gene_genie 0.0.1

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data/README.md

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+[![Build Status](https://travis-ci.org/MEHColeman/gene_genie.svg?branch=master)](https://travis-ci.org/MEHColeman/gene_genie)
+[![Gem Version](https://badge.fury.io/rb/gene_genie.svg)](http://badge.fury.io/rb/gene_genie)
+[![Code Climate](https://codeclimate.com/github/MEHColeman/gene_genie.png)](https://codeclimate.com/github/MEHColeman/gene_genie)
+
+# Gene Genie
+
+Hey, I wrote a genetic algorithm gem. Goals:
+    * Have fun
+    * Be easy and intuitive to use
+    * Be open to extension and experimentation
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+    gem 'gene_genie'
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install gene_genie
+
+## Usage
+Basic usage is designed to be as simple as possible. You provide two things: an exemplar and an evaluator.
+An exemplar is a list of variables along with their possible range of values.
+An evaluator implements a fitness method that returns a numeric value.
+The genetic algorithm will then search for the set of values that maximises the fitness.
+
+```ruby
+require 'gene_genie'
+
+exemplar = {
+  range_of_ints: 1..10,
+  range_of_floats: 1.0..4.5,
+  set_of_items: [:apple, :banana, :orange],
+  ordered_set_of_items: [:one, :two, :three],
+  circular_ordered_set: [:early_morning, :morning, :noon, :afternoon,
+                         :evening, :midnight]
+  }
+```
+
+If you use the simple genie interface, the genetic algorithm will come up with a reasonable best-guesses for various algorthm parameters, but you can dive under the covers to give yourself more flexibility.
+* Population size
+* Gene pools
+* Initialisation
+* Optimisation Criteria
+
+Custom objects for crossover, gene selection, etc.
+
+## Contributing
+
+1. Fork it ( https://github.com/MEHColeman/gene_genie/fork )
+2. Create your feature branch (`git checkout -b my-new-feature`)
+3. Commit your changes (`git commit -am 'Add some feature'`)
+4. Push to the branch (`git push origin my-new-feature`)
+5. Create a new Pull Request

data/lib/gene_genie/gene.rb

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+module GeneGenie
+  # A Gene is the basic unit of the genetic algorithm. Genes hold the
+  # information used to evaluate their fitness.
+  # They are combined into new Genes during the optimisation process.
+  # @since 0.0.1
+  class Gene
+    def initialize(information, fitness_evaluator)
+      @information = information
+      @fitness_evaluator = fitness_evaluator
+    end
+
+    def to_hash
+      @information
+    end
+
+    def fitness
+      @fitness ||= @fitness_evaluator.fitness(@information)
+    end
+
+    def mutate(mutator)
+      @information = mutator.call @information
+      self
+    end
+
+    def combine(other_gene)
+      other_gene_hash = other_gene.to_hash
+      new_hash = {}
+      @information.each do | k, v |
+        new_hash[k] = (rand > 0.5) ? @information[k] : other_gene_hash[k]
+      end
+      Gene.new(new_hash, @fitness_evaluator)
+    end
+
+    def <=>(gene)
+      fitness <=> gene.fitness
+    end
+  end
+end

data/lib/gene_genie/gene_factory.rb

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+require_relative 'gene'
+
+module GeneGenie
+  # GeneFactory
+  # This is a helper class that will create a specified number of genes, given
+  # a template.
+  # The default implementation will produce random genes, but other approaches
+  # could be taken.
+  class GeneFactory
+    def initialize(template, fitness_evaluator)
+      @template = template
+      @fitness_evaluator = fitness_evaluator
+    end
+
+    def create(size = 1)
+      genes = []
+      size.times do
+        hash = create_hash_from_template
+        genes << Gene.new(hash, @fitness_evaluator)
+      end
+
+      genes
+    end
+
+    private
+
+    def create_hash_from_template
+      new_hash = {}
+      @template.each do |k, v|
+        new_hash[k] = rand(v)
+      end
+
+      new_hash
+    end
+  end
+end

data/lib/gene_genie/gene_pool.rb

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+require_relative 'gene_factory'
+require_relative 'mutator/simple_gene_mutator'
+require_relative 'mutator/null_mutator'
+
+module GeneGenie
+  class GenePool
+    def initialize(template, fitness_evaluator, gene_factory,
+                   mutator = NullMutator.new)
+      unless template.instance_of? Hash
+        fail ArgumentError, 'template must be a hash of ranges'
+      end
+      unless fitness_evaluator.respond_to?(:fitness)
+        fail ArgumentError, 'fitness_evaluator must respond to fitness'
+      end
+
+      @template = template
+      @fitness_evaluator = fitness_evaluator
+      @mutator = mutator
+
+      #size = template_evaluator.recommended_size
+      size ||= 10
+      @pool = gene_factory.create(size)
+    end
+
+    # build a GenePool with a reasonable set of defaults.
+    # You only need to specily the minimum no. of parameters
+    def self.build(template, fitness_evaluator)
+      gene_mutator = SimpleGeneMutator.new(template)
+      gene_factory = GeneFactory.new(template, fitness_evaluator)
+      GenePool.new(template, fitness_evaluator, gene_factory,
+                   gene_mutator)
+    end
+
+    def size
+      @pool.size
+    end
+
+    def best
+      @pool.max_by { |gene| gene.fitness }
+    end
+
+    def evolve
+      old_best_fitness = best.fitness
+      new_pool = []
+      size.times do
+        first_gene, second_gene = select_genes
+        new_gene = combine_genes(first_gene, second_gene)
+        new_pool << new_gene.mutate(@mutator)
+      end
+      @pool = new_pool
+      best.fitness > old_best_fitness
+    end
+
+    private
+    # a very simple selection - pick by sorted order
+    # pick two different genes
+    def select_genes
+      selectees = @pool.sort.reverse
+      first, second = nil, nil
+      probability =  [(( 1.0/size ) * 3), 0.8].min
+      while !first || !second do
+        selectees.each do |s|
+          if rand < probability
+            selectees.delete(s)
+            if !first
+              first = s
+              break
+            else
+              second = s
+            end
+          end
+        end
+      end
+      [first, second]
+    end
+
+    def combine_genes(first, second)
+      first.combine(second)
+    end
+  end
+end

