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Haploid vs Diploid Genome in Genetic Algorithms for TSP

Haploid vs Diploid Genome in Genetic Algorithms for TSP

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Published by ijcsis
There exist all types of organisms in nature – haploid, diploid and multiploid. Maximum research works in Genetic Algorithms are carried out using haploids. Diploidy and dominance have not been given due weightage although in maximum complex systems nature uses them. The paper illustrates the previous research work in diploidy and dominance. In this paper, a Genetic Algorithm is proposed to solve Traveling Salesman Problem (TSP) using haploid and diploid genome and to compare their performance in terms of cost and time.
There exist all types of organisms in nature – haploid, diploid and multiploid. Maximum research works in Genetic Algorithms are carried out using haploids. Diploidy and dominance have not been given due weightage although in maximum complex systems nature uses them. The paper illustrates the previous research work in diploidy and dominance. In this paper, a Genetic Algorithm is proposed to solve Traveling Salesman Problem (TSP) using haploid and diploid genome and to compare their performance in terms of cost and time.

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Published by: ijcsis on Nov 02, 2010
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Haploid vs Diploid Genome in Genetic Algorithmsfor TSP
Rakesh Kumar
, Jyotishree
1 Associate Professor, Department of Computer Science & Application, Kurukshetra University, Kurukshetra
Email: rsagwal@rediffmail.com
2 Assistant Professor, Department of Computer Science & Application, Guru Nanak Girls College, Yamuna Nagar 
Email: jyotishreer@gmail.com
There exist all types of organisms in nature –haploid, diploid and multiploid. Maximum research works inGenetic Algorithms are carried out using haploids. Diploidyand dominance have not been given due weightage although inmaximum complex systems nature uses them. The paperillustrates the previous research work in diploidy anddominance. In this paper, a Genetic Algorithm is proposed tosolve Traveling Salesman Problem (TSP) using haploid anddiploid genome and to compare their performance in terms of cost and time.
Genetic algorithms, Diploidy, Dominance
 Genetic Algorithms are considered to be apt for problemsolving involving search. In contrast to other conventionalsearch alternatives, they can be applied to most problems, just focusing on good function specification and a goodchoice of representation and interpretation. Moreover, theexponentially increasing speed/cost ratio of computersmakes them a choice to consider for any search problem.They are based on Darwin’s principle of ‘Survival of fittest’. Most of the research works in genetic algorithmsmake use of haploid genomes, which contain one allele ateach locus. But in nature, many biological organisms,including humans, have diploid genomes having two allelesat each locus and even some organisms have multiploidgenomes having two or more alleles at each locus. Thispaper reviews various implementations of diploidy indifferent applications and implements diploidy in geneticalgorithms to solve the traveling salesman problem.II.
 In natural systems, the total genetic package is calledgenotype and organism formed by interaction of totalgenetic package with its environment is called phenotype.Each individual’s genotype consists of a set of chromosomes having genes which may take some valuecalled allele [10]. Each gene corresponds to a parameter of optimization problem. The simplest genotype in nature ishaploid which has single chromosome. Diploid genome hastwo chromosomes that consist of two set of allelesrepresenting different phenotypic properties.Genotype of diploid organisms contains double theamount of information for same function than the haploids.This leads to lots of redundant information which iseliminated by the use of genetic operator – Dominance. Ata locus, one allele takes precedence over other alleles.Dominant alleles are expressed and denoted by capitalletters and recessive ones by small letters in the phenotype.Dominance can be referred to as genotype to phenotypemapping or genotype reduction mapping [7]. It could berepresented as:AbCDe
ABCDeaBCdeDiploidy and Dominance clearly state that doubleinformation in genotype is reduced by half in its phenotypicrepresentation. Existence of redundant information inchromosomes and then its elimination leads to a thoughtprovoking question. Why does nature keep doubleinformation in genotype and utilizes half of the informationin phenotype? At first, this redundancy of informationseems to be wasteful. But, it is hard fact that nature is notspendthrift. There must be some good reason behind theexistence of diploidy and dominance in nature and keepingredundant information in genotype.Diploidy provides a mechanism for remembering allelesand allele combinations that were previously useful andthat dominance provides an operator to shield thoseremembered alleles from harmful selection in currenthostile environment [7]. This genetic memory of diploidystores the information regarding multiple solutions, butonly one dominant solution is expressed in phenotype.Redundant information is carried along to next generation.Dominance or non-dominance of a particular allele is itself under genetic control and evolves.
