无需微调,用多个AI智能体协作实现药物发现的高效检索生成。
RAG-Enhanced Collaborative LLM Agents for Drug Discovery
- 多智能体协作动态检索生物医学知识库,结合分子上下文生成答案。
- 在多种药物发现任务中超越通用与领域专用模型及传统深度学习方法。
- 适合需要快速整合科学数据、处理复杂开放问题的研究者使用。
大语言模型(LLMs)在加速药物发现方面展现出巨大潜力,但生化数据的专业性通常需要昂贵的领域特定微调,限制了通用模型的应用,并阻碍了实验与研究中持续生成的海量科学数据的快速整合。现实中的科学问题往往复杂且开放,超出模式匹配或静态知识检索的范畴。为此,我们提出CLADD,一个基于检索增强生成(RAG)的代理系统,专为药物发现任务设计。通过多个LLM智能体协作,CLADD能动态从生物医学知识库中检索信息,对查询分子进行上下文建模,并整合相关证据生成响应,无需领域微调。关键在于,我们解决了在生化数据中应用RAG工作流时面临的数据异构性、模糊性和多源集成等挑战。我们在多种药物发现任务中验证了该框架的灵活性与有效性,结果表明其性能优于通用和领域专用模型以及传统深度学习方法。代码已公开于https://github.com/Genentech/CLADD。
原文摘要 · Abstract (English)
Recent advances in large language models (LLMs) have shown great potential to accelerate drug discovery. However, the specialized nature of biochemical data often necessitates costly domain-specific fine-tuning, posing major challenges. First, it hinders the application of more flexible general-purpose LLMs for cutting-edge drug discovery tasks. More importantly, it limits the rapid integration of the vast amounts of scientific data continuously generated through experiments and research. Compounding these challenges is the fact that real-world scientific questions are typically complex and open-ended, requiring reasoning beyond pattern matching or static knowledge retrieval.To address these challenges, we propose CLADD, a retrieval-augmented generation (RAG)-empowered agentic system tailored to drug discovery tasks. Through the collaboration of multiple LLM agents, CLADD dynamically retrieves information from biomedical knowledge bases, contextualizes query molecules, and integrates relevant evidence to generate responses - all without the need for domain-specific fine-tuning. Crucially, we tackle key obstacles in applying RAG workflows to biochemical data, including data heterogeneity, ambiguity, and multi-source integration. We demonstrate the flexibility and effectiveness of this framework across a variety of drug discovery tasks, showing that it outperforms general-purpose and domain-specific LLMs as well as traditional deep learning approaches. Our code is publicly available at https://github.com/Genentech/CLADD.
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