arXiv:2410.03655cs.LGcs.AI2024-10ICML被引 15

通过几何表示条件提升分子生成质量,显著降低计算成本。

Geometric Representation Condition Improves Equivariant Molecule Generation

  • 分两阶段生成:先产几何表示,再据此生成分子。
  • 条件生成任务平均性能提升50%,100步扩散即可达1000步效果。
  • 适合需要高质量分子生成的药物设计场景。

近期分子生成模型在加速科学发现方面展现出巨大潜力,尤其在药物设计领域。然而,这些模型在生成高质量分子方面仍面临挑战,尤其是在需满足特定分子属性的条件下。本文提出GeoRCG框架,通过整合几何表示条件与可证明的理论保证,提升分子生成模型性能。将生成过程分为两阶段:首先生成信息丰富的几何表示,其次基于该表示生成分子。相比单阶段生成,第一阶段生成的易构造表示以目标导向方式引导第二阶段生成高质量分子。以EDM和SemlaFlow为基础生成器,在广泛使用的QM9和GEOM-DRUG数据集上,无条件生成质量显著提升。更关键的是,在具有挑战性的条件分子生成任务中,本框架相较当前最优方法平均性能提升50%;此外,借助表示引导,扩散步骤可减少至仅100步,同时基本保持1000步下的生成质量,大幅降低生成迭代次数。代码已开源。

原文摘要 · Abstract (English)

Recent advances in molecular generative models have demonstrated great promise for accelerating scientific discovery, particularly in drug design. However, these models often struggle to generate high-quality molecules, especially in conditional scenarios where specific molecular properties must be satisfied. In this work, we introduce GeoRCG, a general framework to improve molecular generative models by integrating geometric representation conditions with provable theoretical guarantees. We decompose the generation process into two stages: first, generating an informative geometric representation; second, generating a molecule conditioned on the representation. Compared with single-stage generation, the easy-to-generate representation in the first stage guides the second stage generation toward a high-quality molecule in a goal-oriented way. Leveraging EDM and SemlaFlow as base generators, we observe significant quality improvements in unconditional molecule generation on the widely used QM9 and GEOM-DRUG datasets. More notably, in the challenging conditional molecular generation task, our framework achieves an average 50\% performance improvement over state-of-the-art approaches, highlighting the superiority of conditioning on semantically rich geometric representations. Furthermore, with such representation guidance, the number of diffusion steps can be reduced to as small as 100 while largely preserving the generation quality achieved with 1,000 steps, thereby significantly reducing the generation iterations needed. Code is available at https://github.com/GraphPKU/GeoRCG.

分子生成几何表示扩散模型药物设计

Thank you to arXiv for use of its open access interoperability. PaperDance 不是 arXiv 官方产品;中文卡片由大模型生成,请以原文为准。