MRGBMDAT: A Multi-Relational Graph Encoder Network with Bilinear Fusion for miRNA-Disease Association Type Prediction

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ID: 321863
2026
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Abstract
MOTIVATION: MicroRNAs (miRNAs) are key post-transcriptional regulators involved in diverse biological processes, and their dysregulation is closely associated with the onset and progression of many diseases. Accurate prediction of miRNA-disease association types is therefore essential for understanding disease mechanisms and advancing precision medicine. Although computational methods provide efficient alternatives to wet-lab experiments, existing approaches often focus on binary association prediction, inadequately integrate local semantic dependencies and global topological structures, and suffer from class imbalance. RESULTS: To address these limitations, we propose MRGBMDAT, a multi-relational graph encoder network with bilinear fusion for miRNA-disease association type prediction. Specifically, a multi-relational graph convolution module with bidirectional cross-attention captures global topological structures, while a local subgraph sampling module extracts local semantic dependencies. A bilinear fusion decoder with element-wise attention jointly models their linear and nonlinear interactions. In addition, an iterative feature similarity-based negative sample selection strategy is introduced to alleviate class imbalance. Experimental results on the HMDD v3.2 dataset demonstrate that MRGBMDAT significantly outperforms five state-of-the-art methods across multiple evaluation metrics, exhibiting strong discriminative power and generalization capability. AVAILABILITY AND IMPLEMENTATION: The source code is publicly available at https://github.com/CDMBlab/MRGBMDAT. SUPPLEMENTARY INFORMATION: Supplementary material includes Sections S1-S3, providing additional details on the iterative negative sample selection strategy, dataset description and statistics, and evaluation metrics.
Reference Key
openalex_W7170086487 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Y W Sun, Wenjing Su, Siqi Zhu, Shijia Yan, Xuenan Shi, Junliang Shang, Jin-Xing Liu
Journal BMC Bioinformatics
Year 2026
DOI
10.1093/bioinformatics/btag534
URL
https://doi.org/10.1093/bioinformatics/btag534
Keywords Keywords not found

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