arXiv:2606.30961physics.chem-phcs.LG2026-06

ElemeNet统一建模元素1-100,支持从有机到生物金属体系的分子预测。

ElemeNet: Multiscale Molecular Machine Learning with Uncertainty Quantification Across the Periodic Table

  • 基于E(3)等变与Transformer架构,兼容原子、键、基团级预测
  • 覆盖1-100号元素,支持电荷/自旋条件,模型具备内置不确定性量化
  • 命令行接口简洁,适合非计算背景科研人员使用

深度学习在化学性质预测中取得进展,但现有先进模型多局限于独立代码库,且难以覆盖多样化学物种。本文提出ElemeNet,一个统一的通用分子机器学习软件包,可训练适用于广泛性质与数据集的先进模型,扩展至元素1-100的组合范围。其分子表示支持从有机到金属有机及生物体系的复杂系统,除常见原子、键、分子级预测外,新增基团(moiety)预测能力,并原生支持电荷与自旋态条件。集成E(3)-等变与Transformer架构,同时兼容经典2D模型,所有模块均内置确定性与统计不确定性量化。在有机、无机、配位及生物化学代表性数据集上基准测试显示,性能达当前最优水平,且可扩展至百万级分子。整个工作流通过简洁命令行接口暴露,降低非专家用户使用门槛。我们预计ElemeNet将推动现代深度学习方法在化学与物理科学中的普及应用。

原文摘要 · Abstract (English)

Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species. This work introduces ElemeNet, a unified, general-purpose software package for molecular machine learning. The ElemeNet software package enables the training of advanced ML models for diverse properties and datasets with an enlarged range of elemental compositions. We define molecular representations compatible with elements 1-100, supporting diverse organometallic and biological systems in addition to organic chemistry already well-served by the Chemprop ML toolkit. As well as more common atom-, bond-, and molecule-level predictions, we introduce moiety predictions. We also natively define optional conditioning on charge and spin states. Advanced E(3)-equivariant and transformer architectures are supported, as well as classical 2D models, with all classes including built-in uncertainty quantification through deterministic and statistical measures. We benchmark our protocols for ML model training against representative datasets from organic, inorganic, coordination, and biological chemistry, achieving competitive and SOTA performance relative to literature baselines and favorable scaling to millions of molecules. The entire workflow is exposed through a concise command-line interface, lowering the barrier to entry for non-expert users. We anticipate ElemeNet will empower non-computational researchers to leverage modern deep learning methods across the chemical and physical sciences.

分子机器学习不确定性量化多尺度建模跨周期表

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