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    Gene Expression Programming

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    Sharmila Saravanan
    GEP is a genetic programming technique that uses linear strings of fixed length to represent both genotypes and phenotypes. The genotype string is translated into a nonlinear expression tree that represents the phenotype. This allows GEP to evolve complex solutions like genetic programming while maintaining the simplicity of genetic algorithms. Key benefits of GEP include that the generated solutions are always syntactically valid and genetic operators don't need to ensure syntactic correctness. GEP also allows for multigenic chromosomes that can evolve components of a solution separately, similar to how biological systems and engineering designs decompose problems.

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    Gene Expression Programming

    Uploaded by

    Sharmila Saravanan
    160 views24 pages
    GEP is a genetic programming technique that uses linear strings of fixed length to represent both genotypes and phenotypes. The genotype string is translated into a nonlinear expression tree that represents the phenotype. This allows GEP to evolve complex solutions like genetic programming while maintaining the simplicity of genetic algorithms. Key benefits of GEP include that the generated solutions are always syntactically valid and genetic operators don't need to ensure syntactic correctness. GEP also allows for multigenic chromosomes that can evolve components of a solution separately, similar to how biological systems and engineering designs decompose problems.

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    ppt on gene expression

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    GEP is a genetic programming technique that uses linear strings of fixed length to represent both genotypes and phenotypes. The genotype string is translated into a nonlinear expression tree that represents the phenotype. This allows GEP to evolve complex solutions like genetic programming while maintaining the simplicity of genetic algorithms. Key benefits of GEP include that the generated solutions are always syntactically valid and genetic operators don't need to ensure syntactic correctness. GEP also allows for multigenic chromosomes that can evolve components of a solution separately, similar to how biological systems and engineering designs decompose problems.

    Copyright:

    © All Rights Reserved
    Download as PPT, PDF, TXT or read online from Scribd
    Download as ppt, pdf, or txt
    160 views24 pages

    Gene Expression Programming

    Uploaded by

    Sharmila Saravanan
    GEP is a genetic programming technique that uses linear strings of fixed length to represent both genotypes and phenotypes. The genotype string is translated into a nonlinear expression tree that represents the phenotype. This allows GEP to evolve complex solutions like genetic programming while maintaining the simplicity of genetic algorithms. Key benefits of GEP include that the generated solutions are always syntactically valid and genetic operators don't need to ensure syntactic correctness. GEP also allows for multigenic chromosomes that can evolve components of a solution separately, similar to how biological systems and engineering designs decompose problems.

    Copyright:

    © All Rights Reserved
    Download as PPT, PDF, TXT or read online from Scribd
    Download as ppt, pdf, or txt
    of 24
    At a glance
    Powered by AI
    The key takeaways are that GEP combines features of GA and GP by generating syntactically correct phenotypes without needing corrections to the genetic operators. It also allows for evolving components of a solution rather than just the whole solution.

    GA uses fixed length linear strings while GP uses nonlinear entities of varying sizes and shapes. GEP combines these features by using fixed length linear strings that can be translated into valid nonlinear expression trees. GEP also attempts to more faithfully represent nature by separating the genotype and phenotype.

    In GEP, the genotype is the genetic representation stored in the chromosome, while the phenotype is the physical representation or expression tree resulting from translating the genotype. The fitness is evaluated based on the phenotype, not the genotype directly.

    Gene Expression Programming

    CS678 - Machine Learning


    Grand Valley State University
    by James Bund
    GEP is like GA and GP

    GA: Linear strings of fixed length

    GP: Nonlinear entities of different sizes and shapes

    GEP: Linear strings of fixed length and


    Nonlinear entities of different sizes and shapes
    GEP Algorithm
    Genotype and Phenotype
    Attempts to represent nature more faithfully.
    In GA and GP genotype and phenotype are the same.

    Genotype: Genetic representation


    Phenotype: Physical representation

    Genotype -> Translation -> Phenotype


    String chromosome -> Expression Tree

    Fitness is a judgment of the phenotype


    Reproduction involves the genotype
    Encoding Genotype & Phenotype
    ( a b ) (c d ) 01234567
    Q*+-abcd

    Genotype is a fixed length string.


    Resulting genotype is guaranteed to translate into a valid
    expression tree.
    Open Reading Frames (ORF)
    Biology: Start codons and Stop codons

    GEP: Start at the beginning of the coding sequence


    Stops when the functions have been expressed,
    so usually there are non-coding regions at the end.

