融合序列、图谱和3D结构,提升药物靶点相互作用预测精度
A Triple-Modal Contrastive Learning Framework with Sequence, Graph, and 3D Features for Drug-Target Interaction Prediction

- 构建三模态对比学习框架,整合药物与蛋白的序列、图谱和3D结构特征
- 在三个基准数据集上均超越现有方法,显著提升预测性能
- 适用于新药研发中的靶点识别,尤其适合需多维度结构信息的场景
准确预测药物-靶点相互作用(DTI)对药物发现至关重要。现有方法通常依赖单一模态表示(如序列或图谱),或仅结合两种模态,忽略了3D结构特征。为此,我们提出TriMod-DTI,一种融合药物与蛋白1D序列、2D图谱和3D结构的三模态对比学习框架,获得通用且互补的特征表示。设计特征提取器以跨三模态捕获药物与靶点特征,丰富其表征。进一步提出三模态对比学习策略,在潜在空间中对齐同一分子在不同模态下的表示。通过构建跨模态正负样本对,增强模型判别能力。在三个基准数据集上的实验表明,TriMod-DTI优于当前最先进方法。消融实验证实各模态的贡献。案例研究进一步展示其在DTI预测与药物发现中的实际潜力。
原文摘要 · Abstract (English)
Accurate prediction of drug-target interactions (DTI) is critical for drug discovery. Existing methods often rely on single-modal representations (e.g., sequences or graphs) or combine only two modalities, overlooking 3D structural features. To address this challenge, we propose TriMod-DTI, a triple-modal contrastive learning framework that incorporates 1D sequences, 2D graphs, and 3D structures of drugs and proteins, obtaining the universal and complementary feature representations for DTI prediction. We design a Feature Extractor to capture drug and target features across the three modalities, thereby enriching their representations. We further propose a triple-modal contrastive learning strategy to align different modal representations of the same drug or protein in the latent space. By constructing cross-modal positive and negative sample pairs, this approach enhances the model's discriminative ability. Experiments on three benchmark datasets demonstrate that TriMod-DTI outperforms state-of-the-art methods. The ablation studies validate the contributions of each modality. Moreover, case studies highlight its practical potential for DTI prediction and drug discovery.
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