Theories for mutagenicity: a study in first-order and feature-based induction
Artificial Intelligence - Special volume on empirical methods
Discovering Patterns and Subfamilies in Biosequences
Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology
Verbumculus and the discovery of unusual words
Journal of Computer Science and Technology - Special issue on bioinformatics
An ILP Refinement Operator for Biological Grammar Learning
Inductive Logic Programming
L-Modified ILP Evaluation Functions for Positive-Only Biological Grammar Learning
ILP '08 Proceedings of the 18th international conference on Inductive Logic Programming
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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.