Modeling Polypharmacy and Predicting Drug-Drug Interactions using Deep Generative Models on Multimodal Graphs

Abstract: Latent representations of drugs and their targets produced by contemporary graph autoencoder models have proved useful in predicting many types of node-pair interactions on large networks, including drug-drug, drug-target, and target-target interactions. However, most existing approaches model either the node's latent spaces in which node distributions are rigid or do not effectively capture the interrelations between drugs; these limitations hinder the methods from accurately predicting drug-pair interactions. In this paper, we present the effectiveness of variational graph autoencoders (VGAE) in modeling latent node representations on multimodal networks. Our approach can produce flexible latent spaces for each node type of the multimodal graph; the embeddings are used later for predicting links among node pairs under different edge types. To further enhance the models' performance, we suggest a new method that concatenates Morgan fingerprints, which capture the molecular structures of each drug, with their latent embeddings before preceding them to the decoding stage for link prediction. Our proposed model shows competitive results on three multimodal networks: (1) a multimodal graph consisting of drug and protein nodes, (2) a multimodal graph constructed from a subset of the DrugBank database involving drug nodes under different interaction types, and (3) a multimodal graph consisting of drug and cell line nodes. Our source code is publicly available at https://github.com/HySonLab/drug-interactions.