title: Multi-class Mode of Action Classification of Toxic Compounds Using Logic Based Kernel Methods.
abstract: Toxicity prediction is essential for drug design and development of effective therapeutics. In this paper we present an in silico strategy, to identify the mode of action of toxic compounds, that is based on the use of a novel logic based kernel method. The technique uses support vector machines in conjunction with the kernels constructed from first order rules induced by an Inductive Logic Programming system. It constructs multi-class models by using a divide and conquer reduction strategy that splits multi-classes into binary groups and solves each individual problem recursively hence generating an underlying decision list structure. In order to evaluate the effectiveness of the approach for chemoinformatics problems like predictive toxicology, we apply it to toxicity classification in aquatic systems. The method is used to identify and classify 442 compounds with respect to the mode of action. The experimental results show that the technique successfully classifies toxic compounds and can be useful in assessing environmental risks. Experimental comparison of the performance of the proposed multi-class scheme with the standard multi-class Inductive Logic Programming algorithm and multi-class Support Vector Machine yields statistically significant results and demonstrates the potential power and benefits of the approach in identifying compounds of various toxic mechanisms.
authors.affiliation: School of Information Systems, Computing and Mathematics, Brunel University, Uxbridge, UB8 3 PH, UK. huma.lodhi@brunel.ac.uk.
authors.forename: Huma
authors.initials: H
authors.lastname: Lodhi
authors.affiliation: Department of Computing, Imperial College London, London, SW7 2AZ, UK.
authors.forename: Stephen
authors.initials: S
authors.lastname: Muggleton
authors.affiliation: Structural Bioinformatics Group, Division of Molecular, Biosciences, Imperial College London, London, SW7 2AZ, UK.
authors.forename: Mike J E
authors.initials: MJ
authors.lastname: Sternberg
keywords: Drug design; Inductive logic programming; Molecular modelling; Multi-class classification; Predictive toxicology; Support vector machines