Momentum Contrast-Enhanced Multimodal Representation Learning for Drug Synergy Prediction

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ID: 321457
2026
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Abstract
MOTIVATION: Accurate prediction of synergistic drug combinations can accelerate anticancer combination discovery. Existing methods inadequately model higher-order drug-drug-cell-line interactions and drug-disease associations and remain sensitive to sparse and noisy multi-omics data, limiting generalization to unseen cell lines and drug combinations. RESULTS: We present MoCo-MultiSynergy, a multimodal framework that combines modality-specific momentum contrastive learning with heterogeneous hypergraph modeling. The hypergraph represents synergistic drug-drug-cell-line triplets and drug-disease associations, while gated residual propagation refines node representations. Momentum Contrast modules regularize encoded drug and cell-line representations using latent feature masking and Gaussian perturbation. On the O'Neil and NCI-ALMANAC datasets, MoCo-MultiSynergy achieves the highest AUROC and AUPRC across the evaluated settings, with the largest gains when generalizing to unseen cell lines and drug combinations. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/27167199/MoCo-MultiSynergy.
Reference Key
openalex_W7169533362 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Yu Gu, Xindi Huang, Lifen Shi, Le Chen, Guihua Duan, Cheng Yan
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag530
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