面向非平衡分子表征学习的坐标去噪
Coordinate Denoising for Non-Equilibrium Molecular Representation Learning
把「坐标去噪分数等价于原子力」这一等变图网络中的经典假设推广到非平衡构象，用二阶有限差分构造辅助去噪目标；对做3D点云/等变网络预训练的人，这是一个可复用的、无需预训练即可插入监督流程的辅助损失设计思路。
原文依据 standard coordinate denoising techniques fail because the direct equivalence between denoising scores and atomic forces no longer holds
摘要译文
由模型翻译 · 术语统一 · 请对照原文核对关键结论三维分子表征学习在建模化学结构及其性质方面展现出巨大潜力。然而，现有方法大多隐含地假设分子处于或接近平衡态。该假设在非平衡结构上不再成立——这类结构在分子动力学（MD）轨迹中普遍存在——此时标准的坐标去噪技术会失效，因为去噪分数与原子力之间的直接等价关系不再成立。为弥合这一差距，我们提出非平衡分子上的节点去噪（NDeM），这是一种基于势能面二阶有限差分近似的新型辅助任务。通过显式考虑非平衡态中非零的固有原子力，NDeM 提供了一个理论上严谨、适用于任意分子构象的去噪目标。关键在于，我们的方法被设计为轻量级、架构无关的插件，无需预训练，可无缝集成到各类监督学习流程中。在包括 MD17、QM9 以及大规模 OC20 数据集在内的多个基准上的大量实验表明，NDeM 能够持续提升基线模型，取得极具竞争力的性能，并验证了其在平衡与非平衡两种情形下的鲁棒性。
英文原文摘要 1345 字符
Three-dimensional molecular representation learning has shown great promise in modeling chemical structures and their properties. However, most existing approaches implicitly assume molecules are at or near equilibrium states. This assumption breaks down for non-equilibrium structures--ubiquitous in molecular dynamics (MD) trajectories--where standard coordinate denoising techniques fail because the direct equivalence between denoising scores and atomic forces no longer holds. To bridge this gap, we propose Node Denoising on non-Equilibrium Molecules (NDeM), a novel auxiliary task grounded in a second-order finite difference approximation of the potential energy surface. By explicitly accounting for the non-zero inherent forces in non-equilibrium states, NDeM provides a theoretically sound denoising objective applicable to arbitrary molecular conformations. Crucially, our method is designed as a lightweight, architecture-agnostic plugin that requires no pre-training and can be seamlessly integrated into various supervised learning pipelines. Extensive experiments across diverse benchmarks, including MD17, QM9, and the large-scale OC20 dataset, demonstrate that NDeM consistently improves baseline models, yielding highly competitive performance and validating its robustness across both equilibrium and non-equilibrium regimes.