skip to main content
10.1145/1854776.1854809acmconferencesArticle/Chapter ViewAbstractPublication PagesbcbConference Proceedingsconference-collections
research-article

Ring optimization of edit metric codes in DNA

Published: 02 August 2010 Publication History

Abstract

Error correcting codes over the DNA alphabet are used as embeddable biomarkers. Error correction provides resilience of identification in spite of sequencing errors. Ring optimization is a type of spatially structured evolutionary algorithm derived from models of ring species in nature. This paper compares the performance of a ring optimizer with a standard evolutionary algorithm at searching for large edit metric codes of a given length and able to correct a specified number of errors. The algorithm also incorporates a novel variation operator called Conway crossover that uses Conway's lexicode algorithm as the basis for a binary variation operator. The ring optimizer is found to yield substantially inferior performance. A new type of statistic, last time of innovation is defined and used to compare the two algorithms. Several improvements to the table of best known edit metric codes are presented. Both algorithms yielded improvements to the table, but the improvements due to the ring optimizer were never better than those located by the standard algorithm and worse half of the time.

References

[1]
D. Ashlock. Optimization and Modeling with Evolutionary Computation. Springer-Verlag, New York, 2006.
[2]
D. Ashlock, K. Bryden, and D. McCorkle. Logic function induction with the blender algorithm using function stacks. In Intelligent Engineering Systems Through Artificial Neural Networks, volume 19, pages 189--196, Piscataway, NJ, 2009. IEEE Press.
[3]
D. Ashlock, L. Guo, and F. Qiu. Greedy closure genetic algorithms. In Proceedings of the 2002 Congress on Evolutionary Computation, pages 1296--1301, Piscataway, NJ, 2002. IEEE Press.
[4]
D. Ashlock and S. Houghten. A novel variation operator for more rapid evolution of dna error correcting codes. In Proceedings of the 2005 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pages 53--60, 2005.
[5]
D. Ashlock and S. Houghten. Dna error correcting codes: No crossover. In Proceedings of the 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pages 38--45, 2009.
[6]
D. Ashlock and A. McEachern. Ring optimization of side effect machines. In Intelligent Engineering Systems Through Artificial Neural Networks, volume 19, pages 165--172. ASCME, 2009.
[7]
D. Ashlock and T. VonKonigslow. Evolution of artifical ring species. In Proccedings of the 2008 Congress on Evolutionary Computation, pages 653--659, Piscataway NJ, 2008. IEEE Press.
[8]
D. Ashlock, T. VonKonigslow, E. Clare, and W. Ashlock. Transience in the simulation of ring species. In Proccedings of the 2008 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, pages 256--263, Piscataway NJ, 2008. IEEE Press.
[9]
D. A. Ashlock, K. M. Bryden, and S. Corns. Small population effects and hybridization. In Proceedings of the 2008 Congress on Evolutionary Computation, pages 2642--2648, Piscataway, NJ, 2008. IEEE Press.
[10]
W. Ashlock. Using very small population sizes in genetic programming. In Proceedings of the 2006 Congress on Evolutionary Computation, pages 319--326, Piscataway, NJ, 2006. IEEE Press.
[11]
S. Baker, R. Flack, and S. Houghten. Optimal variable-length edit metric and insertion-deletion correcting codes. Congressus Numerantium, 184:65--80, 2007.
[12]
W. Banzhaf, P. Nordin, R. E. Keller, and F. D. Francone. Genetic Programming: An Introduction: On the Automatic Evolution of Computer Programs and Its Applications. Morgan Kaufmann, San Francisco, 1998.
[13]
J. K. Campbell. Enumeration and Symmetry of Edit Metric Spaces. PhD thesis, Iowa State University, 2005.
[14]
R. Flack and S. Houghten. Generation of good edit codes from classical hammming distance codes. Congressus Numerantium, 190:97--108, 2008.
[15]
R. Flack and S. Houghten. Quaternary edit codes built from classical hammming distance codes. Technical report, Brock University, 2010.
[16]
D. Gusfield. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, Boston, 1997.
[17]
S. Houghten, D. Ashlock, and J. Lenarz. Construction of optimal edit metric codes. In Proceedings of the 2006 IEEE Workshop on Information Theory, pages 259--263, Piscataway, NJ, 2006. IEEE Press.
[18]
D. E. Irwin, S. Bensch, and T. D. Price. Speciation in a ring. Nature, 409:333--337, 2001.
[19]
F. Qiu, T. Wen, D. Ashlock, and P. Schnable. Dna sequence-based bar-codes for tracking the origins of ests from a maize cdna library constructed using multiple mrna sources. Plant Physiology, 133:475--481, 2003.
[20]
Q. Qiu, D. Burns, P. Mukre, and Q. Wu. Hardware acceleration of multi-deme genetic algorithm for the application of dna codeword searching. In Proccedings of the 9th Annual Conference on Genetic and Evolutionary Computation, pages 1349--1356. Association for Computing Machinery, 2007.
[21]
R. C. Stebbins. Speciation in salamanders of the plethodontid genus ensatina. University of California Publications in Zoology, 54:47--124, 1986.
[22]
T. M. Thompson. From Error-Correcting Codes through Sphere Packings to Simple Groups. Cambridge University Press, New York, NY, 2004.

