Immunology as a Metaphor for Computational ... - Napier University

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Chapter 5. EA Based Model — COSDM 115Species 2EASpecies 1EAindividualfitnessPopulationbest representativePopulationDomainmodelbest representativeSpecies 3EAPopulationFigure 5.1: Coevolutionary architecture of the Potter model
Chapter 5. EA Based Model — COSDM 116the fitness evaluation proceeds from the perspective of one of the three species — toevaluate an individual from one species, collaborations are formed with representativesfrom each of the other species. Thus, in the case of the string covering problem describedin chapter 4, individuals in each population represent match strings, and eachspecies contributes one string to the domain model, i.e. the match-set. At any time, thematch-set consists of the string under evaluation, plus the current best string from theother (N-1) populations. The match strength between a match-string Fx and an antigenstring Fy is simply given by summing the number of bits in the same position with thesame value, i,e:S £ Fx¤GFy¥ i L∑1 i f x i y i0 otherwise1 : iThen, to compute the match-strength of the set M, and therefore the fitness ofthe match-set to be assigned back to an individual, the match-strength is calculatedbetween each of the N members of the set and each of the K antigens in the target set,and then the maximum computed strengths with respect to each antigen are averaged:S £ M¥ 1KK∑i 1max S Fm 1 ¤ Ft i ¥H¤§¦©¦¨¦©¤ S £ F m N ¤ Ft i ¥§¥£ £The architecture described by Potter lends itself well to implementing an immunesystem based on an SDM model that is able to successfully store and retrieve largeamounts of data. Whilst the obvious subtasks in COSDM are to locate the best positionand recognition radius of each antibody, there are also complex interactions betweenindividual antibodies as counters are summed across the entire immune system in orderto retrieve a piece of data. These interactions are handled well by the cooperative natureof the architecture.A model of the adapted architecture, COSDM, is shown in figure 5.2. As in theoriginal architecture, multiple populations are evolved. In the case of COSDM, eachpopulation in isolation controls the identity and recognition radius of potential antibodies.A complete immune system is formed by each population contributing oneantibody to a serum which is then evaluated in order to determine how accurately itcan store and recall data currently visible to the system. The serum consists of a memberof the population currently under evaluation, and the best member of each of the
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AbstractThe biological immune syste
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DeclarationI declare that this thes
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Table of Contents1 Introduction 11.
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5.3.1 Default Parameters . . . . .
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List of Figures2.1 ’Lock and Key
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List of Tables2.1 Structural and fu
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Chapter 1IntroductionThe study of b
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Chapter 1. Introduction 3scientists
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Chapter 1. Introduction 5Thus, the
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Chapter 1. Introduction 7of the cha
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Chapter 1. Introduction 94. Analysi
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Chapter 2. Background 11paratopeepi
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Chapter 2. Background 13antigenepit
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£Chapter 2. Background 15low the m
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Chapter 2. Background 17Antigene 0p
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Chapter 2. Background 19maintained
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Chapter 2. Background 23genetically
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Chapter 2. Background 251. Choose a
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Chapter 2. Background 27non-interbr
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Chapter 2. Background 29been made i
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Chapter 2. Background 31patterns wi
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Chapter 2. Background 33reported on
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Chapter 2. Background 35Immunos 81
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Chapter 2. Background 37recognition
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Chapter 2. Background 391. Create a
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Chapter 2. Background 41environment
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Chapter 2. Background 43a)input dat
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Chapter 2. Background 45antibody wi
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Chapter 3. Immune Systems for Sched
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Chapter 6. A Self-Organising SDM
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Chapter 7Conclusion7.1 OverviewThis
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Chapter 7. Conclusion 181however wh
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Chapter 7. Conclusion 183features m
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Chapter 7. Conclusion 185In additio
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Chapter 7. Conclusion 187ter, sched
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Chapter 7. Conclusion 189Clustering
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Chapter 7. Conclusion 191nature in
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Appendix ACoincidences in permutati
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Appendix BExperimental results obta
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Appendix B. Experimental results ob
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Bibliography 203[Cooke and Hunt, 19
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Bibliography 205[Farmer et al., 198
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Bibliography 207[Hart et al., 1998]
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Bibliography 209[Kohonen, 1982b] Ko
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Bibliography 211[Potter and De Jong
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Bibliography 213[Timmis et al., 199
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