QT-Net: Rethinking Evaluation of AI Models in Atomic Chemical Space

원문 초록

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 the atomic environments seen during training strongly affect the performance of molecular property prediction tasks. 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.