Summary
This chapter introduces a class of evolutionary algorithms whose inspiration comes from living processes where cooperation is the main evolutionary strategy. The proposed technique is called Transgenetic Algorithms and is based on two recognized driving forces of evolution: the horizontal gene transfer and the endosymbiosis. These algorithms perform a stochastic search simulating endosymbiotic interactions between a host and a population of endosymbionts. The information exchanging between the host and ensosymbionts is intermediated by agents, called transgenetic vectors, who are inspired on natural mechanisms of horizontal gene transfer. The proposed approach is described and a didactic example with the well-known Traveling Salesman Problem illustrates its basic components. Applications of the proposed technique are reported for two NP-hard combinatorial problems: the Traveling Purchaser Problem and the Bi-objective Minimum Spanning Tree Problem.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Aggarwal, V., Aneja, Y., Nair, K.: Minimal spanning tree subject to a side constraint. Computers & Operations Research 9, 287â296 (1982)
Almeida, C.P., Goldbarg, E.F.G., Gonçalves, R.A., Regattieri, M.D., Goldbarg, M.C.: TA-PFP: A transgenetic algorithm to solve the protein folding problem. In: Proceedings of ISDA 2007 Seventh International Conference on Intelligent Systems Design and Applications, vol. 1, pp. 163â168 (2007)
Applegate, D., Bixby, R., Chvatal, V., Cook, W.: Finding tours in the TSP. Technical Report TR99-05. Department of Computational and Applied Mathematics: Rice University (1999)
Barboza, A.O.: Simulação e técnicas da computação evolucionåria aplicadas a problemas de programação linear inteira mista. D.Sc. Thesis, Universidade Tecnológica Federal do Paranå, Brazil (2005)
Bazlamaçci, C.F., Hindi, K.S.: Minimum-weight spanning tree algorithms: A survey and empirical study. Computers & Operations Research 28, 767â785 (2001)
Bellmore, M., Nemhauser, G.L.: The traveling salesman problem: A survey. Operations Research 16, 538â582 (1968)
Boctor, F.F., Laporte, G., Renaud, J.: Heuristics for the traveling purchaser problem. Computers & Operations Research 30, 491â504 (2003)
Bontoux, B., Feillet, D.: Ant colony optimization for the traveling purchaser problem. Computers & Operations Research 35, 628â637 (2008)
Buchner, P.: Endosymbiosis of animals with plant microorganisms. Wiley Interscience, New York (1965)
Bull, L., Fogarty, T.C.: Artificial symbiogenesis. Artificial Life 2, 269â292 (1995)
Chan, T.-M., Man, K.-F., Tang, K.-S., Kwong, S.A.: Jumping gene algorithm for multiobjective resource management in wideband CDMA. The Computer Journal 48(6), 749â768 (2005)
Chen, I., Dubnau, D.: DNA uptake during bacterial transformation. Nature Reviews Microbiology 2, 241â249 (2004)
Conover, W.J.: Practical nonparametric statistics, 3rd edn. John Wiley & Sons, Chichester (2001)
Daida, J.M., Grasso, C.S., Stanhope, S.A., Ross, S.J.: Symbionticism and complex adaptive systems I: Implications of having symbiosis occur in nature. In: Proceedings of the Fifth Annual Conference on Evolutionary Programming, pp. 177â186 (1996)
Doolittle, W.F.: Lateral genomics. Trends in Genetics 15(12), M5âM8 (1999)
Dutta, C., Pan, A.: Horizontal gene transfer and bacterial diversity. Journal of Biosciences 27, 27â33 (2002)
Eigen, M., Schuster, P.: The hypercycle: A principle of natural selforganization. Naturwissenschafter 64(11), 541â565 (1977)
Fukuda, T., Kubota, N., Shimojima, K.: Virus-evolutionary genetic algorithm and its application to traveling salesmam problem. In: Yao, X. (ed.) Evolutionary Computation, Theory and Applications. World Scientific, Singapore (1999)
Garey, M.R., Johnson, D.S.: Computers and intractability: A guide to the theory of NP-completeness. Freeman, New York (1979)
Goldbarg, E.F.G., Castro, M.P., Goldbarg, M.C.: A transgenetic algorithm for the gas network pipe sizing problem. Computational Methods 1, 893â904 (2006)
Goldbarg, E.F.G., Goldbarg, M.C., Bagi, L.B.: Transgenetic algorithm: A new evolutionary perspective for heuristics design. In: Proceedings of GECCO 2007 Genetic and Evolutionary Computation Conference, pp. 2701â2708 (2007)
Goldbarg, E.F.G., Goldbarg, M.C., Costa, W.E.: Evolutionary algorithms applied to the workover rigs schedule problem. Annals of XI Latin-Iberian American Congress of Operations Research (2002)