Cited By

View all
  • (2017)Hybridization and ring optimization for larger sets of embeddable biomarkers2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)10.1109/CIBCB.2017.8058532(1-8)Online publication date: Aug-2017
  • (2015)Evolving DNA classifiers with extinction based ring optimization2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)10.1109/CIBCB.2015.7300312(1-8)Online publication date: Aug-2015
  • (2015)Lexicode crossover for embeddable biomarkers2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)10.1109/CIBCB.2015.7300291(1-7)Online publication date: Aug-2015
  • Show More Cited By

Index Terms

  1. Ring optimization of edit metric codes in DNA

    Recommendations

    Comments

    Information & Contributors

    Information

    Published In

    cover image ACM Conferences
    BCB '10: Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
    August 2010
    705 pages
    ISBN:9781450304382
    DOI:10.1145/1854776
    Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

    Sponsors

    Publisher

    Association for Computing Machinery

    New York, NY, United States

    Publication History

    Published: 02 August 2010

    Permissions

    Request permissions for this article.

    Check for updates

    Author Tags

    1. DNA
    2. bioinformatics
    3. error correction
    4. evolutionary algorithms
    5. operators

    Qualifiers

    • Research-article

    Conference

    BCB'10
    Sponsor:

    Acceptance Rates

    Overall Acceptance Rate 254 of 885 submissions, 29%

    Contributors

    Other Metrics

    Bibliometrics & Citations

    Bibliometrics

    Article Metrics

    • Downloads (Last 12 months)1
    • Downloads (Last 6 weeks)1
    Reflects downloads up to 17 Jan 2025

    Other Metrics

    Citations

    Cited By

    View all
    • (2017)Hybridization and ring optimization for larger sets of embeddable biomarkers2017 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)10.1109/CIBCB.2017.8058532(1-8)Online publication date: Aug-2017
    • (2015)Evolving DNA classifiers with extinction based ring optimization2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)10.1109/CIBCB.2015.7300312(1-8)Online publication date: Aug-2015
    • (2015)Lexicode crossover for embeddable biomarkers2015 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB)10.1109/CIBCB.2015.7300291(1-7)Online publication date: Aug-2015
    • (2012)Evolutionary approaches to the generation of optimal error correcting codesProceedings of the 14th annual conference on Genetic and evolutionary computation10.1145/2330163.2330320(1135-1142)Online publication date: 7-Jul-2012

    View Options

    Login options

    View options

    PDF

    View or Download as a PDF file.

    PDF

    eReader

    View online with eReader.

    eReader

    Media

    Figures

    Other

    Tables

    Share

    Share

    Share this Publication link

    Share on social media