A multiple kernel learning algorithm for drug-target interaction prediction

BMC Bioinformatics
André C A NascimentoIvan G Costa

Abstract

Drug-target networks are receiving a lot of attention in late years, given its relevance for pharmaceutical innovation and drug lead discovery. Different in silico approaches have been proposed for the identification of new drug-target interactions, many of which are based on kernel methods. Despite technical advances in the latest years, these methods are not able to cope with large drug-target interaction spaces and to integrate multiple sources of biological information. We propose KronRLS-MKL, which models the drug-target interaction problem as a link prediction task on bipartite networks. This method allows the integration of multiple heterogeneous information sources for the identification of new interactions, and can also work with networks of arbitrary size. Moreover, it automatically selects the more relevant kernels by returning weights indicating their importance in the drug-target prediction at hand. Empirical analysis on four data sets using twenty distinct kernels indicates that our method has higher or comparable predictive performance than 18 competing methods in all prediction tasks. Moreover, the predicted weights reflect the predictive quality of each kernel on exhaustive pairwise experiments, which indicates...Continue Reading

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Software Mentioned

SITAR
SIMCOMP
KRONRLS
NETLAPRLS
PKM
R Package Rchemcpp
KRONRL
KBMF
ChEMBL
BLM

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