Minimal Genetic Algorithm
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turtles-own [chromosome ;; a string of digits representing one candidate solution to the problem fitness ;; the numerical value of the chromosomal strings ] globals [best ;; the numerical value of the chromosome closer to the goal worst ;; the numerical value of the chromosome more distant from the goal donor ;; the agent having the best chromosome recipient ;; an agent not having the best chromosome chromcopy ;; the copy of the best chromosome a-split ;; the position of one extreme of a chromosome's fragment b-split ;; the position of the second extreme of a chromosome's fragment counter ;; a counter usefull in different blocks ] ;; ---------- SETUP PROCEDURES ----------------------------------------------------------------------------- ;; ------------------------------------------------------------------------------------------------------------- to setup ;; reset parameters and create a number of agents given by the user clear-all set counter 0 reset-ticks create-turtles turtles-number [ set shape "circle 2" set size 1.8 fd 7 genotype/phenotype-construction ] end to genotype/phenotype-construction ;; the genotype (chromosome) and the corresponding fenotype (fitness) of the agent ;; is initially equal to the worst solution; it is shown as a label set fitness 10 ^ (genes-number - 1) ;; the lowest fitness value is converted into a string: ;; it will be the initial chromosome structure set chromosome word fitness "" ;; chromosome is displayed as a label set label chromosome end ;; ---------- RUNTIME PROCEDURES --------------------------------------------------------------------------- ;; ------------------------------------------------------------------------------------------------------------- to search ;; worse and best fitness value are detected set worst min [fitness] of turtles set best max [fitness] of turtles ;; the problem is resolved when an agent gain the higher value of fitness having a ;; user-specified number of digits if best = 10 ^ genes-number - 1 [show "DONE!!!" stop] ;; when diversity between chromosomes is null, rercombination is skipped if best != worst [rercombination] ;; mutations occur according to a frequency set by the user if random-float 1 < mutation-rate [mutate] tick end to rercombination ;; recombination occurs between the chromosome of a randomly chosen turtle (recipient) and ;; the chromosome of (one of) the most performing turtle (donor) that offers a code's fragment ;; of its chromosome to the first turtle; the two involved agents are highlighted by a link clear-links set donor [who] of one-of turtles with [fitness = best] set recipient [who] of one-of turtles with [fitness != best] ask turtle donor [create-link-to turtle recipient ] set counter 0 set a-split random genes-number set b-split random genes-number set chromcopy [chromosome] of turtle donor ask turtle recipient [ hybridization set fitness read-from-string chromosome set label fitness ] end to hybridization ;; the two selected chromosomal strings give place to hybridization according to a mechanism similar to ;; the crossing-over following to bacterial conjugation; strings are looped, ;; as occur in bacterial chromosomes or plasmids ifelse a-split < b-split [set chromosome replace-item (a-split + counter) chromosome (item (a-split + counter) chromcopy) set counter (counter + 1) if counter < b-split - a-split [hybridization]] [if b-split < a-split [set chromosome replace-item ((a-split + counter) mod genes-number) chromosome (item ((a-split + counter) mod genes-number) chromcopy) set counter (counter + 1) if counter < genes-number - a-split + b-split [hybridization]] ] end to mutate ;; mutations happen randomly with a given frequency on just one digit (gene) ask turtle random turtles-number [set chromosome replace-item random genes-number chromosome word random 10 "" set fitness read-from-string chromosome set label fitness ] end
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Attached files
File | Type | Description | Last updated | |
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Minimal Genetic Algorithm.png | preview | Preview for 'Minimal Genetic Algorithm' | almost 6 years ago, by Cosimo Leuci | Download |
READ_ME.txt | data | attachment | 12 months ago, by Cosimo Leuci | Download |