arXiv:2605.07020cs.LGcs.AI2026-05被引 1

4步生成高质量分子构象,速度比传统方法快250倍

FlashMol: High-Quality Molecule Generation in as Few as Four Steps

论文配图:FlashMol: High-Quality Molecule Generation in as Few as Four Steps
图 1 · 摘自论文原文
  • 用分布匹配蒸馏优化生成过程,重排时间步提升初始质量
  • 在QM9和GEOM-DRUG上实现1000步教师模型的生成质量
  • 适合需要快速筛选分子的大规模药物发现场景

生成化学有效且稳定的3D分子构象对计算药物发现至关重要。传统基于扩散的模型如GeoLDM虽效果好,但需数百步,难以用于大规模虚拟筛选。近期研究将生成步数降至12-50步,但常牺牲样本稳定性。本文提出FlashMol,仅需4步即可生成高质量分子构象。通过将分布匹配蒸馏(DMD)引入分子领域,结合反KL散度最小化目标,并重新设计生成时间步以改善初始化;同时引入Jensen-Shannon散度正则项,缓解DMD的模式聚焦问题,提升多样性。在QM9和GEOM-DRUG数据集上的实验表明,FlashMol达到甚至超越1000步教师模型的性能,采样速度最高提升250倍,同时保持高分子质量。

原文摘要 · Abstract (English)

Generating chemically valid 3D molecular conformations is critical for computational drug discovery. Classical diffusion-based models like GeoLDM perform well but require hundreds of steps, making large-scale in silico screening impractical. Recent efforts on few-step molecular generation have accelerated this process to 12-50 steps, but they often largely sacrifice sample stability. In this work, we present FlashMol, an ultra-fast molecule generative model producing high-quality molecular conformations in as few as 4 steps. To achieve this, we adapt distribution matching distillation (DMD) - a reverse KL-divergence minimization objective - to the molecular domain for effective distillation. Considering the local minimization behavior of DMD, we respace the molecule generation timesteps, providing the generator with much better initialization and enables effective distillation. Additionally, to mitigate the mode-seeking behavior of DMD and improve diversity, we further regularize it with a Jensen-Shannon divergence term, which incorporates the mean-seeking behavior of the forward KL divergence. Extensive experiments on QM9 and GEOM-DRUG datasets demonstrate that FlashMol matches and even surpasses the original 1000-step teacher, achieving up to 250$\times$ acceleration in sampling speed while maintaining high molecular quality.

分子生成扩散模型高效采样药物发现

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