Goldbarg, M.C., Goldbarg, E.F.G., Medeiros Neto, F.D.: Algoritmos evolucionĂĄrios na determinação da configuração de custo mĂnimo de sistemas de co-geração de energia com base no ĂĄ natural. Pesquisa Operacional 25(2), 231â259 (2005)
GouvĂȘa, E.F.: TransgenĂ©tica computacional: Um estudo algorĂtmico. Ph.D. Thesis, Universidade Federal do Rio de Janeiro, Brazil (2001)
Guttin, G., Punnen, A.: The traveling salesman problem and its variations. Kluwer Academic Publishers, Dordrecht (2002)
Hansen, M.P., Jaszkiewicz, A.: Evaluating the quality of approximations to the non-dominated set. Technical Report IMM-REP-1998-7, Technical University, Denmark (1998)
Harvey, I.: The microbial genetic algorithm (unpublished manuscript) (1996), http://citeseer.ist.psu.edu/13824.html
Hillis, D.W.: Co-evolving parasites improve simulated evolution in an optimization procedure. Physica D 42, 228â234 (1999)
Jain, R., Rivera, M.C., Lake, J.A.: Horizontal gene transfer among genomes: The complexity hypothesis. Proceedings of the National Academy of Sciences USA 96, 3801â3806 (1999)
Jain, R., Rivera, M.C., Moore, J.E., Lake, J.A.: Horizontal gene transfer accelerates genome innovation and evolution. Molecular Biology and Evolution 20(10), 1598â1602 (2003)
Kim, J.Y., Kim, Y., Kim, Y.K.: An endosymbiotic evolutionary algorithm for optimization. Applied Intelligence 15, 117â130 (2001)
Kim, Y.K., Kim, J.Y., Kim, Y.: An endosymbiotic evolutionary algorithm for the integration of balancing and sequencing in mixed-model U-lines. European Journal of Operational Research 168, 838â852 (2006)
Knowles, J.D.: Local-search and hybrid evolutionary algorithms for Pareto optimization, PhD Thesis, Department of Computer Science, University of Reading, Reading, UK (2002)
Knowles, J.D., Corne, D.W.: A comparison of encodings and algorithms for multiobjective spanning tree problems. In: Proceedings of the 2001 Congress on Evolutionary Computation (CEC 2001), pp. 544â551 (2001)
Knowles, J.D., Thiele, L., Zitzler, E.: A tutorial on the performance assessment of stochastic multiobjective optimizers, TIK 214, Computer Engineering and Networks Laboratory (TIK), Swiss Federal Institute of Technology (ETH), Zurich (2006)
Kubota, N., Arakawa, T., Fukuda, T., Shimojima, K.: Trajectory generation for redundant manipulator using virus evolutionary genetic algorithm. In: Proceedings of the IEEE International Conference on Robotics and Automation, pp. 205â210 (1997)
Kubota, N., Shimojima, K., Fukuda, T.: Virus-evolutionary genetic algorithm - coevolution of planar grid model. In: Proceedings of the Fifth IEEE International Conference on Fuzzy Systems (FUZZIEEE 1996), vol. 1, pp. 8â11 (1996)
Kutschera, U., Niklas, K.J.: Endosymbiosis, cell evolution, and speciation. Theory in Biosciences 124, 1â24 (2005)
Leite, L.E., Souza Fillho, G., Goldbarg, M.C., Goldbarg, E.F.G.: Comparando algoritmos genĂ©ticos e transgenĂ©ticos para otimizar a configuração de um serviço de distribuição de VĂdeo baseado em replicação mĂłvel. Anais do SBRC2004 22 SimpĂłsio Brasileiro de Redes de Computadores 1, 129â132 (2004)
Margulis, L.: Symbiosis in cell evolution: Microbial communities in the archean and proterozoic eons. W.H. Freeman, New York (1992)
Margulis, L.: Serial endosymbiotic theory (SET) and composite individuality. Microbiology Today 31, 172â174 (2004)
Margulis, L., Sagan, D.: Microcosmos. Summit Books, New York (1986)
Maynard-Smith, J., SzathmĂĄry, E.: The major transitions in evolution. W.H. Freeman, Oxford (1995)
Michalewicz, Z., Fogel, D.B.: How to solve it: Modern heuristics. Springer, Heidelberg (2000)
Mitchell, M.: An introduction to genetic algorithms. MIT Press, Cambridge (1998)
MĂŒhlenbein, H., Voigt, H.-M.: Gene pool recombination in genetic algorithms. In: Proceedings of the Sixth International Conference on Genetic Algorithms, pp. 104â113 (1995)
Novozhilov, A.S., Karev, G.P., Koonin, E.V.: Mathematical modeling of evolution of horizontally transferred genes. Molecular Biology and Evolution 22(8), 1721â1732 (2005)
Perales-GravĂĄn, C., Lahoz-Beltra, R.: An AM radio receiver designed with a genetic algorithm based on a bacterial conjugation genetic operator. IEEE Transactions on Evolutionary Computation 12(2), 1â29 (2008)
Ramos, I.C.O., Goldbarg, M.C., Goldbarg, E.F.G., DĂłria Neto, A.D.: Logistic regression for parameter tuning on an evolutionary algorithm. In: Proceedings of the IEEE CEC 2005 Congress on Evolutionary Computation, vol. 2, pp. 1061â1068 (2005)
