arXiv:2606.03199cs.LGphysics.chem-ph2026-06被引 2

Clari模型将有机晶体结构预测速度提升至秒级,突破传统方法瓶颈。

Fast Organic Crystal Structure Prediction with Unit Cell Flow Matching

论文配图:Fast Organic Crystal Structure Prediction with Unit Cell Flow Matching
图 1 · 摘自论文原文
  • 基于流匹配生成无冗余晶胞,用对位注意力替代三角层
  • 在测试集上解决率超越OXtal,速度提升15-30倍
  • 支持含氢建模与能量排序,适合复杂分子虚拟筛选

有机晶体结构预测(CSP)是有机固态计算模拟的关键,但传统方法每分子需数年CPU时间。生成模型OXtal虽大幅降低开销,但依赖昂贵的三角层建模大块材料,每分子耗时数分钟。本文提出Clari——一个大规模流匹配模型,通过纯对位偏置注意力取代三角层,仅需原子类型和键信息输入,无需RDKit可处理分子,适用于富勒烯、金属配合物等复杂体系。在OXtal测试集上,Clari解决率更高,速度提升15-30倍;因显式建模氢原子,可直接通过能量排序实现推理时缩放,生成150个晶胞选前30名后,解决率进一步提升,仍保持5-8倍加速。我们还引入CSD Teaching Subset作为新测试集以供未来基准。该工作使有机固体的大规模虚拟筛选成为可能。代码已开源。

原文摘要 · Abstract (English)

Organic crystal structure prediction (CSP) is a requirement for computational modelling of organic solids, but traditionally costs several CPU-years per molecule. Generative models such as OXtal dramatically reduce this cost by sampling stable organic crystal structures directly. However, OXtal forgoes explicit lattice parametrization in favour of modelling large crops of the bulk material with expensive triangle layers, which can incur a computational cost of minutes per molecule. In this paper, we reduce this to seconds with Clari, a large-scale flow matching model that generates redundancy-free unit cells and replaces triangle layers with pure pair-bias attention. Clari requires only atom types and bonds as input and does not need an RDKit-sanitizable input molecule, which expands its applicability to challenging chemistries such as fullerenes, metal complexes, and atom clusters. We further ablate key design choices such as auxiliary losses, timestep distributions, noise priors, and self-conditioning. On OXtal's test sets, we surpass OXtal's solve rate while obtaining a speedup of $15$-$30\times$. Because Clari also models explicit hydrogens, it supports inference-time scaling via direct energy ranking, without any decoration or relaxation step. When generating 150 crystals and selecting the top-30 by energy, we further improve solve rate while maintaining a speedup of $5$-$8\times$. We also introduce the CSD Teaching Subset as a new test split of diverse and complex molecules for future benchmarking. Our contributions enable CSP within seconds, making large-scale virtual screening of organic solids practical. Code is available at https://github.com/aspuru-guzik-group/clari.

晶体预测生成模型速度优化分子建模

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