构建330万分子电子密度数据集,推动机器学习在分子力场中的应用
EDBench: Large-Scale Electron Density Data for Molecular Modeling
- 基于PCQM4Mv2构建大规模电子密度数据集,覆盖330万分子
- 模型学习后可高效预测电子密度,精度接近传统DFT计算
- 适用于药物与材料科学中电子级建模,支持预测、检索、生成任务
现有分子机器学习力场(MLFF)多关注原子、分子及简单量子化学性质(如能量、力)的建模,忽视了电子密度ρ(r)在准确理解分子力场中的关键作用。根据霍亨伯格-科恩定理,电子密度唯一决定了多粒子系统的基态性质(如能量、分子结构)。然而,电子密度的计算依赖耗时的第一性原理密度泛函理论(DFT),导致缺乏大规模电子密度数据,限制其在MLFF中的应用。本文提出EDBench,一个大规模、高质量的电子密度数据集,旨在推动电子尺度下的学习研究。基于PCQM4Mv2,EDBench包含330万分子的精确电子密度数据。为全面评估模型对电子信息的理解与利用能力,我们设计了一套以电子密度为核心的基准任务,涵盖预测、检索与生成。对多个先进方法的评估表明,基于EDBench的学习不仅可行,且能达到高精度。此外,学习方法可实现与传统DFT相当的精度,同时显著降低计算成本。EDBench所有数据与基准将公开可用,为电子驱动的药物发现与材料科学奠定坚实基础。
原文摘要 · Abstract (English)
Existing molecular machine learning force fields (MLFFs) generally focus on the learning of atoms, molecules, and simple quantum chemical properties (such as energy and force), but ignore the importance of electron density (ED) $ρ(r)$ in accurately understanding molecular force fields (MFFs). ED describes the probability of finding electrons at specific locations around atoms or molecules, which uniquely determines all ground state properties (such as energy, molecular structure, etc.) of interactive multi-particle systems according to the Hohenberg-Kohn theorem. However, the calculation of ED relies on the time-consuming first-principles density functional theory (DFT) which leads to the lack of large-scale ED data and limits its application in MLFFs. In this paper, we introduce EDBench, a large-scale, high-quality dataset of ED designed to advance learning-based research at the electronic scale. Built upon the PCQM4Mv2, EDBench provides accurate ED data, covering 3.3 million molecules. To comprehensively evaluate the ability of models to understand and utilize electronic information, we design a suite of ED-centric benchmark tasks spanning prediction, retrieval, and generation. Our evaluation on several state-of-the-art methods demonstrates that learning from EDBench is not only feasible but also achieves high accuracy. Moreover, we show that learning-based method can efficiently calculate ED with comparable precision while significantly reducing the computational cost relative to traditional DFT calculations. All data and benchmarks from EDBench will be freely available, laying a robust foundation for ED-driven drug discovery and materials science.
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