Semi-supervised Hierarchical Drug Embedding in Hyperbolic Space

Learning accurate drug representations is essential for tasks such as computational drug repositioning and prediction of drug side effects. A drug hierarchy is a valuable source that encodes knowledge of relations among drugs in a tree-like structure where drugs that act on the same organs, treat the same disease, or bind to the same biological target are grouped together. However, its utility in learning drug representations has not yet been explored, and currently described drug representations cannot place novel molecules in a drug hierarchy. Here, we develop a semi-supervised drug embedding that incorporates two sources of information: (1) underlying chemical grammar that is inferred from chemical structures of drugs and drug-like molecules (unsupervised) and (2) hierarchical relations that are encoded in an expert-crafted hierarchy of approved drugs (supervised). We use the Variational Auto-Encoder (VAE) framework to encode the chemical structures of molecules and use the drug-drug similarity information obtained from the hierarchy to induce the clustering of drugs in hyperbolic space. The hyperbolic space is amenable for encoding hierarchical relations. Both quantitative and qualitative results support that the learned drug embedding can accurately reproduce the chemical structure and recapitulate the hierarchical relations among drugs. Furthermore, our approach can infer the pharmacological properties of novel molecules by retrieving similar drugs from the embedding space. We demonstrate that our drug embedding can predict new uses and discover new side effects of existing drugs. We show that it significantly outperforms comparison methods in both tasks.