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Analysing the Regularity of Genomes Using Compression and Expression Simplification

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Book cover Genetic Programming (EuroGP 2007)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4445))

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Abstract

We propose expression simplification and tree compression as aids in understanding the evolution of regular structure in Genetic Programming individuals. We apply the analysis to two previously-published algorithms, which aimed to promote regular and repeated structure. One relies on subtree duplication operators, the other uses repeated evaluation during a developmental process. Both successfully generated solutions to difficult problems, their success being ascribed to promotion of regular structure. Our analysis modifies this ascription: the evolution of regular structure is more complex than anticipated, and the success of the techniques may have arisen from a combination of promotion of regularity, and other, so far unidentified, effects.

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References

  1. Koza, J.R.: Hierarchical automatic function definition in genetic programming. In: Whitley, L.D. (ed.) Foundations of Genetic Algorithms 2, Vail, Colorado, USA, 24–29 July 1992, pp. 297–318. Morgan Kaufmann, San Francisco (1992)

    Google Scholar 

  2. Spector, L.: Evolving control structures with automatically defined macros. In: Siegel, E.V., Koza, J.R. (eds.) Working Notes for the AAAI Symposium on Genetic Programming, 10-12 November 1995, pp. 99–105. MIT Press, Cambridge (1995)

    Google Scholar 

  3. Woodward, J.R.: Modularity in genetic programming. In: Ryan, C., Soule, T., Keijzer, M., Tsang, E.P.K., Poli, R., Costa, E. (eds.) EuroGP 2003. LNCS, vol. 2610, pp. 254–263. Springer, Heidelberg (2003)

    Chapter  Google Scholar 

  4. Koza, J.R.: Genetic Programming II: Automatic Discovery of Reusable Programs. MIT Press, Cambridge (May 1994)

    MATH  Google Scholar 

  5. Schlosser, G., Wagner, G.E.: Modularity in Development and Evolution. University of Chicago Press, Chicago (2004)

    Google Scholar 

  6. Lathrop, J.I.: Compression depth and genetic programs. In: Koza, J.R., Deb, K., Dorigo, M., Fogel, D.B., Garzon, M., Iba, H., Riolo, R.L. (eds.) Genetic Programming 1997, Proceedings of the Second Annual Conference, Stanford University, CA, USA, 13-16 July 1997, pp. 370–379. Morgan Kaufmann, San Francisco (1997)

    Google Scholar 

  7. Svangard, N., Nordin, P.: Automated aesthetic selection of evolutionary art by distance based classification of genomes and phenomes using the universal similarity metric. In: Raidl, G.R., Cagnoni, S., Branke, J., Corne, D.W., Drechsler, R., Jin, Y., Johnson, C.G., Machado, P., Marchiori, E., Rothlauf, F., Smith, G.D., Squillero, G. (eds.) EvoWorkshops 2004. LNCS, vol. 3005, pp. 447–456. Springer, Heidelberg (2004)

    Google Scholar 

  8. Blickle, T., Thiele, L.: Genetic programming and redundancy. In: Hopf, J. (ed.) Genetic Algorithms within the Framework of Evolutionary Computation, Workshop at KI-94, Saarbrücken, Germany, pp. 33–38. Max-Planck-Institut für Informatik, Saarbrücken (MPI-I-94-241) (1994)

    Google Scholar 

  9. Mori, N., McKay, R., Nguyen, X., Essam, D.: How different are genetic programs: New methods for studying diversity and complexity in genetic programming (in preparation, 2007)

    Google Scholar 

  10. Cleary, J., Witten, I.: Data compression using adaptive coding and partial string matching. IEEE Transactions on Communications 32, 396–402 (1984)

    Article  Google Scholar 

  11. Ziv, J., Lempel, A.: Compression of individual sequences via variable-rate coding. IEEE Transactions on Information Theory 24, 530–536 (1978)

    Article  MATH  MathSciNet  Google Scholar 

  12. Cheney, J.: Compressing xml with multiplexed hierarchical models. In: IEEE Data Compression Conference, Snowbird, Utah, pp. 163–172. IEEE Computer Society Press, Los Alamitos (2002)

    Google Scholar 

  13. Hooper, D., Flann, N.S.: Improving the accuracy and robustness of genetic programming through expression simplification. In: Koza, J.R., et al. (eds.) Proceedings of the First Annual Conference: Genetic Programming 1996, Stanford University, CA, USA, 28–31 July, p. 428. MIT Press, Cambridge (1996)

    Google Scholar 

  14. Ekart, A.: Shorter fitness preserving genetic programs. In: Fonlupt, C., Hao, J.-K., Lutton, E., Schoenauer, M., Ronald, E. (eds.) AE 1999. LNCS, vol. 1829, pp. 73–83. Springer, Heidelberg (2000)

    Chapter  Google Scholar 

  15. Wong, P., Zhang, M.: Algebraic simplification of genetic programs during evolution. Technical Report CS-TR-06-7, Computer Science, Victoria University of Wellington, New Zealand (2006)

    Google Scholar 

  16. Hoai, N.X., McKay, R.I., Essam, D., Hao, H.T.: Genetic transposition in tree-adjoining grammar guided genetic programming: The duplication operator. In: Keijzer, M., Tettamanzi, A.G.B., Collet, P., van Hemert, J.I., Tomassini, M. (eds.) EuroGP 2005. LNCS, vol. 3447, pp. 18–119. Springer, Heidelberg (2005)

    Google Scholar 

  17. Hoang, T., Essam, D., McKay, R., Nguyen, X.: Developmental evaluation in genetic programming: A tag-based framework. In: Procceedings of the third Asia-Pacific Workshop on Genetic Programming, VietNam Military Technical Academy, Hanoi, VietNam, October 12-14 (2006)

    Google Scholar 

  18. Kang, M., Shin, J., Hoang, T., McKay, R., Essam, D., Mori, N., Nguyen, X.: Code duplication and developmental evaluation in genetic programming. In: 10th Asia-Pacific Workshop on Intelligent and Evolutionary Systems, Seoul, Korea (2006)

    Google Scholar 

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Marc Ebner Michael O’Neill Anikó Ekárt Leonardo Vanneschi Anna Isabel Esparcia-Alcázar

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Shin, J. et al. (2007). Analysing the Regularity of Genomes Using Compression and Expression Simplification. In: Ebner, M., O’Neill, M., Ekárt, A., Vanneschi, L., Esparcia-Alcázar, A.I. (eds) Genetic Programming. EuroGP 2007. Lecture Notes in Computer Science, vol 4445. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71605-1_23

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  • DOI: https://doi.org/10.1007/978-3-540-71605-1_23

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-71602-0

  • Online ISBN: 978-3-540-71605-1

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