用推理增强大模型预测药物审批,既准又透明。
DrugReasoner: Interpretable Drug Approval Prediction with a Reasoning-augmented Language Model
- 基于大模型构建推理系统,结合分子特征与相似化合物对比。
- 验证集AUC达0.732,测试集F1达0.718,优于传统方法。
- 输出可解释的推理链条,适合医药研发决策参考。
药物发现过程复杂且资源密集,早期预测审批结果对优化研发投入至关重要。尽管传统机器学习和深度学习在药物审批预测中展现潜力,但其可解释性不足限制了实际应用。本文提出DrugReasoner,一种基于LLaMA架构并使用组相对策略优化(GRPO)微调的推理型大语言模型,用于预测小分子药物的审批概率。DrugReasoner融合分子描述符,并通过与结构相似的已批准及未批准化合物进行比较推理,生成预测结果、逐步推理过程及置信度评分。在验证集上,DrugReasoner取得0.732的AUC和0.729的F1分数,在测试集上分别为0.725和0.718,优于逻辑回归、支持向量机和k近邻等传统基线模型,性能与XGBoost相当。在外部独立数据集上,其表现超越基线及近期提出的ChemAP模型,实现0.728的AUC和0.774的F1分数,同时保持高精确率与均衡敏感性,展现出在真实场景中的鲁棒性。结果表明,DrugReasoner不仅具备竞争力的预测精度,更通过可解释的推理输出提升透明度,解决了人工智能辅助药物研发中的关键瓶颈。本研究凸显了推理增强型大语言模型在可解释性与有效性方面的潜力,为制药决策提供新工具。
原文摘要 · Abstract (English)
Drug discovery is a complex and resource-intensive process, making early prediction of approval outcomes critical for optimizing research investments. While classical machine learning and deep learning methods have shown promise in drug approval prediction, their limited interpretability constraints their impact. Here, we present DrugReasoner, a reasoning-based large language model (LLM) built on the LLaMA architecture and fine-tuned with group relative policy optimization (GRPO) to predict the likelihood of small-molecule approval. DrugReasoner integrates molecular descriptors with comparative reasoning against structurally similar approved and unapproved compounds, generating predictions alongside step-by-step rationales and confidence scores. DrugReasoner achieved robust performance with an AUC of 0.732 and an F1 score of 0.729 on the validation set and 0.725 and 0.718 on the test set, respectively. These results outperformed conventional baselines, including logistic regression, support vector machine, and k-nearest neighbors and had competitive performance relative to XGBoost. On an external independent dataset, DrugReasoner outperformed both baseline and the recently developed ChemAP model, achieving an AUC of 0.728 and an F1-score of 0.774, while maintaining high precision and balanced sensitivity, demonstrating robustness in real-world scenarios. These findings demonstrate that DrugReasoner not only delivers competitive predictive accuracy but also enhances transparency through its reasoning outputs, thereby addressing a key bottleneck in AI-assisted drug discovery. This study highlights the potential of reasoning-augmented LLMs as interpretable and effective tools for pharmaceutical decision-making.
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