Sign-aware Graph Contrastive Learning for Drug Repositioning.
Journal:
IEEE journal of biomedical and health informatics
Published Date:
May 20, 2025
Abstract
Drug repositioning, which identifies new therapeutic potential of approved drugs, is pivotal in accelerating drug discovery. Recently, growing efforts are devoted to applying graph neural networks (GNNs) for effectively modeling drug-disease associations (DDAs). However, current GNN-based methods are generally designed for unsigned graphs and fail to gain complementary insights provided by negative links. Despite the proposal of sign-aware GNNs in general fields, there exist two intractable challenges when indiscriminately deploying prior solutions into drug repositioning. (i) How to explicitly connect the nodes within the same set (disease-disease and drug-drug)? (ii) How to design the contrastive learning objective for signed graphs? To this end, we propose a novel sign-aware graph contrastive learning approach, namely SIGDR, which takes both the positive and negative links from signed biological networks into consideration to identify underlying DDAs. To handle the first challenge, we measure the drug and disease similarity and form signed unipartite graphs according to similarity scores. For the second challenge, a signed bipartite graph is then constructed from the annotated DDA dataset. Through dividing above obtained signed graphs into positive and negative subgraphs respectively, we devise the inter-view contrastive learning auxiliary task to enhance the consistency of node representations derived from partitioned subgraphs with the same link type. Extensive experiments conducted on three benchmarks under 10-fold cross-validation demonstrate the model effectiveness. Source code and datasets are available at https://github.com/OleCui/paper_SIGDR.
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