skip to main content
10.1145/1569901.1570044acmconferencesArticle/Chapter ViewAbstractPublication PagesgeccoConference Proceedingsconference-collections
research-article

Evolving stochastic processes using feature tests and genetic programming

Published:08 July 2009Publication History

ABSTRACT

The synthesis of stochastic processes using genetic programming is investigated. Stochastic process behaviours take the form of time series data, in which quantities of interest vary over time in a probabilistic, and often noisy, manner. A suite of statistical feature tests are performed on time series plots from example processes, and the resulting feature values are used as targets during evolutionary search. A process algebra, the stochastic π-calculus, is used to denote processes. Investigations consider variations of GP representations for a subset of the stochastic π-calculus, for example, the use of channel unification, and various grammatical constraints. Target processes of varying complexity are studied. Results show that the use of grammatical GP with statistical feature tests can successfully synthesize stochastic processes. Success depends upon a selection of appropriate feature tests for characterizing the target behaviour, and the complexity of the target process.

References

  1. P. Angeline. Evolving Predictors for Chaotic Time Series. In Proc. SPIE: Application and Science of Computational Intelligence, volume 3390, pages 170--180, 1998.Google ScholarGoogle ScholarCross RefCross Ref
  2. R. Blossey, L. Cardelli, and A. Phillips. A Compositional Approach to the Stochastic Dynamics of Gene Networks. Trans. in Comp. Sys. Bio (TCSB), 3939:99--122, 2006. Google ScholarGoogle ScholarDigital LibraryDigital Library
  3. A. Borrelli, I. De Falco, A. Della Cioppa, M. Nicodemi, and G. Trautteura. Performance of genetic programming to extract the trend in noisy data series. Physica A: Statistical and Theoretical Physics, 370(1):104--108, 2006.Google ScholarGoogle ScholarCross RefCross Ref
  4. D.-Y. Cho, K.-H. Cho, and B.-T. Zhang. Identification of biochemical networks by S--tree based genetic programming. Bioinformatics, 22(13):1631--1640, 2006. Google ScholarGoogle ScholarDigital LibraryDigital Library
  5. D. Chu. Evolving genetic regulatory networks for systems biology. In D. Srinivasan and L. Wang, editors, Proc. CEC 2007, pages 875--882, Singapore, 25--28 Sept. 2007. IEEE Press.Google ScholarGoogle Scholar
  6. B. Drennan and R. Beer. Evolution of repressilators using a biologically-motivated model of gene expression. In L. R. et al., editor, Artificial Life X: Proc. Tenth Intl. Conf. on the Simulation and Synthesis of Living Systems, pages 22--27. MIT Press, August 2006.Google ScholarGoogle Scholar
  7. D. Gillespie. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem, 81:2340--2361, 1977.Google ScholarGoogle ScholarCross RefCross Ref
  8. J. Imada. Evolutionary synthesis of stochastic gene network models using feature--based search spaces. Master's thesis, Department of Computer Science, Brock University, 2009.Google ScholarGoogle Scholar
  9. J. Imada and B. Ross. Using Feature-based Fitness Evaluation in Symbolic Regression with Added Noise. In Proc. GECCO 2008 Late Breaking Papers, July 2008. Google ScholarGoogle ScholarDigital LibraryDigital Library
  10. J. Kitagawa and H. Iba. Identifying Metabolic Pathways and Gene Regulation Networks with Evolutionary Algorithms. In G. Fogel and D. Corne, editors, Evolutionary Computation in Bioinformatics, pages 255--278. Morgan Kaufmann, 2003.Google ScholarGoogle ScholarCross RefCross Ref
  11. J. Koza. Genetic Programming: On the Programming of Computers by Means of Natural Selection. MIT Press, 1992. Google ScholarGoogle ScholarDigital LibraryDigital Library
  12. J. Koza, M. Keane, M. Streeter, W. Mydlowec, J. Yu, and G. Lanza. Genetic Programming IV: Routine Human-Competitive Machine Intelligence. Kluwer Academic Publishers, 2003. Google ScholarGoogle ScholarDigital LibraryDigital Library
  13. A. Leier, P. Kuo, W. Banzhaf, and K. Burrage. Evolving noisy oscillatory dynamics in genetic regulatory networks. In P. C. et al., editor, EuroGP 2006, volume 3905 of LNCS, pages 290--299. Springer, 2006. Google ScholarGoogle ScholarDigital LibraryDigital Library
