Automated learning of a detector for the cores of a-helices in protein sequences via genetic programming   [GP]

by

Handley, S.

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Info: Proceedings of the 1994 IEEE World Congress on Computational Intelligence (Conference proceedings), 1994, p. 474-479
Keywords:genetic algorithms, genetic programming
Abstract:
I used Koza's genetic programming to evolve programs [GP] that classified contiguous regions of proteins as being a-helix cores or not. I snipped positive and negative examples of a-helix core regions out of a set of 90 proteins. These proteins were chosen from the Brookhaven Protein Data Bank to be non-homologous. The fitness of the programs was defined as the correlation coefficient between the observed and the predicted a-helicity of the above regions. The fittest program produced by the genetic programming system [GP] that predicted the training set at least as well as the testing set had a correlation of 0.4818 between the observed classifications and the classifications predicted by the program (on the proteins in the testing set).
URL(s):(G)zipped postscript

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BibTex:
@InProceedings{Handley:1994:alAHGP,
  author =       "S. Handley",
  title =        "Automated learning of a detector for the cores of
                 a-helices in protein sequences via genetic
                 programming",
  booktitle =    "Proceedings of the 1994 IEEE World Congress on
                 Computational Intelligence",
  year =         "1994",
  volume =       "1",
  pages =        "474--479",
  address =      "Orlando, Florida, USA",
  month =        "27-29 " # jun,
  publisher =    "IEEE Press",
  URL =          "http://www-leland.stanford.edu/~shandley/postscript/helix_segments_paper.ps.gz",
  keywords =     "genetic algorithms, genetic programming",
  size =         "6 pages",
  abstract =     "I used Koza's genetic programming to evolve programs
                 that classified contiguous regions of proteins as being
                 a-helix cores or not. I snipped positive and negative
                 examples of a-helix core regions out of a set of 90
                 proteins. These proteins were chosen from the
                 Brookhaven Protein Data Bank to be non-homologous. The
                 fitness of the programs was defined as the correlation
                 coefficient between the observed and the predicted
                 a-helicity of the above regions. The fittest program
                 produced by the genetic programming system that
                 predicted the training set at least as well as the
                 testing set had a correlation of 0.4818 between the
                 observed classifications and the classifications
                 predicted by the program (on the proteins in the
                 testing set).",
}