用图像增强分子片段序列,提升药物相互作用预测精度
ImageDDI: Image-enhanced Molecular Motif Sequence Representation for Drug-Drug Interaction Prediction
- 将分子拆分为功能片段,结合局部与全局图像信息建模
- 在多个数据集上超越现有最优模型,2D/3D图像增强均表现优异
- 适合药物研发中需要精准预测副作用的场景
为减少多药联用带来的意外副作用和相互作用风险,准确识别和预测药物-药物相互作用(DDI)成为深度学习领域的重要任务。现有方法受限于功能片段表示学习能力不足,因DDI本质源于片段间的相互作用,而非整体分子结构。本文提出ImageDDI框架,通过全局与局部结构联合表征一对药物:先将分子分段为功能片段,构建序列并使用基于Transformer的编码器进行嵌入;再融合分子图像中的纹理、阴影、颜色及平面空间关系等全局视觉信息,增强空间表征。通过自适应特征融合机制,动态调整视觉与序列特征的融合过程,提升模型泛化能力。实验表明,ImageDDI在多个公开数据集上优于当前最优方法,且在2D与3D图像增强场景下均保持竞争力。
原文摘要 · Abstract (English)
To mitigate the potential adverse health effects of simultaneous multi-drug use, including unexpected side effects and interactions, accurately identifying and predicting drug-drug interactions (DDIs) is considered a crucial task in the field of deep learning. Although existing methods have demonstrated promising performance, they suffer from the bottleneck of limited functional motif-based representation learning, as DDIs are fundamentally caused by motif interactions rather than the overall drug structures. In this paper, we propose an Image-enhanced molecular motif sequence representation framework for \textbf{DDI} prediction, called ImageDDI, which represents a pair of drugs from both global and local structures. Specifically, ImageDDI tokenizes molecules into functional motifs. To effectively represent a drug pair, their motifs are combined into a single sequence and embedded using a transformer-based encoder, starting from the local structure representation. By leveraging the associations between drug pairs, ImageDDI further enhances the spatial representation of molecules using global molecular image information (e.g. texture, shadow, color, and planar spatial relationships). To integrate molecular visual information into functional motif sequence, ImageDDI employs Adaptive Feature Fusion, enhancing the generalization of ImageDDI by dynamically adapting the fusion process of feature representations. Experimental results on widely used datasets demonstrate that ImageDDI outperforms state-of-the-art methods. Moreover, extensive experiments show that ImageDDI achieved competitive performance in both 2D and 3D image-enhanced scenarios compared to other models.
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