Rethinking the Role of Frames for SE(3)-Invariant Crystal Structure Modeling

Abstract

Crystal structure modeling with graph neural networks is essential for various applications in materials informatics, and capturing SE(3)-invariant geometric features is a fundamental requirement for these networks. A straightforward approach is to model with orientation-standardized structures through structure-aligned coordinate systems, or “frames.” However, unlike molecules, determining frames for crystal structures is challenging due to their infinite and highly symmetric nature. In particular, existing methods rely on a statically fixed frame for each structure, determined solely by its structural information, regardless of the task under consideration. Here, we rethink the role of frames, *questioning whether such simplistic alignment with the structure is sufficient*, and propose the concept of *dynamic frames*. While accommodating the infinite and symmetric nature of crystals, these frames provide each atom with a dynamic view of its local environment, focusing on actively interacting atoms. We demonstrate this concept by utilizing the attention mechanism in a recent transformer-based crystal encoder, resulting in a new architecture called **CrystalFramer**. Extensive experiments show that CrystalFramer outperforms conventional frames and existing crystal encoders in various crystal property prediction tasks.