Size-Generalizable RNA Structure Evaluation by Exploring Hierarchical Geometries

Zongzhao Li, Jiacheng Cen, Wenbing Huang, Taifeng Wang, Le Song

Keywords: RNA Structure, RNA Evaluation, Geometric Deep Learning, Graph Neural Networks

Abstract: Understanding the 3D structure of RNA is essential for deciphering its function and developing RNA-based therapeutics. Geometric Graph Neural Networks (GeoGNNs) that conform to the $\mathrm{E}(3)$-symmetry have advanced RNA structure evaluation, a crucial step toward RNA structure prediction. However, existing GeoGNNs are still defective in two aspects: 1. inefficient or incapable of capturing the full geometries of RNA; 2. limited generalization ability when the size of RNA significantly differs between training and test datasets. In this paper, we propose EquiRNA, a novel equivariant GNN model by exploring the three-level hierarchical geometries of RNA. At its core, EquiRNA effectively addresses the size generalization challenge by reusing the representation of nucleotide, the common building block shared across RNAs of varying sizes. Moreover, by adopting a scalarization-based equivariant GNN as the backbone, our model maintains directional information while offering higher computational efficiency compared to existing GeoGNNs. Additionally, we propose a size-insensitive $K$-nearest neighbor sampling strategy to enhance the model's robustness to RNA size shifts. We test our approach on our created benchmark as well as an existing dataset. The results show that our method significantly outperforms other state-of-the-art methods, providing a robust baseline for RNA 3D structure modeling and evaluation.

Primary Area: applications to physical sciences (physics, chemistry, biology, etc.)

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Submission Number: 10008