用伪力场生成分子构象,速度快且无需昂贵计算。
Generative Pseudo-Force Fields for Molecular Generation

- 构建基于参考结构的二次伪势能面,无需真实能量计算即可训练力场。
- 256次函数评估下100%有效率,仅6次就超50%有效率,显著优于扩散模型。
- 可实时生成药物分子,支持自定义结构约束,适合分子设计场景。
生成稳定分子构象通常需在物理现实性与采样效率间权衡。机器学习力场(MLFF)虽能通过物理力松弛生成稳定构象,但依赖昂贵的从头算训练数据;扩散模型(DMs)仅从平衡数据学习,却依赖噪声调度和时间步条件。本文提出生成式伪力场(GPFF),通过在参考平衡结构基础上训练二次伪势能面,无需对扰动构象进行从头算计算,即可通过高斯噪声扰动生成非平衡训练数据。我们证明GPFF是方差爆炸型扩散模型的时间步无关变体:预测的伪力即为得分,而力的大小隐含噪声水平,因此无需时间步条件。该方法可直接替代标准扩散采样(如祖先法、Heun法),并支持更高效的自适应算法及受力场启发的直接去噪方案。所有采样算法均支持任意结构先验与几何约束。在QM9数据集上,GPFF在256次神经函数评估(NFE)时达到100%有效性,仅6次评估即超50%有效性,全面优于各类扩散基线。结合定制先验,我们在药物设计场景中实现分子的实时生成,展示出快速准确的生成能力。
原文摘要 · Abstract (English)
Generating stable molecular conformations typically forces a tradeoff between the physical realism of energy-based relaxation and the sampling efficiency of data-driven generative models. While machine learning force fields (MLFFs) can sample stable conformations by relaxing molecular geometries according to physical forces, they require costly ab-initio training data. Conversely, diffusion models (DMs) learn from equilibrium data alone but are dependent on noise schedules and time-step conditioning. In this work, we propose generative pseudo-force fields (GPFFs) to bridge these paradigms by training an MLFF on a quadratic pseudo-potential energy surface relative to reference equilibrium structures. Because no ab-initio calculations are required for the perturbed geometries, non-equilibrium training data can be generated on the fly by perturbing the equilibria with Gaussian noise. We show that GPFFs constitute a time-step-agnostic variant of variance exploding DMs: the score comes from the predicted pseudo-forces but because force magnitudes implicitly encode the noise level, no time-step conditioning is needed. Our GPFF can hence be used as a drop-in replacement in standard diffusion sampling (ancestral, Heun) but also facilitates more efficient, adaptive variants and an MLFF inspired direct denoising scheme. Our proposed sampling algorithms support arbitrary structural priors and geometric constraints. On QM9, GPFF has 100 % validity at 256 neural function evaluations (NFE) and over 50 % at just 6 NFE, outperforming diffusion baselines across all samplers. Combined with custom priors, we showcase the fast and accurate generation process of our method in a molecular editor for a drug design setting, where a molecule is generated in real time.
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