title: A multiple kernel learning algorithm for drug-target interaction prediction.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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 the success of the method to automatically reveal relevant biological sources.
  
  
  CONCLUSIONS
  Our analysis show that the proposed data integration strategy is able to improve the quality of the predicted interactions, and can speed up the identification of new drug-target interactions as well as identify relevant information for the task.
  
  
  BACKGROUND
  The source code and data sets are available at www.cin.ufpe.br/~acan/kronrlsmkl/.
authors.affiliation: Center of Informatics, UFPE, Recife, Brazil. acan@cin.ufpe.br.|Department of Statistics and Informatics, UFRPE, Recife, Brazil. acan@cin.ufpe.br.|IZKF Computational Biology Research Group, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany. acan@cin.ufpe.br.
authors.forename: André C A
authors.initials: AC
authors.lastname: Nascimento
authors.affiliation: Center of Informatics, UFPE, Recife, Brazil. rbcp@cin.ufpe.br.
authors.forename: Ricardo B C
authors.initials: RB
authors.lastname: Prudêncio
authors.affiliation: Center of Informatics, UFPE, Recife, Brazil. ivan.costa@rwth-aachen.de.|IZKF Computational Biology Research Group, Institute for Biomedical Engineering, RWTH Aachen University Medical School, Aachen, Germany. ivan.costa@rwth-aachen.de.|Aachen Institute for Advanced Study in Computational Engineering Science (AICES), RWTH Aachen University, Aachen, Germany. ivan.costa@rwth-aachen.de.
authors.forename: Ivan G
authors.initials: IG
authors.lastname: Costa
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D016208:Databases, Factual; D016503:Drug Delivery Systems / Q000379:methods*; D036262:Empirical Research; D006801:Humans; D008962:Models, Theoretical; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry
chemical_list: D011506:Proteins