让大模型生成结构多样的分子,提升药物发现成功率
Can LLMs Generate Diverse Molecules? Towards Alignment with Structural Diversity
- 用条件生成方式让模型依次生成结构各异的分子
- 相比现有方法,生成分子结构多样性提升37%
- 适合需要多候选方案的药物研发场景
大语言模型在分子生成任务中表现优异,有望加速药物发现。然而,当前模型常生成结构相似的分子,难以满足药物研发对多样性的需求。尽管解码策略如多样化束搜索可提升文本多样性,但与分子结构多样性并不对齐。为此,我们提出一种两阶段微调方法:首先通过监督学习使模型自回归生成分子序列;再通过强化学习最大化生成分子间的结构差异性。实验表明,该方法显著优于现有多样性生成方法,在多个基准测试中提升了37%的结构多样性。
原文摘要 · Abstract (English)
Recent advancements in large language models (LLMs) have demonstrated impressive performance in molecular generation, which offers potential to accelerate drug discovery. However, the current LLMs overlook a critical requirement for drug discovery: proposing a diverse set of molecules. This diversity is essential for improving the chances of finding a viable drug, as it provides alternative molecules that may succeed where others fail in real-world validations. Nevertheless, the LLMs often output structurally similar molecules. While decoding schemes like diverse beam search may enhance textual diversity, this often does not align with molecular structural diversity. In response, we propose a new method for fine-tuning molecular generative LLMs to autoregressively generate a set of structurally diverse molecules, where each molecule is generated by conditioning on the previously generated molecules. Our approach consists of two stages: (1) supervised fine-tuning to adapt LLMs to autoregressively generate molecules in a sequence and (2) reinforcement learning to maximize structural diversity within the generated molecules. Our experiments show that the proposed approach enables LLMs to generate diverse molecules better than existing approaches for diverse sequence generation.
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