Measuring Performance when Positives are Rare

S. H. Muggleton, C.H. Bryant, and A. Srinivasan

This paper presents a new method of measuring performance when positives are rare and investigates whether Chomskylike grammar representations are useful for learning accurate comprehensible predictors of members of biological sequence families. The positive-only learning framework of the Inductive Logic Programming (ILP) system CProgol is used to generate a grammar for recognising a class of proteins known as human neuropeptide precursors (NPPs). As far as these authors are aware, this is both the first biological grammar learnt using ILP and the first real-world scientific application of the positive-only learning framework of CProgol. Performance is measured using both predictive accuracy and a new cost function, Relative Advantage (RA). The RA results show that searching for NPPs by using our best NPP predictor as a filter is more than 100 times more efficient than randomly selecting proteins for synthesis and testing them for biological activity. The highest RAwas achieved by amodel which includes grammar-derived features. This RA is significantly higher than the best RA achieved without the use of the grammar-derived features.

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