Introduction to Genesis

1
Introduction to Genesis

• The Genesis Software
• Introduction
• Genesis (GENEtic Search Implementation System)
• Mature, robust and well written GA software.
• Easy to use all that is normally required is
  the provision of a fitness function.
• For educational use only.
• Written in C.
• Installation
• The software and User's Guide are available in
  the course notes
• Follow the instructions p. 91 for downloading
  and installing Genesis

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Introduction to Genesis

• Use of Software --- Overview
• for a particular GA run
• establish the gene and chromosome structure GA
  Setup
• establish the operating parameters for the GA
  run GA Setup
• write the fitness function as a C function,
  that takes a set of parameters and returns
  fitness
• run the batch file GO, which requires two
  parameters --- the name of the file containing
  the fitness function (something'.c) and the file
  suffix for the parameters and chromosome/gene
  structures
• compilation errors in your fitness function
  will be reported when you run GO.

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Introduction to Genesis

• GA Setup
• The setup program is run to specify the genetic
  structure (chromosome and genes) for a problem
  and the GA parameters such as the Number of
  Trials and the Mutation Rate.
• Values in indicate the default value if
  ltEntergt is pressed
• The program first prompts for information on the
  genetic structure. This information is stored
  in the template file
• File Suffix
• Identifier for the problem, this is attached to
  the end of all files names, for example if the
  suffix is europe1 then some of the files are
  in.europe, template.europe1, rep.europe1 ltetcgt
• Floating Point Representation y Always use y
• Number of Genes The total number of genes in the
  chromosome

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Introduction to Genesis

• GA Setup (cont'd)
• For each Gene
• Minimum Value Minimum value for the gene
  permitted (integer or floating point)
• Maximum Value Maximum value for the gene
  permitted (integer or floating point)
• Number of Values
• Must be a power of 2 eg 2, 4, 8, 16, ...
• The values will be evenly distributed between
  Minimum and Maximum
• Example 1 Minimum 0, Maximum 3, Number of
  Values 4 Gene values will be 0, 1, 2, 3.
• Example 2 Minimum 0, Maximum 1, Number of
  Values 4 Gene values will be 0, 0.3333, 0.6667,
  1.0
• Output Format
• ''C" type format string. Use n.0f for integers
  and n.df for floating point numbers, where n is
  the number of characters to be displayed and d is
  the number of decimal places. eg 2.0f, 7.2f
• Repetition
• The number of genes in sequence that are
  identical to the above

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Introduction to Genesis

• GA setup (cont'd)
• The program then prompts for information on the
  GA parameters. This information is stored in the
  in file. They are
• o Number of Experiments 1 (always 1)
• o Number of Trials 1000
• o Population Size 50
• o Crossover Rate 0.6
• o Mutation Rate 0.001
• o ...
• o Number of Trials between Data Collections 100
• o ...
• o Options cefgl (use these normally)
• o Random Seed 123456789
• o ...
• See the Running the Programs section of the
  User's Guide for more information
• See the Options section of the User's Guide for
  more information

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Introduction to Genesis

• Fitness Function
• The fitness function (evaluation function) must
  be written by the developer in C
• The function must be named eval and have the
  parameters specified below. The function returns
  the fitness value as a floating point number to
  the GA
• The vect and genes parameters are normally used
  instead of str and length
• fitness skeleton
• double eval(str, length, vect, genes)
• char str / string representation /
• int length / length of bit string /
• double vect / floating point
  representation /
• int genes / number of elements in vect
  /
• double fitness / could be declared as an
  integer, but if so remember to cast it as a
  double when returning the value i.e. return
  (double) fitness /
• ltdeclaration of local variablesgt
• ltYOUR C CODE goes in here!gt

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Introduction to Genesis

• Files
• The files used by Genesis are discussed in the
  Files section of the User's Guide
• The main files have the prefix
• o in describes the GA parameters, created using
  setup
• o template describes the chromosome structure,
  created using setup
• o rep report summarizing the GA run
• o min the best chromosomes found by the GA
• o log logs the start and end times of runs