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Published Conference Proceedings - Paper
January 2006

Pertinent Background Knowledge for Learning Protein Grammars

Bryant, C & Fredouille, D & Wilson, A & Jayawickreme, C & Jupe, S & Topp, S 2006, Pertinent Background Knowledge for Learning Protein Grammars, in: Furnkranz, J & Scheffer, T & Spiliopoulou, M (eds.), 'Proceedings of the 17th European Conference on Machine Learning', Springer-Verlag, Berlin, Germany, pp.54-65.


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.


Lecture Notes in Artificial Intelligence, No. 4212


SEEK Members

External Authors

C.K. Jayawickreme

S. Jupe

D Fredouille

A Wilson

S. Topp


Non-SEEK Editors

T. Scheffer

M. Spiliopoulou

J. Furnkranz

Publication Details

Conference Proceedings
Bryant, C & Fredouille, & Wilson, & Jayawickreme, & Jupe, & Topp, eds. 2006, Proceedings of the 17th European Conference on Machine Learning, Springer-Verlag, Berlin, Germany, pp.54-65.