基于精确转动惯量约束生成分子3D结构,提升解析精度与效率
Stiefel Flow Matching for Moment-Constrained Structure Elucidation
- 在Stiefel流形上构建生成模型,严格满足转动惯量约束
- 相比传统方法,对大分子在GEOM数据集上成功率更高、采样更快
- 适合需要高精度分子结构解析的化学与天体化学研究者
分子结构解析是理解化学现象的基础,应用于天然产物、合成样品、法医样本及星际介质中的分子识别。本文研究仅凭分子式和转动惯量矩预测全原子3D结构的任务,源于旋转光谱可精确测量这些矩。现有生成模型虽能近似满足转动惯量条件,但未能利用实验提供的多位数精度。我们首次证明:具有固定转动惯量的n原子点云空间嵌入于Stiefel流形St(n,4)。为此提出Stiefel Flow Matching生成模型,实现精确约束下的结构解析。同时,通过求解在Stiefel流形上的等变最优传输近似解,学习更简洁高效的生成流。实验表明,强制精确约束的模型在高维流形(如GEOM数据集中的大分子)上,比欧氏扩散模型具有更高的成功率达和更快的采样速度。
原文摘要 · Abstract (English)
Molecular structure elucidation is a fundamental step in understanding chemical phenomena, with applications in identifying molecules in natural products, lab syntheses, forensic samples, and the interstellar medium. We consider the task of predicting a molecule's all-atom 3D structure given only its molecular formula and moments of inertia, motivated by the ability of rotational spectroscopy to measure these moments. While existing generative models can conditionally sample 3D structures with approximately correct moments, this soft conditioning fails to leverage the many digits of precision afforded by experimental rotational spectroscopy. To address this, we first show that the space of $n$-atom point clouds with a fixed set of moments of inertia is embedded in the Stiefel manifold $\mathrm{St}(n, 4)$. We then propose Stiefel Flow Matching as a generative model for elucidating 3D structure under exact moment constraints. Additionally, we learn simpler and shorter flows by finding approximate solutions for equivariant optimal transport on the Stiefel manifold. Empirically, enforcing exact moment constraints allows Stiefel Flow Matching to achieve higher success rates and faster sampling than Euclidean diffusion models, even on high-dimensional manifolds corresponding to large molecules in the GEOM dataset.
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