Optimal Use of Expert Knowledge in Ant Colony Optimization for the Analysis of Epistasis in Human Disease

  • Casey S. Greene
  • Jason M. Gilmore
  • Jeff Kiralis
  • Peter C. Andrews
  • Jason H. Moore
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5483)

Abstract

The availability of chip-based technology has transformed human genetics and made routine the measurement of thousands of DNA sequence variations giving rise to an informatics challenge. This challenge is the identification of combinations of interacting DNA sequence variations predictive of common diseases. We have previously developed Multifactor Dimensionality Reduction (MDR), a method capable of detecting these interactions, but an exhaustive MDR analysis is exponential in time complexity and thus unsuitable for an interaction analysis of genome-wide datasets. Therefore we look to stochastic search approaches to find a suitable wrapper for the analysis of these data. We have previously shown that an ant colony optimization (ACO) framework can be successfully applied to human genetics when expert knowledge is included. We have integrated an ACO stochastic search wrapper into the open source MDR software package. In this wrapper we also introduce a scaling method based on an exponential distribution function with a single user-adjustable parameter. Here we obtain expert knowledge from Tuned ReliefF (TuRF), a method capable of detecting attribute interactions in the absence of main effects, and perform a power analysis at different parameter settings. We show that the expert knowledge distribution parameter, the retention factor, and the weighting of expert knowledge significantly affect the power of the method.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Casey S. Greene
    • 1
  • Jason M. Gilmore
    • 1
  • Jeff Kiralis
    • 1
  • Peter C. Andrews
    • 1
  • Jason H. Moore
    • 1
  1. 1.Dartmouth CollegeLebanonUSA

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