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Updated: Jul 21, 2025

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
Published on: December 1, 2020
Tensor-Reduced Atomic Density Representations
James P Darby1,2, Dávid P Kovács2, Ilyes Batatia2,3
1Warwick Centre for Predictive Modelling, School of Engineering, University of Warwick, Coventry, CV4 7AL, United Kingdom.
Abstract:
Density-based representations of atomic environments that are invariant under Euclidean symmetries have become a widely used tool in the machine learning of interatomic potentials, broader data-driven atomistic modeling, and the visualization and analysis of material datasets. The standard mechanism used to incorporate chemical element information is to create separate densities for each element and form tensor products between them. This leads to a steep scaling in the size of the representation as the number of elements increases. Graph neural networks, which do not explicitly use density representations, escape this scaling by mapping the chemical element information into a fixed dimensional space in a learnable way. By exploiting symmetry, we recast this approach as tensor factorization of the standard neighbour-density-based descriptors and, using a new notation, identify connections to existing compression algorithms. In doing so, we form compact tensor-reduced representation of the local atomic environment whose size does not depend on the number of chemical elements, is systematically convergable, and therefore remains applicable to a wide range of data analysis and regression tasks.
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