提出可解释的假说生成框架,提升药物肝损伤预测的透明度与机制洞察。
An explainable hypothesis-driven approach to Drug-Induced Liver Injury with HADES

- 构建假说驱动的预测框架,结合分子特征与毒性通路证据。
- 在测试集上达0.68的ROC-AUC,优于现有模型,且在新数据上仍具稳定性。
- 适合需要可解释性决策的药物研发人员,推动精准毒理学发展。
药物诱导肝损伤(DILI)仍是临床试验中后期失败的主要原因。现有计算模型多依赖二分类任务,限制了泛化能力,且缺乏机制解释以支持转化决策。本文主张将DILI预测视为可解释的假说生成问题。为此,我们构建了DILER基准数据集,通过文献挖掘为精选分子添加机制性肝毒性假说。进一步提出HADES系统,一个能生成透明可审计推理链条的智能体,整合分子级预测、代谢物分解、结构理解及毒性通路证据,实现机制性DILI风险评估。在DILER基准上,HADES在二分类任务中表现更优:测试集ROC-AUC为0.68(对比DILI-Predictor的0.63),2021年后数据集为0.59(对比0.50)。更重要的是,首次建立机制假说生成基线,HADES获得0.16的假说对齐模糊杰卡德指数,揭示该任务的复杂性,并凸显可解释方法在预测毒理学中的必要性。
原文摘要 · Abstract (English)
Drug-induced liver injury (DILI) remains a leading cause of late-stage clinical trial attrition. However, existing computational predictors primarily rely on binary classification, a framing that limits generalization and yields no mechanistic insight to guide translational decisions. We argue that DILI prediction is better posed as an explainable hypothesis-generation problem. To support this shift, we introduce the DILER Benchmark, a dataset that extends beyond binary labels by augmenting a curated set of molecules with mechanistic hepatotoxicity hypotheses derived from biomedical literature. We further present HADES, an agentic system designed to generate transparent and auditable reasoning traces. By combining molecular-level predictions, metabolite decomposition, structural understanding, and toxicity pathway evidence, HADES mechanistically assesses DILI risk. Evaluated on the DILER Benchmark, HADES outperforms existing models in binary classification, achieving a ROC-AUC of 0.68 on the Test Set and 0.59 on the challenging Post-2021 Set, compared with 0.63 and 0.50 for DILI-Predictor, respectively. More importantly, we establish a baseline for mechanistic hypothesis generation, where HADES achieves a Hypothesis Alignment Fuzzy Jaccard Index of 0.16. This result underscores the inherent complexity of the task while highlighting the need for advanced explainable approaches in predictive toxicology.
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