Pertinent background knowledge for learning protein grammars

Abstract

We are interested in using Inductive Logic Programming (ILP) to infer grammars representing sets of protein sequences. ILP takes as input both examples and background knowledge predicates. This work is a first step in optimising the choice of background knowledge predicates for predicting the function of proteins. We propose methods to obtain different sets of background knowledge. We then study the impact of these sets on inference results through a hard protein function inference task: the prediction of the coupling preference of GPCR proteins. All but one of the proposed sets of background knowledge are statistically shown to have positive impacts on the predictive power of inferred rules, either directly or through interactions with other sets. In addition, this work provides further confirmation, after the work of Muggleton et al., 2001 that ILP can help to predict protein functions. © Springer-Verlag Berlin Heidelberg 2006.