arXiv:2602.00539cs.LG2026-02

构建首个统一的药物相互作用预测基准,解决数据与评估标准不一问题。

OpenDDI: A Comprehensive Benchmark for DDI Prediction

  • 整合6个主流数据集与多模态药物表示,新增3个大模型增强数据集。
  • 统一20个前沿模型在3项任务上的评估,涵盖质量、泛化、鲁棒性等维度。
  • 提供10条关键洞见,指导药物相互作用研究方向,适合算法与医药交叉研究者。

药物-药物相互作用(DDI)显著影响治疗效果与患者安全。由于实验发现成本高、耗时长,计算方法成为必要手段。当前主流方法将DDI预测建模为基于药物图的链接预测任务,但进展受限于两大挑战:(1) 数据质量不足:多数研究依赖小规模数据集与单模态药物表征;(2) 评估标准不统一:场景不一致、指标多样、基线差异大。为此,我们提出OpenDDI,一个全面的DDI预测基准。具体而言,(1) 从数据角度,统一6个常用DDI数据集与2种现有药物表征形式,并新增3个大规模大模型增强数据集及一种覆盖5个模态的多模态药物表征;(2) 从评估角度,统一20个最先进的模型基线,在3个下游任务上采用标准化协议,评估数据质量、有效性、泛化能力、鲁棒性与效率。基于OpenDDI,我们进行了全面评估,得出10条有价值洞见,揭示当前局限,为该快速发展的领域提供关键指引。代码已开源:https://github.com/xiaoriwuguang/OpenDDI。

原文摘要 · Abstract (English)

Drug-Drug Interactions (DDIs) significantly influence therapeutic efficacy and patient safety. As experimental discovery is resource-intensive and time-consuming, efficient computational methodologies have become essential. The predominant paradigm formulates DDI prediction as a drug graph-based link prediction task. However, further progress is hindered by two fundamental challenges: (1) lack of high-quality data: most studies rely on small-scale DDI datasets and single-modal drug representations; (2) lack of standardized evaluation: inconsistent scenarios, varied metrics, and diverse baselines. To address the above issues, we propose OpenDDI, a comprehensive benchmark for DDI prediction. Specifically, (1) from the data perspective, OpenDDI unifies 6 widely used DDI datasets and 2 existing forms of drug representation, while additionally contributing 3 new large-scale LLM-augmented datasets and a new multimodal drug representation covering 5 modalities. (2) From the evaluation perspective, OpenDDI unifies 20 SOTA model baselines across 3 downstream tasks, with standardized protocols for data quality, effectiveness, generalization, robustness, and efficiency. Based on OpenDDI, we conduct a comprehensive evaluation and derive 10 valuable insights for DDI prediction while exposing current limitations to provide critical guidance for this rapidly evolving field. Our code is available at https://github.com/xiaoriwuguang/OpenDDI

药物相互作用图神经网络多模态基准测试

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