A Simple Genetic Algorithm for Biomarker Mining

  • Dusan Popovic
  • Alejandro Sifrim
  • Georgios A. Pavlopoulos
  • Yves Moreau
  • Bart De Moor
Part of the Lecture Notes in Computer Science book series (LNCS, 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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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Dusan Popovic
    • 1
  • Alejandro Sifrim
    • 1
  • Georgios A. Pavlopoulos
    • 1
  • Yves Moreau
    • 1
  • Bart De Moor
    • 1
  1. 1.ESAT-SCD / IBBT-KU Leuven Future Health DepartmentKatholieke Universiteit LeuvenLeuvenBelgium

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