    0123456789
    Q*+-abcdef
    Head and Tail Regions
    t = h (n-1) + 1

    t = tail length
    h = head length
    n = maximum number of arguments to a function

    012345678901234567890
    +Q-/b*aaQbaabaabbaaab
    Multigenic Chromosomes
    Hierarchical discovery technique

    012345678012345678
    Q*Q+bbaaa*-babaabb
    Multigenic Chromosomes
    012345678901201234567890120123456789012
    IIAIca3aa2acuNNAOab2u3c31cAu12ua3112cac

    13 = h + t
    t = h (n-1) + 1

    h = 4, t = 9
    Replication

    Replication is copying without modification.


    Mutation
    012345678012345678012345678
    -+-+abaaa/bb/ababb*Q*+aaaba

    012345678012345678012345678
    Q+-+abaaa/bbQababb*b*+aaaba

    Resulting ET will be valid as long as the tail doesnt contain functions.


    Insertion Sequence (IS)
    Transposition
    012345678901234567890012345678901234567890
    *-+*a-+a*bbabbaabababQ**+abQbb*aabbaaaabba

    012345678901234567890012345678901234567890
    *-+*a-bba+babbaabababQ**+abQbb*aabbaaaabba

    The position and the length of the IS must be determined.


    Resulting ET will be valid, because the change is upstream.
    Root Insertion Sequence (RIS)
    Transposition
    012345678901234567890012345678901234567890
    -ba*+-+-Q/abababbbaaaQ*b/+bbabbaaaaaaaabbb

    012345678901234567890012345678901234567890
    -ba*+-+-Q/abababbbaaa+bbQ*b/+bbaaaaaaaabbb

    The position and the length of the RIS must be determined.


    Resulting ET will be valid, because the change is upstream.
    Gene Transposition

    012345678012345678012345678
    *a-*abbab-QQ/aaabbQ+abababb

    012345678012345678012345678
    -QQ/aaabb*a-*abbabQ+abababb

    No effect on genes, but can change the linking of genes.


    1-Point Recombination
    012345678012345678
    -b+Qbbabb/aQbbbaab
    /-a/ababb-ba-abaaa

    012345678012345678
    -b+/ababb-ba-abaaa
    /-aQbbabb/aQbbbaab

    Second gene was not modified.


    Both offspring will always be valid.
    2-Point Recombination
    0123456789001234567890
    +*a*bbcccac*baQ*acabab
    *cbb+cccbcc++**bacbaab

    0123456789001234567890
    +*a*bbccbcc++*Q*acabab
    *cbb+ccccac*ba*bacbaab

    Both offspring will always be valid.


    Gene Recombination
    012345678012345678012345678
    /aa-abaaa/a*bbaaab/Q*+aaaab
    /-*/abbabQ+aQbabaa-Q/Qbaaba

    012345678012345678012345678
    /aa-abaaaQ+aQbabaa/Q*+aaaab
    /-*/abbab/a*bbaaab-Q/Qbaaba
    Block Stacking (SpellBot) Example
    EQ=E TOS=t
    DO=D TCB=c
    MTT=T NBN=n
    MTS=S
    NOT=N

    EQ(DO(MTT(TOS), NOT(TOS)), DO(MTS(NBN), NOT(NBN)))

    012345601234560123456
    DTNttttDSNnnnncNStcnc
    Advantages of GEP over GA and GP
    GAs have less complexity in what they can express.

    GPs are harder to work with because their operators must


    be smart enough to ensure syntactically correct offspring.

    GEP combine these two features by having the ease of


    working with them as GAs and the complexity of GPs.
    Generated phenotypes are always syntactically correct and
    dont need to be corrected.
    The genetic operators dont need to handle complex
    language syntax.
    Multigenic Chromosome Benefits
    Evolving components of a solution not just solutions.

    Separation of tasks and abstraction of details like in the


    engineering done by humans.

    Similar to:
    Structured Programming
    Functions
    Object Oriented
    Design Patterns
    You Can Have Extra Genes
    Best Fitness vrs. Average Fitness
    References
    Gene Expression Programming: A New Adaptive Algorithm for Solving Problems
    by Candida Ferreira
    http://www.gene-expression-programming.com/webpapers/gep.pdf

    Gene Expression Programming


    http://www.gene-expression-programming.com

    GeneXproTools
    http://www.gepsoft.com

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