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USING PROGRAM SLICING AND SEQUENCE ALIGNMENT TO ANALYZE ORGANISMS OF AVIDA, A DIGITAL EVOLUTION PLATFORM

Hu, Hanqing
http://rave.ohiolink.edu/etdc/view?acc_num=miami1331015337

Abstract Details

2012, Master of Computer Science, Miami University, Computer Science and Software Engineering.
Digital evolution is a form of evolutionary computation closely associated with artificial life in which a population of self-replicating computer programs that are subject to mutations and natural selection exists in a user-defined computational environment. Each organism comprises an evolved genome (program) of assembly-like instructions and a virtual CPU on which the genome executes. Since each genome is produced by a sequence of random mutations over evolutionary time, the encoding of behavior within the genome is often obscure, making manual analysis tedious and time-consuming. In this thesis, we present a methodology for analyzing digital organisms using program understanding and Bioinformatics techniques, including program slicing and sequence alignment, both of which we have adapted for the digital evolution context. We apply this approach to a set of evolved genomes and demonstrate how dependency analysis and slicing facilitate identification of known patterns and operations embedded within the genomes.
Jerry Gannod, PhD (Advisor)
John Karro, PhD (Other)
James Kiper, PhD (Other)
Computer Science
Avida; Digital Evolution; Genetic Algorithm; Program Slicing; Sequence Alignment; Program Understanding

Recommended Citations

Citations

  • Hu, H. (2012). USING PROGRAM SLICING AND SEQUENCE ALIGNMENT TO ANALYZE ORGANISMS OF AVIDA, A DIGITAL EVOLUTION PLATFORM [Master's thesis, Miami University]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=miami1331015337

    APA Style (7th edition)

  • Hu, Hanqing. USING PROGRAM SLICING AND SEQUENCE ALIGNMENT TO ANALYZE ORGANISMS OF AVIDA, A DIGITAL EVOLUTION PLATFORM. 2012. Miami University, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=miami1331015337.

    MLA Style (8th edition)

  • Hu, Hanqing. "USING PROGRAM SLICING AND SEQUENCE ALIGNMENT TO ANALYZE ORGANISMS OF AVIDA, A DIGITAL EVOLUTION PLATFORM." Master's thesis, Miami University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=miami1331015337

    Chicago Manual of Style (17th edition)

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© 2012, all rights reserved.
This open access ETD is published by Miami University and OhioLINK.