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 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 not only achieves state-of-the-art performance in Davis and KIBA datasets but also reaches cutting-edge performance in the cross-domain applications across different bio-activity types and different protein classes. We also demonstrate that EnsembleDLM achieves a good performance (Pearson correlation coefficient and concordance index > 0.8) in the new domain with approximately 50% transfer learning data, i.e., the training set has twice as much data as the test set.

Toward Robust 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.