Cold-Start Problems in Data-Driven Prediction of Drug–Drug Interaction Effects

Combining drugs, a phenomenon often referred to as polypharmacy, can induce additional adverse effects. The identification of adverse combinations is a key task in pharmacovigilance. In this context, in silico approaches based on machine learning are promising as they can learn from a limited number of combinations to predict for all. In this work, we identify various subtasks in predicting effects caused by drug–drug interaction. Predicting drug–drug interaction effects for drugs that already exist is very different from predicting outcomes for newly developed drugs, commonly called a cold-start problem. We propose suitable validation schemes for the different subtasks that emerge. These validation schemes are critical to correctly assess the performance. We develop a new model that obtains AUC-ROC [Formula: see text] for the hardest cold-start task up to AUC-ROC [Formula: see text] for the easiest one on the benchmark dataset of Zitnik et al. Finally, we illustrate how our predictions can be used to improve post-market surveillance systems or detect drug–drug interaction effects earlier during drug development.