Toward Drug-Target Interaction Prediction via Ensemble Modeling and Transfer Learning.

Drug-target interaction (DTI) prediction plays a crucial role in drug discovery, and deep learning approaches have achieved state-of-the-art performance in this field. We introduce an ensemble of deep learning models (EnsembleDLM) for robust DTI prediction. EnsembleDLM only uses the sequence information of chemical compounds and proteins, and it aggregates the predictions from multiple deep neural networks. This approach reduces the chance of overfitting, yields an unbiased prediction, and achieves state-of-the-art performance in Davis and KIBA datasets. EnsembleDLM also reaches state-of-the-art performance in cross-domain applications and decent cross-domain performance (Pearson correlation coefficient and concordance index > 0.8) with transfer learning using approximately twice the amount of test data in the new domain.