用多维特征融合与注意力机制预测药物协同作用,提升抗癌治疗潜力。
MD-Syn: Synergistic drug combination prediction based on the multidimensional feature fusion method and attention mechanisms
- 融合一维和二维特征,通过注意力机制捕捉关键交互信息。
- 5折交叉验证下AUROC达0.919,优于现有方法。
- 模型可解释性强,适合药物研发人员快速筛选有效组合。
联合用药在复杂疾病治疗中展现出良好疗效,并有望降低耐药性。然而,药物组合数量庞大,传统实验难以全面筛选。本文提出MD-Syn,一种基于多维特征融合与多头注意力机制的计算框架。给定药物对-细胞系三元组,该模型同时考虑一维与二维特征空间,包含一维特征嵌入模块(1D-FEM)、二维特征嵌入模块(2D-FEM)及深度神经网络分类器,用于协同药物组合预测。在5折交叉验证中,MD-Syn的AUROC达到0.919,优于当前最优方法;在两个独立数据集上亦表现稳定。多头注意力机制不仅学习不同特征维度的表示,还能聚焦关键交互特征,增强模型可解释性。总结而言,MD-Syn是一种可解释的框架,可结合化学物质与癌细胞系基因表达谱,优先筛选协同药物对。为促进社区使用,我们开发了在线预测门户(https://labyeh104-2.life.nthu.edu.tw/),支持用户自定义化合物进行协同效应预测。
原文摘要 · Abstract (English)
Drug combination therapies have shown promising therapeutic efficacy in complex diseases and have demonstrated the potential to reduce drug resistance. However, the huge number of possible drug combinations makes it difficult to screen them all in traditional experiments. In this study, we proposed MD-Syn, a computational framework, which is based on the multidimensional feature fusion method and multi-head attention mechanisms. Given drug pair-cell line triplets, MD-Syn considers one-dimensional and two-dimensional feature spaces simultaneously. It consists of a one-dimensional feature embedding module (1D-FEM), a two-dimensional feature embedding module (2D-FEM), and a deep neural network-based classifier for synergistic drug combination prediction. MD-Syn achieved the AUROC of 0.919 in 5-fold cross-validation, outperforming the state-of-the-art methods. Further, MD-Syn showed comparable results over two independent datasets. In addition, the multi-head attention mechanisms not only learn embeddings from different feature aspects but also focus on essential interactive feature elements, improving the interpretability of MD-Syn. In summary, MD-Syn is an interpretable framework to prioritize synergistic drug combination pairs with chemicals and cancer cell line gene expression profiles. To facilitate broader community access to this model, we have developed a web portal (https://labyeh104-2.life.nthu.edu.tw/) that enables customized predictions of drug combination synergy effects based on user-specified compounds.
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