arXiv:2410.20182cs.LGcs.AI2024-10被引 2

用轻量适配器连接文本与分子模型,实现文本到分子的精准生成。

Chemical Language Model Linker: blending text and molecules with modular adapters

  • 通过少量适配参数融合预训练文本与分子模型,避免从头训练。
  • 使用SMILES表示时生成效果更优,即使不保证分子合法性。
  • 提供过滤后的PubChem数据集,支持更可信的生成评估。

大语言模型和多模态模型的发展使从文本描述生成新分子成为可能,有望改变依赖大规模化学筛选的范式。然而,现有融合文本与分子的多模态模型通常需从零训练,消耗大量计算资源且难以扩展。为此,本文提出轻量级适配器策略——化学语言模型链接器(ChemLML),在保持分子嵌入空间专一性的同时,实现基于文本描述的条件分子生成。ChemLML仅需微调少量适配参数,即可适配多种预训练文本模型。实验发现,分子表示方式(SMILES vs SELFIES)对生成性能影响显著,其中SMILES虽不保证分子有效性,但表现更优。本文还指出直接使用完整PubChem数据集进行生成评估存在偏差,并公开了一个经筛选的测试集。最后,通过生成候选蛋白抑制剂并进行对接评估,验证了ChemLML在实际应用中的潜力,成功生成具有膜渗透性的候选分子。

原文摘要 · Abstract (English)

The development of large language models and multi-modal models has enabled the appealing idea of generating novel molecules from text descriptions. Generative modeling would shift the paradigm from relying on large-scale chemical screening to find molecules with desired properties to directly generating those molecules. However, multi-modal models combining text and molecules are often trained from scratch, without leveraging existing high-quality pretrained models. Training from scratch consumes more computational resources and prohibits model scaling. In contrast, we propose a lightweight adapter-based strategy named Chemical Language Model Linker (ChemLML). ChemLML blends the two single domain models and obtains conditional molecular generation from text descriptions while still operating in the specialized embedding spaces of the molecular domain. ChemLML can tailor diverse pretrained text models for molecule generation by training relatively few adapter parameters. We find that the choice of molecular representation used within ChemLML, SMILES versus SELFIES, has a strong influence on conditional molecular generation performance. SMILES is often preferable despite not guaranteeing valid molecules. We raise issues in using the entire PubChem dataset of molecules and their associated descriptions for evaluating molecule generation and provide a filtered version of the dataset as a generation test set. To demonstrate how ChemLML could be used in practice, we generate candidate protein inhibitors and use docking to assess their quality and also generate candidate membrane permeable molecules.

分子生成多模态适配器SMILES

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