arXiv:2512.05287cs.LG2025-12

用图注意力网络预测药物与微RNA关联,准确率超95%。

DMAGT: Unveiling miRNA-Drug Associations by Integrating SMILES and RNA Sequence Structures through Graph Transformer Models

  • 将药物和miRNA构建成图结构,用Transformer学习特征与关系
  • 在3个数据集上最高达95.24%的AUC,优于现有方法
  • 成功验证14个潜在关联,助力抗癌药靶点发现

由于miRNA在基因调控中的作用,靶向miRNA的药物研发成为新方向。但传统实验成本高、效率低,难以全面探索药物与miRNA的潜在关联。为此,我们提出基于多层图神经网络的DMAGT模型,将药物-miRNA关联转化为图结构,利用Word2Vec对药物分子结构和miRNA碱基序列进行嵌入,再通过图变换器模型学习嵌入特征与关系结构,最终预测关联。在ncDR、RNAInter、SM2miR三个数据集上测试,最大AUC达95.24±0.05。对比实验表明其性能更优。针对5-Fluorouracil和Oxaliplatin两种药物,从20个高置信度关联中成功验证了14个。结果表明,DMAGT在预测药物-miRNA关联方面具有优异性能与稳定性,为miRNA靶向药物开发提供新路径。

原文摘要 · Abstract (English)

MiRNAs, due to their role in gene regulation, have paved a new pathway for pharmacology, focusing on drug development that targets miRNAs. However, traditional wet lab experiments are limited by efficiency and cost constraints, making it difficult to extensively explore potential associations between developed drugs and target miRNAs. Therefore, we have designed a novel machine learning model based on a multi-layer transformer-based graph neural network, DMAGT, specifically for predicting associations between drugs and miRNAs. This model transforms drug-miRNA associations into graphs, employs Word2Vec for embedding features of drug molecular structures and miRNA base structures, and leverages a graph transformer model to learn from embedded features and relational structures, ultimately predicting associations between drugs and miRNAs. To evaluate DMAGT, we tested its performance on three datasets composed of drug-miRNA associations: ncDR, RNAInter, and SM2miR, achieving up to AUC of $95.24\pm0.05$. DMAGT demonstrated superior performance in comparative experiments tackling similar challenges. To validate its practical efficacy, we specifically focused on two drugs, namely 5-Fluorouracil and Oxaliplatin. Of the 20 potential drug-miRNA associations identified as the most likely, 14 were successfully validated. The above experiments demonstrate that DMAGT has an excellent performance and stability in predicting drug-miRNA associations, providing a new shortcut for miRNA drug development.

药物发现图神经网络miRNA预测模型

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