Using expert knowledge in initialization for genome-wide analysis of epistasis using genetic programming

Abstract

In human genetics it is now possible 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 may be examined as interacting DNA sequence variations. The machine learning challenge is to e.ectively explore interactions in these datasets to identify combinations of variations which are predictive of common human diseases. Genetic programming is a promising approach to this problem. The goal of this study is to examine the role that an expert knowledge aware initializer can play in the framework of genetic programming. We show that this expert knowledge aware initializer outperforms both a random initializer and an enumerative initializer.