title: SELF-BLM: Prediction of drug-target interactions via self-training SVM.
abstract: Predicting drug-target interactions is important for the development of novel drugs and the repositioning of drugs. To predict such interactions, there are a number of methods based on drug and target protein similarity. Although these methods, such as the bipartite local model (BLM), show promise, they often categorize unknown interactions as negative interaction. Therefore, these methods are not ideal for finding potential drug-target interactions that have not yet been validated as positive interactions. Thus, here we propose a method that integrates machine learning techniques, such as self-training support vector machine (SVM) and BLM, to develop a self-training bipartite local model (SELF-BLM) that facilitates the identification of potential interactions. The method first categorizes unlabeled interactions and negative interactions among unknown interactions using a clustering method. Then, using the BLM method and self-training SVM, the unlabeled interactions are self-trained and final local classification models are constructed. When applied to four classes of proteins that include enzymes, G-protein coupled receptors (GPCRs), ion channels, and nuclear receptors, SELF-BLM showed the best performance for predicting not only known interactions but also potential interactions in three protein classes compare to other related studies. The implemented software and supporting data are available at https://github.com/GIST-CSBL/SELF-BLM.
authors.affiliation: School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, 123 Cheomdangwgi-ro, Buk-gu, Gwangju, Republic of Korea.
authors.forename: Jongsoo
authors.initials: J
authors.lastname: Keum
authors.affiliation: School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology, 123 Cheomdangwgi-ro, Buk-gu, Gwangju, Republic of Korea.
authors.forename: Hojung
authors.initials: H
authors.lastname: Nam
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D006801:Humans; D020407:Internet; D008962:Models, Theoretical; D058990:Molecular Targeted Therapy / Q000379:methods; D004364:Pharmaceutical Preparations / Q000008:administration & dosage / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D011506:Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism*; D043562:Receptors, G-Protein-Coupled / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D015203:Reproducibility of Results; D060388:Support Vector Machine
chemical_list: D004364:Pharmaceutical Preparations; D011506:Proteins; D043562:Receptors, G-Protein-Coupled