MVSGDR: multi-view stacked graph convolutional network for drug repositioning

Abstract

Abstract Drug repositioning (DR) presents a cost-effective strategy for drug development by identifying novel therapeutic applications for existing drugs. Current computational approaches remain constrained by their inability to synergize localized substructure patterns with global network semantics, leading to overreliance on data augmentation to mitigate latent drug–disease association (DDA) information gaps. To address these limitations, we present multi-view stacked graph convolutional network (MVSGDR), a novel DR framework featuring three technical innovations: (i) multi-view stacked module that enables depth-wise feature enhancement through hierarchical aggregation of multi-hop neighborhood interactions across distinct graph convolutional layers; (ii) bi-level subgraph transformer module that decomposes DDAs into METIS (a graph partitioning tool) informative subgraphs for breadth-wise analysis of external and internal subgraph drug–disease relationships; and (iii) negative sampling balancing strategy that mitigates sample imbalance through negative sample synthesis. Extensive 10-fold cross-validation experiments across four benchmark datasets confirm MVSGDR’s superior performance, demonstrating its statistically significant improvements over existing methods. Moreover, case studies further validate MVSGDR’s potential utility through identification of previously unreported DDAs with supporting literature evidence.