  14. H. Liu and H. Motoda. Feature Selection for Knowledge Discovery and Data Mining. Kluwer Academic Publishers, 1998. Google ScholarGoogle ScholarDigital LibraryDigital Library
  15. R. Milner. Communication and Concurrency. Prentice Hall, 1989. Google ScholarGoogle ScholarDigital LibraryDigital Library
  16. A. Nanopoulos, R. Alcock, and Y. Manolopoulos. Feature-based classification of time-series data. In Information processing and technology, pages 49--61. Nova Science Publishers, Inc., Commack, NY, USA, 2001. Google ScholarGoogle ScholarDigital LibraryDigital Library
  17. A. Phillips. The stochastic pi machine, 2008. http://research.microsoft.com/ aphillip/spim/. Last accessed Dec 9, 2008.Google ScholarGoogle Scholar
  18. A. Phillips and L. Cardelli. A Correct Abstract Machine for the Stochastic Pi-calculus. In Proc. Bioconcur'04, 2004.Google ScholarGoogle Scholar
  19. C. Priami. Stochastic pi-Calculus. The Computer Journal, 38(7):579--589, 1995.Google ScholarGoogle ScholarCross RefCross Ref
  20. C. Priami, A. Regev, E. Shapiro, and W. Silverman. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters, 80:25--31, 2001. Google ScholarGoogle ScholarDigital LibraryDigital Library
  21. R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, 2007.Google ScholarGoogle Scholar
  22. K. Rodriguez-Vazquez and P. J. Fleming. Evolution of mathematical models of chaotic systems based on multiobjective genetic programming. Knowledge and Information Systems, 8(2):235--256, Aug. 2005. Google ScholarGoogle ScholarDigital LibraryDigital Library
  23. B. Ross. Logic-based Genetic Programming with Definite Clause Translation Grammars. New Generation Computing, 19(4):313--337, 2001. Google ScholarGoogle ScholarDigital LibraryDigital Library
  24. B. Ross. Using Genetic Programming to Synthesize Monotonic Stochastic Processes. In Proceedings CI-2007, July 2007. Google ScholarGoogle ScholarDigital LibraryDigital Library
  25. B. Ross and J. Imada. Using Multi-objective Genetic Programming to Synthesize Stochastic Processes. In Genetic Programming -- Theory and Practice, May 2009.Google ScholarGoogle Scholar
  26. R. Schwaerzel and T. Bylander. Predicting currency exchange rates by genetic programming with trigonometric functions and high-order statistics. In M. Cattolico, editor, GECCO 2006, pages 955--956. ACM, 2006. Google ScholarGoogle ScholarDigital LibraryDigital Library
  27. F. Streichert, H. Planatscher, C. Spieth, H. Ulmer, and A. Zell. Comparing genetic programming and evolution strategies on inferring gene regulatory networks. In K. et al., editor, GECCO-2004, volume 3102 of LNCS, pages 471--480, Seattle, WA, 2004. Springer-Verlag.Google ScholarGoogle Scholar
  28. S. Strogatz. Nonlinear Dynamics and Chaos. Westview Press, 1994.Google ScholarGoogle Scholar
  29. X. Wang, K. Smith, and R. Hyndman. Characteristic-based clustering for time series data. Data Min. Knowl. Discov., 13(3):335--364, 2006. Google ScholarGoogle ScholarDigital LibraryDigital Library
  30. W. Zhang, G. Yang, and Z.Wu. Genetic Programming-based Modeling on Chaotic Time Series. In Proc. 3rd Intl Conf. on Machine Learning and Cybernetics, pages 2347--2352. IEEE, 2004.Google ScholarGoogle ScholarCross RefCross Ref

Recommendations

Comments

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Sign in
  • Published in

    cover image ACM Conferences
    GECCO '09: Proceedings of the 11th Annual conference on Genetic and evolutionary computation
    July 2009
    2036 pages
    ISBN:9781605583259
    DOI:10.1145/1569901

    Copyright © 2009 ACM

    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]

    Publisher

    Association for Computing Machinery

    New York, NY, United States

    Publication History

    • Published: 8 July 2009

    Permissions

    Request permissions about this article.

    Request Permissions

    Check for updates

    Qualifiers

    • research-article

    Acceptance Rates

    Overall Acceptance Rate1,669of4,410submissions,38%

    Upcoming Conference

    GECCO '24
    Genetic and Evolutionary Computation Conference
    July 14 - 18, 2024
    Melbourne , VIC , Australia

PDF Format

View or Download as a PDF file.

PDF

eReader

View online with eReader.

eReader