(IJCSIS) International Journal of Computer Science and Information Security,Vol. 8, No. 7, October 2010234http://sites.google.com/site/ijcsis/ISSN 1947-5500
Diploidy increases diversity in GAs by allowingrecessive genes to survive in a population and becomeactive at some later time when changes in the environmentmake them more desirable. One drawback of diploidy isthat the mechanics of a diploid GA requires twice as muchcomputational effort as the mechanics of a haploid GAbecause we have twice as many alleles to deal with [16].III.
 In 1967, Bagley used concept of diploidy to model apopulation of individuals with dominance map, therebycarrying hidden trait without expressing it [1]. Bagleyadded an evolvable dominance value to each gene. In 1967,Rosenberg simulated the evolution of a simple biochemicalsystem in which single-celled organisms capable of producing enzymes were represented in diploid fashion andwere evolved over time to produce appropriate chemicalconcentrations. Any dominance effect was result of presence or absence of particular enzyme [22].In 1971, Hollstein used a dominance schedule andsuggested that diploidy did not offer a significant advantageto fitness. He described two simple evolving dominancemechanisms [9]. In the first scheme, each binary gene wasdescribed by two genes, a modifier gene and functionalgene. Hollstein further replaced this two-locus evolvingdominance by simpler one-locus scheme by introducingthird allele at each locus and named it as triallelic scheme.This triallelic scheme was analysed for its steady stateperformance by Holland in 1975 and it turned out to beclearest, simplest Hollstein-Holland triallelic scheme forarticial genetic search. It combined dominance map andallele information at a single position [10].Many experiments on function optimization werecarried out by A. Brindle in 1981 with different dominanceschemes. She did not consider artificial dominance anddiploidy as taken in earlier experiments and developed sixnew dominance schemes [2]. In 1987, D.E. Goldberg andR.E. Smith used diploid representations and a dominanceoperator in GA’s to improve performance of non-stationaryproblems in function optimization. They used threeschemes: a simple haploid GA, a diploid GA with a fixeddominance map (1 dominates 0) and applied them to a l7-object, blind, nonstationary 0-1 knapsack problem wherethe weight constraint is varied in time as a periodic stepfunction [6]. They proved the superiority of diploidy overhaploidy in a nonstationary knapsack problem.In 1992, R.E. Smith & D.E. Goldberg extended theirresearch and showed that a diploid GA maintained extradiversity at loci where alternative alleles were emphasizedin the recent past [18]. In 1994, F. Greene useddiploid/dominance in genetic search. Diploid chromosomeswere computed separately and were evaluated to producetwo intermediate phenotypes. Mapping function was calleddominance map or dominance function and fitness wasreferred to as sub-fitness [8]. Experiment was performedusing diploid chromosome C++ object compatible toGenitor and arithmetic crossover was implemented on itand they identified the changing global optima.In 1994, C. Ryan avoided the use of dominancealtogether and introduced two new schemes - additivediploidy and polygenic inheritance. Additive diploidyscheme excelled in non-binary GAs as it can be applied toGAs with any number of phenotypes. The implementationof high level diploidy is referred to as the degree of Nness,where N is the number of the last phenotype [15]. In 1995,K.P. Ng and K.C. Wong proposed dominance changemechanism in which dominance relationships betweenalleles could change over time. They extended themultiallele approach to dominance computation by addinga fourth value for a recessive 0. Thus 1 dominates 0 and oand 0 dominates i and o. When both allele values for a geneare dominant or recessive, then one of the two values ischosen randomly to be the dominant value. They alsosuggested that the dominance of all of the components inthe genome should be reversed when the fitness value of anindividual falls by 20% or more between generations andsystem is not suitable for domains where changes are small[13].In 1996, Callebrata etal compared the behavior of haploid and diploid populations of ecological neuralnetworks in fixed and changing environments. Theyshowed that diploid genotypes were better than haploidones in terms of fitness and diploid genotypes retainedbetter changes in environment. They analysed the effect of mutation on both type of populations [3]. They concludedthat diploids had lower average fitness but higher peak fitness than haploids. In 1996, E. Collingwood, D. Corne &P. Ross studied the use of multiploidy in GAs for twoknown test problems namely, the Indecisive(k) problemand the max problem. In their multiploid model, they usedp chromosomes and a simple mask which specifieddominant gene at a locus in each chromosome and furtherthis mask helped to derive the phenotype. On testing thetwo problems at same population size, they analyzed thatthe multiploid algorithms outperformed haploid algorithms[5]. Multiploid GA was able to recover from early geneticdrift, thereby good genes managed to remain in population,shielded from harmful over-selection of bad genes.In 1997, Calabretta etal used a 2-bit dominance modifiergene for each locus apart from structural genes expressingneural network [4]. They compared the adaptation ability of haploid and diploid individuals in varying environment andfound that diploid populations performed better and wereable to tolerate sudden environment changes, thusexhibiting less reduction in fitness. In 1998, J. Lewis, E.Hart and G. Ritchie tested various diploid algorithms, withand without mechanisms for dominance change on twovariations of nonstationary problems. Comparison showedthat diploid scheme did not perform well and on adding
