用刚性片段生成三维分子，速度更快且更紧凑。
3D Molecule Generation from Rigid Motifs via SE(3) Flows
- 将分子视为刚性片段集合，用SE(3)等变模型生成3D结构。
- 生成速度提升2至10倍，原子稳定性优于现有方法。
- 适合需要高效生成与压缩分子表示的药物设计场景。
三维分子结构生成通常以原子为单位进行，但分子图生成常以片段为单元。受基于框架的蛋白质结构生成启发，本文将碎片化思想拓展至三维分子，将一般分子视为刚性基团的集合。利用该表示，采用SE(3)等变生成建模实现从刚性片段出发的全新3D分子生成。在评估中，结果在多个基准上达到或超越当前最优水平，在GEOM-Drugs数据集上表现出更高的原子稳定性；同时生成步数减少2至10倍，分子表示压缩达3.5倍，相比标准原子级方法显著提升效率。
原文摘要 · Abstract (English)
Three-dimensional molecular structure generation is typically performed at the level of individual atoms, yet molecular graph generation techniques often consider fragments as their structural units. Building on the advances in frame-based protein structure generation, we extend these fragmentation ideas to 3D, treating general molecules as sets of rigid-body motifs. Utilising this representation, we employ SE(3)-equivariant generative modelling for de novo 3D molecule generation from rigid motifs. In our evaluations, we observe comparable or superior results to state-of-the-art across benchmarks, surpassing it in atom stability on GEOM-Drugs, while yielding a 2x to 10x reduction in generation steps and offering 3.5x compression in molecular representations compared to the standard atom-based methods.
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