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1.1 Biological Background

Evolutionary Algorithms in Theory and Practice. 1.1 Biological Background. 발표자 : 김정집. 1.Organic Evolution and Problem Solving. interdisciplinary research field biology, artificial intelligence, numerical optimization, and decision support organic evolution

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1.1 Biological Background

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  1. Evolutionary Algorithms in Theory and Practice 1.1 Biological Background 발표자 : 김정집

  2. 1.Organic Evolution and Problem Solving • interdisciplinary research field • biology, artificial intelligence, numerical optimization, and decision support • organic evolution • collective learning process within a population of individuals • individual • a search point • container of current knowledge about the “laws” of the environment • fitness value, recombination, mutation, and selection

  3. Different Mainstreams • three different Mainstreams • Evolution Strategies (ESs) • Genetic Algorithms (GAs) • Evolutionary Programming(EP) • Index • sec 1.1 biological background • sec 1.2 impact on AI, and ML • sec 1.3 a global optimization algorithm as random search algorithm • sec 1.4 overview of the history of Eas

  4. 1.1 Biological Background • Darwinian theory of evolution(Charles Darwin) • natural selection • mutation on phentypes -> selection under limited environmental conditions -> advantageous organisms survives

  5. Neodarwinism • synthetic theory of evolution • genes • transfer units of heredity • changed by mutations • population • evolving unit • consists of a common gene pool • indirect fitness • natural selection as no active driving force • What is mapping from genotype to phenotype?

  6. Adaptation • denotes a general advantage in ecological or physiological efficiency • nongenetic-somatic adaptation • genetic adaptation • “To What” • any major kind of environment (adaptive zone) • ecological niche ( the set of possible environments that permit survival of a species)

  7. Adaptive surface • possible biological trait combinations • natural analogy to the optimization problem • climbing the hill nearest to the starting point • genetic drift • random decrease or increase of biological trait frequencies • dynamically changing by means of environment-population interactions

  8. Schematic diagram of an adaptive surface

  9. 1.1.1 Life and Information Processing • DNA: 2strands • nucleotide base • Adenine(A), Thymine(T), Cytosine(C), Guanine(G) • purine base (A or G) • pyrimidine base ( T or C)

  10. creates the phenotype from the genotype • protein biosynthesis • mapping genotype to phenotype • polygeny - m:1 • pleiotropy - 1:m • epistasis • alphabet of amino acids : 20 different one • mRNA(1 strand):transcription,nucleus->ribosomes • tRNA:translation in ribosome

  11. the genetic code

  12. protein biosynthesis

  13. central dogma of molecular genetics • DNA->RNA->Protein • the proof of the incorrectness of Lamarckism

  14. Hierarchy of the genetic information

  15. 1.1.2 Meiotic Heredity • mitosis • cell division with identical genetic material • phylogeny(evolution) • meiotic cell division

  16. Meiosis(I)

  17. Meiosis(II)

  18. crossover • position(s) at random • in nature, 1~8 points • haploid case(*) • haploid gameter->diploid zygote->haploid cell • recombination and mutaion occur in zygote

  19. one-point crossover

  20. characteristics of meiosis

  21. 1.1.3 mutations • DNA-replication is overwhelmingly exact but not perfect • for a specific gene of the human genome, Pm=6*10-6~8*10-6 • by origin • normal-in the replication process • exogenous factors

  22. classes of mutations • by location • somatic • generative • usual deviations • gene mutations • chromosome mutations • genome mutations

  23. gene , genome mutations • gene mutations • small mutations • little variation-do not negatively effect • large mutations • cause phenotype deviations • progressive(constructive) mutations • cause crossings of boundaries between species • genome mutations • not been tested as an extension of EAs

  24. chromosome mutations • losses of chromosome regions • deficiencies and deletions • doubling of chromosome regions • duplications • reorganization of chromosomes • translocations and inversions

  25. terminal and internal segment losses

  26. duplication event

  27. inversion event

  28. 1.1.4 Molecular Darwinism • human genome • consists of one billion nucleotide bases • 4^1,000,000,000 possibilities • random emergence of self-reproducing units can be called impossible • explain the efficiency of biological evolution

  29. necessary conditions for Darwinian selection • Metabolism • Self-reproduction • Mutation

  30. Eigen’s equations • Eigen’s equations for the dynamical behavior of species • : build-up term resulting from self-replication • : term incorporating destruction • : transition probability from class k to I • : growth and shrinking processes of the total number of individuals

  31. Under the assumption of a constant overall organization • buffering the concentrations Ai of energy-rich substances, s.t. AiQi=const • total size of the system is limited • excess productivity • excess productivity must be compensated by transportation through the flow

  32. Average excess productivity • Eigen’s eq. Can be transferred to where , selective value of a species I

  33. only those species having Wi above E(t) • will grow the number • shifting E(t) to an optimum • representing Maximum selective value of all species

  34. The selection criterion • allow growing of a new species m to become the dominant one • the quasi-species • the currently dominant species together with its stationary distribution of mutants emerging from this species

  35. A maximum length s.t. the information can be preserved by reproduction • the ratio of the wild-type(dominant species) reproduction rate to the average reproduction rate of the rest

  36. Experimental results • lmax is no longer than hundred nucleotide bases • Darwinian selection • N=kN • In principle, any new species can grow and become the dominant ones. • Eigen’s concept of a hypercycle • N=kN2 • does not allow for diversity of species

  37. Summary of experiments • Summary of experiments • coexistent evolution according to the principle of Darwiniam selection • Hypercyclic system stabilized. • Hypercuclic selection optimizes the system. Only one universal genetic code is produced • The first biological cells emerge • Darwiniam evolution leads to the development of the known variety of species

  38. Using a birth and death model, an approximate analytical expression for the dependence of the error threshold • more approximated form

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