(IJCSIS) International Journal of Computer Science and Information Security,Vol. 8, No. 7, October 2010235http://sites.google.com/site/ijcsis/ISSN 1947-5500
dominance change mechanism, performance improvedsignificantly. Further, extending the additive dominancescheme with change improved the performanceconsiderably [12]. They concluded that some form of dominance mechanism is needed along with diploidy toallow flexible response to change.In 2002, S. Ayse, Yilmaz, Annie S. Wu, proposed a newdiploid scheme without dominance on integerrepresentation. In their research, they evolved all diploidindividuals without using any haploid stage and comparedperformance for TSP as their test problem. They concludedthat simple haploid GA outperformed diploid GA [21]. In2003, C. Ryan, J.J. Collins, D. Wallin extended their work and proposed the Shades scheme – a new version of haploidy that incorporates the characteristics of diploidscheme in haploid genetic algorithms but with lesser cost.Performance of Shades scheme was analyzed andcompared to two diploid schemes – tri-allelic andDominance change mechanism scheme in two dynamicproblems domains. Shades-3 outperformed both the diploidschemes in both Osmera’s dynamic problem andconstrained knapsack problem. Shades-2 outperformedshades -3 in knapsack problem [16].In 2003, Robert Schafer presented a GA protocol as atool to approach dynamic systems having reciprocalindividual-environment interaction and then applied on amodel problem in which a population of simulatedcreatures lived and metabolized in a three-gas atmosphere[17]. In 2005, Shane Lee and Hefin Rowlands described adiploid genetic algorithm, which favoured robust localoptima rather than a less robust global optimum in aproblem space. Diploid chromosomes were created withtwo binary haploid chromosomes, which were then used tocreate a schema. The schema was then used to measure thefitness of a family of solutions. [11].In 2007, Shengxiang Yang proposed an adaptivedominance learning scheme for diploid genetic algorithmsin dynamic environments. In this scheme, the genotype tophenotype mapping in each gene locus was controlled by adominance probability [20]. The proposed dominancescheme was experimentally compared to two other schemesfor diploid genetic algorithms and results validated theefficiency of the dominance learning scheme. Out of thetwo schemes, additive diploidy scheme proved to be betterthan the Ng-Wong dominance scheme. In 2009, Dan Simonutilized diploidy and dominance in genetic algorithms toimprove performance in time-varying optimizationproblems. He used the scaled One Max problem to provideadditional theoretical basis for the superior time-varyingperformance of diploid GAs. The analysis confirmed thatdiploidy increases diversity, and provided somequantitative results for diversity increase as a function of the GA population characteristics [19].IV.
 The Travelling Salesman Problem (TSP) is a classicalcombinatorial optimization problem, which is known to beNP-Hard problem. The problem is to find the shortest touror Hamiltonian path through a set of N vertices so that eachvertex is visited exactly once [14]. To find an optimalsolution involves searching in a solution space that growsexponentially with number of cities. So, certain kind of heuristic techniques are applied to reduce the search spaceand direct search to the areas with the highest probability of good solutions. One such heuristics technique is geneticalgorithms (GAs).The problem is solved under following assumptions:
Each city is connected to every other city,
Each city has to be visited exactly once,
The salesman’s tour starts and ends at the samecity.Based on the above assumptions, a simple geneticalgorithm is formulated to solve the problem.
[N is number of cities and M is number of maximumgenerations, GP is generation pool ]1
Create an initial population P(i) of GPchromosomes having length N.4
Evaluate the fitness of each chromosome in P(i).5
While i <M do6
Perform selection i.e. choose at random apair of parents from P(i).7
Exchange strings by crossover to createtwo offsprings.8
Insert offsprings in P(i+1)9
Repeat steps 6 to 8 until P(i+1) is full10
Replace P(i) with P(i+1).11
Evaluate the fitness of each chromosomein P(i+1)12
Final result is best chromosome created duringthe search.14
 The algorithm is further coded in MATLAB for itsimplementation using both haploid and diploid genome set.The code was implemented first for 10 cities. The cost of different paths was computed for fifteen consecutive runsand then compared.
(IJCSIS) International Journal of Computer Science and Information Security,Vol. 8, No. 7, October 2010236http://sites.google.com/site/ijcsis/ISSN 1947-5500

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