Ant colony optimization for genome-wide genetic analysis

Abstract

In human genetics it is now feasible to measure large numbers of DNA sequence variations across the human genome. Given current knowledge about biological networks and disease processes it seems likely that disease risk can best be modeled by interactions between biological components, which can be examined as interacting DNA sequence variations. The machine learning challenge is to effectively explore interactions in these datasets to identify combinations of variations which are predictive of common human diseases. Ant colony optimization (ACO) is a promising approach to this problem. The goal of this study is to examine the usefulness of ACO for problems in this domain and to develop a prototype of an expert knowledge guided probabilistic search wrapper. We show that an ACO approach is not successful in the absence of expert knowledge but is successful when expert knowledge is supplied through the pheromone updating rule. © 2008 Springer-Verlag Berlin Heidelberg.