end

data/lib/karyotype.rb

@@ -1,20 +1,30 @@
 require 'chromosome'
+require 'digest/md5'
+# This class represent a karyotype, which could be seen as a set of
+# chromosomes representing a specific individual of a population
 class Karyotype
   attr_accessor :chromosomes
   attr_accessor :fitness
+  
   def initialize(genome, chromosomes_description)
     @genome = genome
     @chromosomes_description = chromosomes_description
   end
   private :initialize
+  
+  # Copy self and all its chromosomes to a new karyotype
   def copy
     karyotype = Karyotype.new(@genome, @chromosomes_description)
     karyotype.chromosomes = self.chromosomes.map{|chromosome| chromosome.copy}
     karyotype
   end
+  
   def to_s
     @genome.gene_positions.keys.map{|gn| "#{gn}=>#{self[gn]}"}.join';'
   end
+  
+  # Create a random karyotype from a specific genome an its associated
+  # chromosomes description
   def Karyotype.create_random_from(genome, chromosomes_description)
     karyotype = Karyotype.new(genome, chromosomes_description)
     karyotype.chromosomes = chromosomes_description.map {|description|
@@ -23,21 +33,49 @@ class Karyotype
     karyotype
   end
   
+  # Return the allele value of a specific named gene
+  # We strongly recommand using symbols as gene name
   def [](gene_name)
     return nil if @chromosomes.nil?
-    chromosome_position, gene_position = @genome.get_gene_position(gene_name)
+    chromosome_position, gene_position =
+      @genome.get_gene_position(gene_name)
     return nil if chromosome_position.nil? || gene_position.nil?
     return @chromosomes[chromosome_position][gene_position].value
   end
   
+  # Breeding function
+  # Create a new karyotype based on self and an other
   def +(other)
-    child = copy
-    other.chromosomes.each_with_index {
-      |chromosome, index| child.chromosomes[index] = chromosome if rand(2) == 0
+    child = Karyotype.new(@genome, @chromosomes_description)
+    child.chromosomes = []
+    other.chromosomes.each_with_index { |chromosome, index|
+      child_chromosome = nil
+      # Randomly copy chromosomes from dad or mom to child
+      if (rand(100) / 100.0) < @genome.cross_over_rate then
+        # Crossing over required
+        child_chromosome =
+          Chromosome.cross_over(chromosome, chromosomes[index])
+      else
+        # Standard breeding via random selection
+        child_chromosome = (rand(2)==0?chromosome : chromosomes[index]).copy
+      end
+      child.chromosomes.push(child_chromosome)
     }
     child
   end
   
+  # Aggregate all the allele into a md5 hash value
+  def to_md5()
+    if (@hash_value.nil?) then
+      @hash_value = @chromosomes.map{ |chromosome|
+        chromosome.aggregated_alleles
+      }.join(";")
+      @hash_value = Digest::MD5.hexdigest(@hash_value)
+    end
+    @hash_value
+  end
+  
+  # Randomly mutate an allele of a randomly selected chromosome
   def mutate
     @chromosomes[rand @chromosomes.size].mutate
     self

data/lib/population.rb

@@ -4,17 +4,54 @@ class Population
   DEFAULT_MUTATION_RATE = 0.01
   DEFAULT_KEEP_ALIVE_RATE = 0.1
   DEFAULT_EVOLVE_ITERATIONS = 1
+  DEFAULT_FORCE_FITNESS_RECALCULATION = false
+
+  attr_accessor :fitness_target, :karyotypes, :force_fitness_recalculation
+  attr_reader :mutation_rate, :keep_alive_rate
+  
+  # mutation rate setter function
+  # Accept values in the range [0,1]
+  def mutation_rate=(value)
+    raise "mutation_rate value must be included in [0,1]" unless value.between?(0,1)
+    @mutation_rate = value
+  end
   
-  attr_accessor :mutation_rate, :keep_alive_rate, :fitness_target, :karyotypes
+  # keep alive rate setter function
+  # Accept values in the range [0,1]
+  def keep_alive_rate=(value)
+    raise "mutation_rate value must be included in [0,1]" unless value.between?(0,1)
+    @keep_alive_rate = value
+  end 
+
 
