arXiv:2604.16648cs.LGq-bio.QM2026-04被引 3

用质谱生成分子结构,训练和推理都可大规模扩展。

FRIGID: Scaling Diffusion-Based Molecular Generation from Mass Spectra at Training and Inference Time

论文配图:FRIGID: Scaling Diffusion-Based Molecular Generation from Mass Spectra at Training and Inference Time
图 1 · 摘自论文原文
  • 通过指纹和化学式中间表示,让扩散模型从质谱生成分子
  • 推理时通过碎片校验提升精度,顶1准确率超18%且三倍领先
  • 适合做小分子结构解析的科研人员,尤其关注效率与精度

串联质谱在未知小分子鉴定中至关重要,但高通量结构解析仍具挑战。尽管近期自回归与图扩散模型在从头解析中展现潜力,其性能受限于训练与推理阶段的低可扩展性。本文提出FRIGID框架,采用新型扩散语言模型,基于质谱与中间指纹表示及确定的化学式生成分子结构,并在数亿未标注结构上进行训练。我们进一步展示前向碎片模型如何通过识别谱图不一致的片段,在推理时实现高效扩展:通过针对性重掩码与去噪修正。尽管基线扩散模型已表现优异,推理时扩展显著提升准确率,在挑战性MassSpecGym基准上达到18%以上顶1准确率,且在NPLIB1上使领先方法顶1准确率提升三倍。实证分析表明,FRIGID的性能随推理计算量呈对数线性增长,为从头结构解析开辟新方向。FRIGID代码已公开于https://github.com/coleygroup/FRIGID。

原文摘要 · Abstract (English)

Tandem mass spectrometry is prominent in scientific discovery workflows for identifying unknown small molecules, yet high-throughput structural elucidation remains challenging. While recent autoregressive and graph diffusion models have shown promise in de novo elucidation, performance remains limited by poor scalability during both training and inference time. In this work, we present FRIGID, a framework with a novel diffusion language model that generates molecular structures conditioned on mass spectra via intermediate fingerprint representations and determined chemical formulae, training at the scale of hundreds of millions of unlabeled structures. We then demonstrate how forward fragmentation models enable inference-time scaling by identifying spectrum-inconsistent fragments and refining them through targeted remasking and denoising. While FRIGID already achieves strong performance with its diffusion base, inference-time scaling significantly improves its accuracy, surpassing 18% Top-1 accuracy on the challenging MassSpecGym benchmark and tripling the Top-1 accuracy of the leading methods on NPLIB1. Further empirical analyses show that FRIGID exhibits log-linear performance scaling with increasing inference-time compute, opening a promising new direction for continued improvements in de novo structural elucidation. FRIGID code is publicly available at https://github.com/coleygroup/FRIGID.

分子生成扩散模型质谱解析

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