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IAPR International Conference on Pattern Recognition in Bioinformatics

PRIB 2012: Pattern Recognition in Bioinformatics pp 222–232Cite as

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  2. Pattern Recognition in Bioinformatics
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A Simple Genetic Algorithm for Biomarker Mining

A Simple Genetic Algorithm for Biomarker Mining

  • Dusan Popovic23,
  • Alejandro Sifrim23,
  • Georgios A. Pavlopoulos23,
  • Yves Moreau23 &
  • …
  • Bart De Moor23 
  • Conference paper
  • 1637 Accesses

  • 4 Citations

Part of the Lecture Notes in Computer Science book series (LNBI,volume 7632)

Abstract

We present a method for prognostics biomarker mining based on a genetic algorithm with a novel fitness function and a bagging-like model averaging scheme. We demonstrate it on publicly available data sets of gene expressions in colon cancer tissue specimens and assess the relevance of the discovered biomarkers by means of a qualitative analysis. Furthermore, we test performance of the method on the cancer recurrence prediction task using two independent external validation sets. The obtained results correspond to the top published performances of gene signatures developed specially for the colon cancer case.

Keywords

  • genetic algorithm
  • feature selection
  • biomarker discovery
  • gene expressions
  • colon
  • cancer
  • gene signature
  • k-nearest neighbours
  • bagging

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Author information

Authors and Affiliations

  1. ESAT-SCD / IBBT-KU Leuven Future Health Department, Katholieke Universiteit Leuven, Kasteelpark Arenberg 10, box 2446, 3001, Leuven, Belgium

    Dusan Popovic, Alejandro Sifrim, Georgios A. Pavlopoulos, Yves Moreau & Bart De Moor

Authors
  1. Dusan Popovic
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  2. Alejandro Sifrim
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  3. Georgios A. Pavlopoulos
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  4. Yves Moreau
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  5. Bart De Moor
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Editor information

Editors and Affiliations

  1. Institute of Medical Science, University of Tokyo, 4-6-1, Shirokanedai, 108-8639, Minato-ku, Tokyo, Japan

    Tetsuo Shibuya

  2. Department of Mathematical Informatics, The University of Tokyo, 7-3-1 Hongo, 113-8654, Bunkyo-ku, Tokyo, Japan

    Hisashi Kashima

  3. Department of Comouter Science, Tokyo Institute of Technology, 2-12-1 Ookayamama, 152-8550, Meguro-ku, Tokyo, Japan

    Jun Sese

  4. Bioinformatics Project, National Institute of Biomedical Innovation, 7-6-8 Saito-Asagi, 567-0085, Suita, Osaka, Japan

    Shandar Ahmad

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© 2012 Springer-Verlag Berlin Heidelberg

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Popovic, D., Sifrim, A., Pavlopoulos, G.A., Moreau, Y., De Moor, B. (2012). A Simple Genetic Algorithm for Biomarker Mining. In: Shibuya, T., Kashima, H., Sese, J., Ahmad, S. (eds) Pattern Recognition in Bioinformatics. PRIB 2012. Lecture Notes in Computer Science(), vol 7632. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-34123-6_20

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