data/lib/gene_genie/genie.rb

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+require_relative 'gene_pool'
+
+# Namespace for GeneGenie genetic algorithm optimisation gem
+# @since 0.0.1
+module GeneGenie
+
+  # Top level, basic interface for GA optimisation.
+  # Genie will attempt to optimise based on best-guess defaults if none are
+  # provided
+  # @since 0.0.1
+  class Genie
+
+    DEFAULT_NO_OF_GENERATIONS = 50
+    IMPROVEMENT_THRESHOLD = 0.1 # %
+
+    def initialize(template, fitness_evaluator)
+      @template = template
+      @fitness_evaluator = fitness_evaluator
+      @gene_pool = GenePool.build(template, fitness_evaluator)
+    end
+
+    # Optimise the genes until the convergence criteria are met.
+    # A reasonable set of defaults for criteria will be applied.
+    # @param [Integer] number_of_generations
+    def optimise(number_of_generations = 0)
+      previous_best = best_fitness
+
+      # optimise
+      if number_of_generations > 0
+        evolve_n_times(number_of_generations)
+      else
+        optimise_by_strategy
+      end
+
+      @best_fitness = @fitness_evaluator.fitness(best)
+
+      @best_fitness > previous_best
+    end
+    alias_method :optimize, :optimise
+
+    def best
+      @gene_pool.best.to_hash
+    end
+
+    def best_fitness
+      @gene_pool.best.fitness
+    end
+
+    private
+    def evolve_n_times(n)
+      n.times { @gene_pool.evolve }
+    end
+
+    def optimise_by_strategy
+      DEFAULT_NO_OF_GENERATIONS.times do
+        current_fitness = best_fitness
+        @gene_pool.evolve
+      end
+      DEFAULT_NO_OF_GENERATIONS.times do
+        current_fitness = best_fitness
+        @gene_pool.evolve
+        break if best_fitness < current_fitness *
+          (1 + (IMPROVEMENT_THRESHOLD / 100 ))
+      end
+    end
+  end
+end

data/lib/gene_genie/mutator/null_mutator.rb

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+module GeneGenie
+  # A NullMutator does no mutation on the gene
+  # @since 0.0.1
+  class NullMutator
+    def initialize(*_)
+    end
+
+    def call(hash)
+      hash
+    end
+  end
+end

data/lib/gene_genie/mutator/simple_gene_mutator.rb

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+module GeneGenie
+  # A SimpleGeneMutator loops through each member of a hash, and has a 1%
+  # chance of swapping the value for another valid value (based on the
+  # template)
+  # @since 0.0.1
+  class SimpleGeneMutator
+    def initialize(template, mutation_rate = 0.01)
+      @template = template
+      @mutation_rate = mutation_rate
+    end
+
+    def call(hash)
+      hash.each do |k, v|
+        if rand < @mutation_rate
+          hash[k] = rand(@template[k])
+        end
+      end
+      hash
+    end
+  end
+end
+

data/lib/gene_genie/version.rb

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+module GeneGenie
+  VERSION = '0.0.1'
+end

data/lib/gene_genie.rb

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+require_relative 'gene_genie/genie'

metadata

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+--- !ruby/object:Gem::Specification
+name: gene_genie
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Mark Coleman
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2015-08-28 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.6'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest-spec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ">="
+      - !ruby/object:Gem::Version
+        version: '0'
+description: JUST A PROTOTYPE WORK IN PROGRESS! Optimise anything that responds to
+  'fitness' and takes a hash
+email:
+- m@rkcoleman.co.uk
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- README.md
+- lib/gene_genie.rb
+- lib/gene_genie/gene.rb
+- lib/gene_genie/gene_factory.rb
+- lib/gene_genie/gene_pool.rb
+- lib/gene_genie/genie.rb
+- lib/gene_genie/mutator/null_mutator.rb
+- lib/gene_genie/mutator/simple_gene_mutator.rb
+- lib/gene_genie/version.rb
+homepage: https://github.com/MEHColeman/gene_genie
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.4.5
+signing_key: 
+specification_version: 4
+summary: Genetic algorithm optimisation gem
+test_files: []