arXiv:2502.12638q-bio.QMcs.LG2025-02ICLR被引 26

结合1D语言模型与3D扩散模型,生成高精度且化学有效的分子结构。

NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation

  • 先用1D SELFIES语言模型生成合法分子,再用3D扩散模型预测构象。
  • 在GEOM-DRUGS上实现26%的3D FCD提升,QM9-2014上平均增益13%。
  • 适合药物发现与材料设计领域,尤其关注分子结构生成质量的研究者。

三维分子生成对药物发现和材料设计至关重要。以往工作多聚焦于3D扩散模型以建模连续构象,但忽略了基于1D SELFIES的语言模型(LM)的优势——可生成100%合法分子,并利用大规模1D分子数据集。为此,我们提出基础模型NExT-Mol:将1D语言模型与3D扩散模型结合。NExT-Mol首先使用大规模预训练的分子语言模型生成1D分子表示,再通过3D扩散模型预测其三维构象。通过扩大语言模型规模、优化扩散神经架构及应用1D到3D迁移学习,显著提升性能。结果表明,该1D语言模型在分布相似性上优于基线且保证分子有效性,3D扩散模型在构象预测上达到领先水平。在GEOM-DRUGS数据集上,NExT-Mol实现26%的3D FCD相对提升;在QM9-2014数据集上,条件生成任务平均相对增益达13%。代码与预训练权重已开源。

原文摘要 · Abstract (English)

3D molecule generation is crucial for drug discovery and material design. While prior efforts focus on 3D diffusion models for their benefits in modeling continuous 3D conformers, they overlook the advantages of 1D SELFIES-based Language Models (LMs), which can generate 100% valid molecules and leverage the billion-scale 1D molecule datasets. To combine these advantages for 3D molecule generation, we propose a foundation model -- NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation. NExT-Mol uses an extensively pretrained molecule LM for 1D molecule generation, and subsequently predicts the generated molecule's 3D conformers with a 3D diffusion model. We enhance NExT-Mol's performance by scaling up the LM's model size, refining the diffusion neural architecture, and applying 1D to 3D transfer learning. Notably, our 1D molecule LM significantly outperforms baselines in distributional similarity while ensuring validity, and our 3D diffusion model achieves leading performances in conformer prediction. Given these improvements in 1D and 3D modeling, NExT-Mol achieves a 26% relative improvement in 3D FCD for de novo 3D generation on GEOM-DRUGS, and a 13% average relative gain for conditional 3D generation on QM9-2014. Our codes and pretrained checkpoints are available at https://github.com/acharkq/NExT-Mol.

分子生成扩散模型语言模型药物发现

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