Inferring potential adverse drug reactions is an important and challenging task for the drug discovery and healthcare industry. Many previous studies in computational pharmacology have proposed utilizing multi-source drug information to predict drug side effects have and achieved initial success. However, most of the prediction methods mainly rely on direct similarities inferred from drug information and cannot fully utilize the drug information about the impact of protein–protein interactions (PPI) on potential drug targets. Moreover, most of the methods are designed for specific tasks. In this work, we propose a novel heterogeneous network embedding approach for learning drug representations called SDHINE, which integrates PPI information into drug embeddings and is generic for different adverse drug reaction (ADR) prediction tasks. To integrate heterogeneous drug information and learn drug representations, we first design different meta-path-based proximities to calculate drug similarities, especially target propagation meta-path-based proximity based on PPI network, and then construct a semi-supervised stacking deep neural network model that is jointly optimized by the defined meta-path proximities. Extensive experiments with three state-of-the-art network embedding methods on three ADR prediction tasks demonstrate the effectiveness of the SDHINE model. Furthermore, we compare the drug representations in terms of drug differentiation by mapping the representations into 2D space; the results show that the performance of our approach is superior to that of the comparison methods.
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