Evidential Deep Learning for Guided Drug-Target Interaction Prediction

Drug-target interaction (DTI) prediction is a crucial component of drug discovery. Recent deep learning methods show great potential in this field but also encounter substantial challenges. These include generating reliable confidence estimates for predictions, enhancing robustness when handling novel, unseen DTIs, and mitigating the tendency toward overconfident and incorrect predictions. To solve these problems, we propose EviDTI, a novel approach utilizing evidential deep learning (EDL) for uncertainty quantification in neural network-based DTI prediction. EviDTI integrates multiple data dimensions, including drug 2D topological graphs and 3D spatial structures, and target sequence features. Through EDL, EviDTI provides uncertainty estimates for its predictions. Experimental results on three benchmark datasets demonstrated the competitiveness of EviDTI against five state-of-the-art baseline models. In addition, our study shows that EviDTI can calibrate prediction errors. More importantly, well-calibrated uncertainty information enhanced the efficiency of drug discovery by prioritizing DTIs with higher confident predictions for experimental validation. In a case study focused on tyrosine kinase inhibitors (TKIs), uncertainty-guided predictions identified novel potential inhibitors targeting FAK and FLT3. These results underscore the potential of evidential deep learning as a robust tool for uncertainty quantification in DTI prediction and its broader implications for accelerating drug discovery.