+  # Run the fitness function for all karyotypes, and sort it by fitness
   def evaluate
-    @karyotypes.each { |k| k.fitness = @fitness_calculator.call(k) if k.fitness.nil? }
+    if @force_fitness_recalculation then
+      @karyotypes.each do |karyotype|
+        karyotype.fitness = @fitness_calculator.call(karyotype)
+        @fitness_hash[karyotype.to_md5()] = karyotype.fitness
+      end
+    else     
+      @karyotypes.each do |karyotype|
+        if karyotype.fitness.nil? then
+          if @fitness_hash[karyotype.to_md5()].nil? then
+            karyotype.fitness = @fitness_calculator.call(karyotype)
+            @fitness_hash[karyotype.to_md5()] = karyotype.fitness
+          else
+            karyotype.fitness = @fitness_hash[karyotype.to_md5()]
+          end
+        end
+      end
+    end
     @karyotypes.sort! { |x,y| y.fitness <=> x.fitness }
   end
-  
+
   private :evaluate
-  
+
   def initialize(size, genome, fitness_calculator)
+    raise "size must be strictly positive." if size < 1
+    @fitness_hash = {}
+    @force_fitness_recalculation = DEFAULT_FORCE_FITNESS_RECALCULATION
     @mutation_rate = DEFAULT_MUTATION_RATE
     @keep_alive_rate = DEFAULT_KEEP_ALIVE_RATE
     @genome = Genome.new(genome)
@@ -22,22 +59,30 @@ class Population
     @karyotypes = Array.new(size){ @genome.create_random_karyotype }
     evaluate
   end
-  
+
   def set_mutation_rate(rate)
-    @mutation_rate = rate
+    raise "mutation_rate value must be included in [0,1]" unless rate.between?(0,1)
+    
+    @mutation_rate= rate
     self
   end
-  
+
   def set_keep_alive_rate(rate)
+    raise "keep_alive_rate must be included in [0,1]" unless rate.between?(0,1)
     @keep_alive_rate = rate
     self
   end
-  
+
   def set_fitness_target(target)
     @fitness_target = target
     self
   end
-  
+
+  def set_force_fitness_recalculation(target)
+    @force_fitness_recalculation = target
+    self
+  end
+
   def size
     @karyotypes.size
   end
@@ -45,49 +90,57 @@ class Population
   def linear_random_select
     @karyotypes[rand @karyotypes.size]
   end
-    
+
   def create_random_mutation
     linear_random_select.copy.mutate
   end
 
   private :linear_random_select, :create_random_mutation
 
-  def random_select
+  def fitness_weighted_random_select
     @karyotypes[
-      @karyotypes.size - Integer(Math.sqrt(Math.sqrt(1 + rand(@karyotypes.size**4 - 1))))
+      @karyotypes.size -
+        Integer(Math.sqrt(Math.sqrt(1 + rand(@karyotypes.size**4 - 1))))
     ]
   end
   
   def random_breed
-    random_select + random_select
+    fitness_weighted_random_select + fitness_weighted_random_select
   end
 
-private :random_select, :random_breed
-  
+  private :fitness_weighted_random_select, :random_breed
+
+  # This function make ou population evolving by:
+  # * Selecting and breeding the fittest karyotypes
+  # * Running the fitness evaluation on all the newly created karyotyopes
+  # The selection process include three subprocesses:
+  # * Selecting the fittest individuals to keep alive
+  # * Mutating randomly (linear) selected individuals
+  # * Breeding randomly (fitness weighted) selected individuals
   def evolve(iterations = DEFAULT_EVOLVE_ITERATIONS)
     i = 1
     while (i <= iterations) &&
       (@fitness_target.nil? || @fitness_target > @karyotypes[0].fitness) do
-      evolve_impl
-      i += 1
+        evolve_impl
+        i += 1
     end
     self
   end
-  
+
   def evolve_impl
     new_population = []    
-    
+
     # Keeping alive a specific amount of the best karyotypes
     keep_alive_count = Integer(@karyotypes.size * @keep_alive_rate)
     if keep_alive_count > 0 then
       @karyotypes[0, keep_alive_count].each {|karyotype| new_population.push(karyotype)}
     end
-        
+
     mutation_count = Integer(@karyotypes.size * @mutation_rate)
     (0..mutation_count-1).each {
       new_population.push create_random_mutation
     }
-    
+
     remaining = @karyotypes.size-mutation_count-keep_alive_count
     (0..remaining-1).each {
       child = random_breed

metadata

@@ -1,16 +1,16 @@
 --- !ruby/object:Gem::Specification
 name: gegene
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.1.0
 platform: ruby
 authors:
 - Alexandre Ignjatovic
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2013-10-27 00:00:00.000000000 Z
+date: 2013-11-01 00:00:00.000000000 Z
 dependencies: []
-description: Framework for fast genetic algorithm development
+description: Framework for genetic algorithm fast development
 email: alexandre.ignjatovic@gmail.com
 executables: []
 extensions: []
@@ -26,6 +26,7 @@ files:
 - example/adding_gene_type.rb
 - example/one_max.rb
 - example/simple.rb
+- LICENSE.txt
 homepage: https://github.com/bankair/gegene
 licenses:
 - MIT
@@ -46,7 +47,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
       version: '0'
 requirements: []
 rubyforge_project: 
-rubygems_version: 2.1.4
+rubygems_version: 2.1.10
 signing_key: 
 specification_version: 4
 summary: Genetic algorithm helpers