META-DDIE: predicting drug–drug interaction events with few-shot learning

Abstract Drug–drug interactions (DDIs) are one of the major concerns in pharmaceutical research, and a number of computational methods have been developed to predict whether two drugs interact or not. Recently, more attention has been paid to events caused by the DDIs, which is more useful for investigating the mechanism hidden behind the combined drug usage or adverse reactions. However, some rare events may only have few examples, hindering them from being precisely predicted. To address the above issues, we present a few-shot computational method named META-DDIE, which consists of a representation module and a comparing module, to predict DDI events. We collect drug chemical structures and DDIs from DrugBank, and categorize DDI events into hundreds of types using a standard pipeline. META-DDIE uses the structures of drugs as input and learns the interpretable representations of DDIs through the representation module. Then, the model uses the comparing module to predict whether two representations are similar, and finally predicts DDI events with few labeled examples. In the computational experiments, META-DDIE outperforms several baseline methods and especially enhances the predictive capability for rare events. Moreover, META-DDIE helps to identify the key factors that may cause DDI events and reveal the relationship among different events.