Background: There has been paid more and more attention to supervised classification models in the area of predicting drug-target interactions (DTIs). However, in terms of classification, unavoidable missing DTIs in data would cause three issues which have not yet been addressed appropriately by former approaches. Directly labeled as negatives (non-DTIs), missing DTIs increase the confusion of positives (DTIs) and negatives, aggravate the imbalance between few positives and many negatives, and are usually discriminated as highly-scored false positives, which influence the existing measures sharply.
Results: Under the framework of local classification model (LCM), this work focuses on the scenario of predicting how possibly a new drug interacts with known targets. To address the first two issues, two strategies, Spy and Super-target, are introduced accordingly and further integrated to form a two-layer LCM. In the bottom layer, Spy-based local classifiers for protein targets are built by positives, as well as reliable negatives identified among unlabeled drug-target pairs. In the top layer, regular local classifiers specific to super-targets are built with more positives generated by grouping similar targets and their interactions. Furthermore, to handle the third issue, an additional performance measure, Coverage, is presented for assessing DTI prediction. The experiments based on benchmark datasets are finally performed under five-fold cross validation of drugs to evaluate this approach. The main findings are concluded as follows. (1) Both two individual strategies and their combination are effective to missing DTIs, and the combination wins the best. (2) Having the advantages of less confusing decision boundary at the bottom layer and less biased decision boundary at the top layer, our two-layer LCM outperforms two former approaches. (3) Coverage is more robust to missing interactions than other measures and is able to evaluate how far one needs to go down the list of targets to cover all the proper targets of a drug.
Conclusions: Proposing two strategies and one performance measure, this work has addressed the issues derived from missing interactions, which cause confusing and biased decision boundaries in classifiers, as well as the inappropriate measure of predicting performance, in the scenario of predicting interactions between new drugs and known targets.