Riera-Ledesma, J., Salazar-GonzĂĄlez, J.J.: A heuristic approach for the traveling purchaser problem. European Journal of Operational Research 162, 142â152 (2005)
Rocha, D.A.M., Goldbarg, E.F.G., Goldbarg, M.C.: A memetic algorithm for the biobjective minimum spanning tree problem. In: Gottlieb, J., Raidl, G.R. (eds.) EvoCOP 2006. LNCS, vol. 3906, pp. 222â233. Springer, Heidelberg (2006)
Rocha, D.A.M., Goldbarg, E.F.G., Goldbarg, M.C.: A new evolutionary algorithm for the bi-objective minimum spanning tree. In: Proceedings of ISDA 2007 Seventh International Conference on Intelligent Systems Design and Applications, pp. 735â740 (2007)
Rosenkrantz, D.J., Stearns, R.E., Lewis II, P.M.: An analysis of several heuristics for the traveling salesman problem. SIAM Journal on Computing 6, 563â581 (1977)
Rosin, C.D., Belew, R.K.: New methods for competitive coevolution. Evolutionary Computation 5(1), 1â29 (1997)
Schmidt, C., Goldbarg, E.F.G., Goldbarg, M.C.: A hybrid transgenetic algorithm for the prize collecting Steiner tree problem. In: Proceedings of ISDA 2007 Seventh International Conference on Intelligent Systems Design and Applications, vol. 1, pp. 271â276 (2007)
Shapiro, J.A.: Transposable elements as the key to a 21st century view of evolution. Genetica 107, 171â179 (1999)
SimĂ”es, A.B., Costa, E.: Transposition: A biologically inspired mechanism to use with genetic algorithms. In: Proceedings of the Fourth International Conference of Neural Networks and Genetic Algorithms, pp. 178â186 (1999)
SimĂ”es, A.B., Costa, E.: Transposition versus crossover: An empirical study. In: Proceedings of the Genetic and Evolutionary Compuation Conference (GECCO 1999), pp. 612â619 (1999)
SimĂ”es, A.B., Costa, E.: On biologically inspired genetic operators: Transformation in the standard genetic algorithm. In: Proceedings of the Genetic and Evolutionary Computation Conference (GECCO 2001), pp. 584â591 (2001)
SimĂ”es, A.B., Costa, E.: An evolutionary approach to the zero/one knapsack problem: Testing ideas from biology. In: Proceedings of the Fifth International Conference on Neural Networks and Genetic Algorithms (ICANNGA 2001), pp. 22â25 (2001)
Smith, P.W.H.: Finding hard satisfiability problems using bacterial conjugation. In: Proceedings of the AISB96 Workshop on Evolutionary Computing, pp. 236â244 (1996)
Theissen, U., Martin, W.: The difference between organelles and endosymbionts. Current Biology 16(24), R1016âR1017 (2006)
Timmis, J.N., Ayliffe, M.A., Huang, C.Y., Martin, W.: Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nature Reviews Genetic 5, 123â135 (2004)
Vothknecht, U.C., Soll, J.: Protein import: The hitchhikers guide into chloroplasts. Biological Chemistry 381, 887â897 (2000)
Wernegreen, J.J.: For better or worse: genomic consequences of intracellular mutualism and parasitism. Genetics & Development 15, 572â583 (2005)
Yeung, S.-H., Ng, H.-K., Man, K.-F.: Multi-criteria design methodology of a dielectric resonator antenna with jumping genes evolutionary algorithm. International Journal of Electronics and Communication (AEĂ) 62, 266â276 (2008)
Zaneveld, J.R., Nemergut, D.R., Knight, R.: Are all horizontal gene transfers created equal? Prospects for mechanism-based studies of HGT patterns. Microbiology 154, 1â15 (2008)
Zhou, G., Gen, M.: Genetic algorithm approach on multi-criteria minimum spanning tree problem. European Journal of Operational Research 114, 141â152 (1999)
Zitzler, E., Thiele, L.: Multiobjective evolutionary algorithms: A comparative case study and the strength Pareto approach. IEEE Transactions on Evolutionary Computation 3(4), 257â271 (1999)
Zitzler, E., Thiele, L., Laumanns, M., Fonseca, C.M., Fonseca, V.G.: Performance assessment of multiobjective optimizers: An analysis and review. IEEE Transactions on Evolutionary Computation 7(2), 117â132 (2003)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Goldbarg, E.F.G., Goldbarg, M.C. (2009). Transgenetic Algorithm: A New Endosymbiotic Approach for Evolutionary Algorithms. In: Abraham, A., Hassanien, AE., Siarry, P., Engelbrecht, A. (eds) Foundations of Computational Intelligence Volume 3. Studies in Computational Intelligence, vol 203. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-01085-9_14
Download citation
DOI: https://doi.org/10.1007/978-3-642-01085-9_14
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-01084-2
Online ISBN: 978-3-642-01085-9
eBook Packages: EngineeringEngineering (R0)