Abstract
In this work, we present results on analyzing the behavior of a parallel distributed genetic algorithm over different LAN technologies. Our goal is to offer a study on the potential impact in the search mechanics when shifting between LANs. We will address three LANs: a Fast Ethernet network, a Gigabit Ethernet network, and a Myrinet network. We also study the importance of several parameters of the migration policy. The whole analysis will use the DNA fragment assembly problem to show the actual power and utility of the proposed distributed technique.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
E. Alba. Parallel evolutionary algorithms can achieve super-linear performace. Information Processing Letters, 82:7–13, 2002.
E. Alba. Parallel Metaheuristics: A New Class of Algorithms. Wiley, 2005.
E. Alba, C. Cotta, M. Díaz, E. Soler, and J.M. Troya. MALLBA: Middleware for a geographically distributed optimization system. Technical report, Dpto. Lenguajes y Ciencias de la Computatión, Universidad de Malága (internal report), 2000.
E. Alba, F. Luna, and A. J. Nebro. Advances in parallel heterogeneous genetic algorithms for continuous optimization. International Journal of Applied Mathematics and Computer Science, 14(3):317–333, 2004.
E. Alba and the MALLBA Group. MALLBA: A library of skeletons for combinatorial optimisation. In R. Feldmann B. Monien, editor, Proceedings of the Euro-Par, volume 2400 of LNCS, pages 927–932, Paderborn (GE), 2002. Springer–Verlag.
E. Alba and M. Tomassini. Parallelism and Evolutionary Algorithms. IEEE Transactions on Evolutionary Computation, 6(5):443–462, October 2002.
C.F. Allex. Computational Methods for Fast and Accurate DNA Fragment Assembly. UW technical report CS-TR-99–1406, Department of Computer Sciences, University of Wisconsin-Madison, 1999.
N.J. Boden, D. Cohen, R.E. Felderman, A.E. Kulawik, C.L. Seitz, J. Seizovic, and W. Su. Myrinet A Gigabit Per Second Local Area Network. IEEE Micro, pages 29–36, 1995.
E. Cantú-Paz. Efficient and Accurate Parallel Genetic Algorithms. Kluwer Academic Press, 2000.
M.L. Engle and C. Burks. Artificially generated data sets for testing DNA fragment assembly algorithms. Genomics, 16, 1993.
Message Passing Interface Forum. MPI: A message–passing interface standard. Technical Report UT-CS-94–230, 1994.
D.E. Goldberg and K. Deb. A comparative analysis of selection schemes used in genetic algorithms. In G.J.E. Rawlins, editor, Foundations of Genetic Algorithms, pages 69–93. Morgan Kaufmann, 1991.
S. Kim. A structured Pattern Matching Approach to Shotgun Sequence Assembly. PhD thesis, Computer Science Department, The University of Iowa, 1997.
C. Notredame and D.G. Higgins. SAGA: sequence alignment by genetic algorithm. Nucleic Acids Research, 24:1515–1524, 1996.
R. Parsons, S. Forrest, and C. Burks. Genetic algorithms, operators, and DNA fragment assembly. Machine Learning, 21:11–33, 1995.
R. Parsons and M.E. Johnson. A case study in experimental design applied to genetic algorithms with applications to DNA sequence assembly. American Journal of Mathematical and Management Sciences, 17:369–396, 1995.
P.A. Pevzner. Computational molecular biology: An algorithmic approach. The MIT Press, London, 2000.
J. Setubal and J. Meidanis. Introduction to Computational Molecular Biology, chapter 4 - Fragment Assembly of DNA, pages 105–139. University of Campinas, Brazil, 1997.
D. Whitely. The GENITOR algorithm and selection pressure: Why rank-based allocation of reproductive trials is best. In J.D. Schaffer, editor, Proceedings of the Third International Conference on Genetic Algorithms, pages 116–121. Morgan Kaufmann, 1989.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2006 Springer
About this chapter
Cite this chapter
Alba, E., Luque, G. (2006). Performance of Distributed GAs on DNA Fragment Assembly. In: Nedjah, N., Mourelle, L.d., Alba, E. (eds) Parallel Evolutionary Computations. Studies in Computational Intelligence, vol 22. Springer, Berlin, Heidelberg . https://doi.org/10.1007/3-540-32839-4_5
Download citation
DOI: https://doi.org/10.1007/3-540-32839-4_5
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-32837-7
Online ISBN: 978-3-540-32839-1
eBook Packages: EngineeringEngineering (R0)