提出原子层面的分布外评估协议,验证新模型对化学性质预测的提升
QT-Net: Rethinking Evaluation of AI Models in Atomic Chemical Space

- 按SOAP描述符聚类原子环境,仅用训练未见类别评估性能
- 新模型QT-Net在QM9外分子上提升原子电荷与多极矩预测精度
- 适用于需要原子级化学先验的分子机器学习研究
原子性质如部分电荷或多极矩包含有意义的化学信息,可辅助下游分子性质预测,但其作为机器学习目标时缺乏原子层级的合理分布外评估协议。本文提出一种保留评估协议:通过SOAP描述符对原子环境聚类,并仅计算训练中未见簇标签的指标。采用5×5交叉验证与Tukey's HSD进行统计严谨比较,评估了E(3)-等变与非等变、旋转增强模型在预测H、C、N、O原子电子分布和多极矩的表现。基于结果,我们提出量子拓扑神经网络(QT-Net),一种旋转增强的非等变图神经网络。实验表明,QT-Net能从训练集外的QM9分子中推断原子性质,且这些推断属性作为输入特征可提升下游分子性质预测效果。进一步验证中,由QT-Net原子输出计算的分子偶极矩与QM9真实值高度一致。代码与数据已公开,含基于JAX的QT-Net实现,支持将学习到的量子拓扑原子属性作为原子尺度分子机器学习的归纳偏置。
原文摘要 · Abstract (English)
Atomic properties such as partial charges or multipoles encode chemically meaningful information that can inform downstream molecular property prediction, but their evaluation as machine learning targets has been complicated by the absence of a principled out-of-distribution evaluation protocol at the atomic level. In this work, we propose a held-out evaluation protocol that clusters atomic environments by SOAP descriptors and computes metrics accounting only for cluster labels unseen during training. Following this procedure, we use 5$\times$5 cross-validation and Tukey's HSD to run a statistically rigorous comparison of E(3)-equivariant against non-equivariant, rotationally augmented models for predicting electron populations and multipoles of H, C, N, and O atoms. Building on our results, we introduce the Quantum Topological Neural Network (QT-Net), a rotationally augmented, non-equivariant graph neural network. We show that QT-Net can be used to infer properties of atoms in molecules from QM9 outside our training set, and that these inferred properties can yield improvement when used as input features for downstream molecular property prediction. To further validate the framework, molecular dipole moments computed from QT-Net's per-atom outputs recover the ground-truth values reported in QM9. We release all code and data, including a JAX implementation of QT-Net, to support the broader use of learned QTA properties as inductive biases for atomic-scale molecular machine learning.
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