用生成边增强关系感知,提升未知分子的蛋白-核酸互作预测能力
EGRL: Edge generation-guided relation-aware learning for RNA-protein interaction prediction

- 通过隐式关系学习与图生成器自动发现互作模式
- 冷启动场景下AUROC达0.867,优于现有方法8.6%
- 适合新药物靶点发现与稀疏数据场景
RNA-蛋白互作(RPI)在调控细胞功能中至关重要。传统湿实验成本高、耗时长,深度学习提供高效计算替代方案。图神经网络(GNN)因其天然建模能力备受关注,但现有方法多依赖同质图或预定义元路径,难以应对数据稀疏和冷启动问题。为此,提出边生成引导的关系感知学习框架EGRL:通过隐式元路径学习捕捉关系语义;设计多关系感知注意力机制自适应融合互作模式;引入图生成器预测潜在(软)边以支持冷启动节点;采用多特征融合预测器进行最终互作评分。EGRL联合主任务损失与辅助生成器损失训练。在四个基准数据集上评估显示,整体性能具有竞争力,尤其在冷启动场景表现优异:对未知分子的受试者工作特征曲线下面积(AUROC)达0.867,精确率-召回率曲线下面积(AUPR)达0.861,较先前最优方法分别提升8.6%和5.0%。代码将很快开源。
原文摘要 · Abstract (English)
RNA-Protein Interactions (RPIs) are critical for regulating cellular functions. While traditional wet-lab experiments for RPI detection are costly and time-consuming, Deep Learning (DL) methods provide an efficient computational alternative for RPI Prediction (RPIP). In particular, Graph Neural Networks (GNNs) are promising, as they naturally model RPI networks. However, existing GNN-based methods often rely on homogeneous graphs or predefined meta-paths, which limit their ability to handle data sparsity and to generalize to cold-start scenarios involving unknown molecules. To address these limitations, we propose Edge Generation-guided Relation-aware Learning (EGRL), a novel framework with several key components: implicit meta-path learning to capture relational semantics without handcrafted paths; a multi-relation-aware attention mechanism for adaptive fusion of interaction patterns; a graph generator that predicts potential ("soft") edges to support cold-start nodes; and a multi-feature fusion predictor for final interaction scoring. EGRL is jointly trained with a primary task loss and an auxiliary generator loss. Comprehensive evaluations on four benchmark datasets demonstrate that EGRL achieves competitive overall performance. More importantly, it exhibits superior generalization in cold-start settings, achieving an Area Under the Receiver Operating Characteristic curve (AUROC) of 0.867 and an Area Under the Precision-Recall curve (AUPR) of 0.861 on unknown molecules, corresponding to improvements of 8.6% in AUROC and 5.0% in AUPR over prior state-of-the-art methods. The code will be released soon.
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