Harnessing Genetics Genetic Algorithms (GA) Genetic Algorithms - - PDF document

Christian Jacob, University of Calgary

CPSC 607 Christian Jacob

• Dept. of Computer Science
• Dept. of Biochemistry & Molecular Biology

University of Calgary

Harnessing Genetics

Genetic Algorithms

Christian Jacob, University of Calgary

John H. Holland 1975 David Goldberg 1989

Genetic Algorithms (GA)

Christian Jacob, University of Calgary

GA Dualism: Binary Encoding

Genotype

{1,0,1,1,0,1,0,0,1,0,1,1} {0,1,1,1,1,0,0,1,0,0,0,1} {0,0,1,1,0,1,1,1,0,1,0,0} ... {1,1,0,0,0,1,0,1,0,1,0,0} ... {1,0,1,0,0,1,1,1,0,1,1,1} {0,0,1,1,0,1,1,1,0,1,0,0} {1,0,0,1,0,1,1,1,0,0,0,1}

Decoding

Interpretation

Phenotype

Christian Jacob, University of Calgary {1,1,1,1,0,1,0,1,0,0,0,0} {0,1,1,1,0,0,1,1,0,1,1,0}

Mutation

{0,1,1,1,0,1,0,1,0,0,0,0} {1,1,1,1,0,0,1,1,0,1,1,0}

Crossover

How Genetic Algorithms W

• rk

{1,1,0,0,0,1,0,1,0,1,0,0} {0,0,1,1,0,1,1,1,0,1,0,0}

Selection

{1,0,1,1,0,1,0,0,1,0,1,1} {0,1,1,1,1,0,0,1,0,0,0,1} {1,1,0,0,0,1,0,1,0,1,0,0} ... {1,0,1,0,0,1,1,1,0,1,1,1} {0,0,1,1,0,1,1,1,0,1,0,0} {1,0,0,1,0,1,1,1,0,0,0,1}

Interpretation Evaluation

2 4 6

• Ind. 40
• Ind. 37
• Ind. 5
• Ind. 2

{1,0,1,1,0,1,0,0,1,0,1,1} {0,1,1,1,1,0,0,1,0,0,0,1} {1,1,0,0,0,1,0,1,0,1,0,0} ... {1,0,1,0,0,1,1,1,0,1,1,1} {0,0,1,1,0,1,1,1,0,1,0,0} {1,0,0,1,0,1,1,1,0,0,0,1}

Insert in Genepool

Christian Jacob, University of Calgary

Evolution with V arying Objective Function

Generation 0 Generation 10 Generation 11 Generation 30

Christian Jacob, University of Calgary

Generation 0 to Generation 10

Evolution with V arying Objective Function

Christian Jacob, University of Calgary

Generation 11 to Generation 30

Evolution with V arying Objective Function

Christian Jacob, University of Calgary

Comparison of Genetic Operators

Initial Population Mutation Recombination Inversion Deletion Duplication Christian Jacob, University of Calgary Initial Population Mutation Recombination Inversion Deletion Duplication

Comparison of Genetic Operators

Christian Jacob, University of Calgary Initial Population Mutation Recombination Inversion Deletion Duplication

Comparison of Genetic Operators

Christian Jacob, University of Calgary Initial Population Mutation Recombination Inversion Deletion Duplication

Comparison of Genetic Operators

Christian Jacob, University of Calgary Initial Population Mutation Recombination Inversion Deletion Duplication

Comparison of Genetic Operators

Christian Jacob, University of Calgary Initial Population Mutation Recombination Inversion Deletion Duplication

Comparison of Genetic Operators

Christian Jacob, University of Calgary Initial Population Mutation Recombination Inversion Deletion Duplication

Comparison of Genetic Operators

Christian Jacob, University of Calgary Initial Population Mutation Recombination Inversion Deletion Duplication

Comparison of Genetic Operators

Christian Jacob, University of Calgary {1,1,1,1,0,1,0,1,0,0,0,0} {0,1,1,1,0,0,1,1,0,1,1,0}

Mutation

{0,1,1,1,0,1,0,1,0,0,0,0} {1,1,1,1,0,0,1,1,0,1,1,0}

Crossover

GA Dualism

{1,1,0,0,0,1,0,1,0,1,0,0} {0,0,1,1,0,1,1,1,0,1,0,0}

Selection

{1,0,1,1,0,1,0,0,1,0,1,1} {0,1,1,1,1,0,0,1,0,0,0,1} {1,1,0,0,0,1,0,1,0,1,0,0} ... {1,0,1,0,0,1,1,1,0,1,1,1} {0,0,1,1,0,1,1,1,0,1,0,0} {1,0,0,1,0,1,1,1,0,0,0,1}

Interpretation Evaluation

2 4 6

• Ind. 40
• Ind. 37
• Ind. 5
• Ind. 2

{1,0,1,1,0,1,0,0,1,0,1,1} {0,1,1,1,1,0,0,1,0,0,0,1} {1,1,0,0,0,1,0,1,0,1,0,0} ... {1,0,1,0,0,1,1,1,0,1,1,1} {0,0,1,1,0,1,1,1,0,1,0,0} {1,0,0,1,0,1,1,1,0,0,0,1}

Insert in Genepool

Christian Jacob, University of Calgary Decoding Interpretation

Phenotype

GA Dualism Dualism in Nature

Genotype

Christian Jacob, University of Calgary

Genotype

GA Dualism Dualism in Nature

Transcription Translation Development Morphogenesis

Phenotype

Christian Jacob, University of Calgary

Genotype

Genetic Algorithms & Programming

Transcription Translation Development Morphogenesis

Phenotype

Program Code

Christian Jacob, University of Calgary

Genotype

Genetic Algorithms & Programming

Transcription Translation Development Morphogenesis

Phenotype

Program Code

Christian Jacob, University of Calgary

References

• Genetic Algorithms:

– Goldberg, D. (1989). Genetic Algorithms in Search, Optimization, and Machine Learning. Reading, MA, Addison- Wesley. – Holland, J. H. (1975). Adaptation in Natural and Artificial

• Systems. Ann Arbor, MI, University of Michigan Press.

– Holland, J. H. (1992). Adaptation in Natural and Artificial

• Systems. Cambridge, MA, MIT Press (originally published in

1975). – Jacob, C. (2001). Illustrating Evolutionary Computation with

• Mathematica. San Francisco, CA, Morgan Kaufmann

Publishers (Chapter 3).