Rigid Protein-Protein Docking via Equivariant Elliptic-Paraboloid Interface Prediction. - Ziyang Yu 002; Wenbing Huang 001; Yang Liu 005 (ICLR, 2024)

Equivariant Pretrained Transformer for Unified Geometric Learning on Multi-Domain 3D Molecules. - Rui Jiao; Xiangzhe Kong; Ziyang Yu 002; Wenbing Huang 001; Yang Liu 005 (CoRR, 2024)

A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications. - Jiaqi Han; Jiacheng Cen; Liming Wu; Zongzhao Li; Xiangzhe Kong; Rui Jiao; Ziyang Yu 002; Tingyang Xu; Fandi Wu; Zihe Wang; Hongteng Xu; Zhewei Wei; et al. (CoRR, 2024)

Force-Guided Bridge Matching for Full-Atom Time-Coarsened Dynamics of Peptides. - Ziyang Yu 002; Wenbing Huang 001; Yang Liu 005 (CoRR, 2024)

UniSim: A Unified Simulator for Time-Coarsened Dynamics of Biomolecules. - Ziyang Yu 002; Wenbing Huang 001; Yang Liu 005 (CoRR, 2025)

A survey of geometric graph neural networks: data structures, models and applications. - Jiaqi Han; Jiacheng Cen; Liming Wu; Zongzhao Li; Xiangzhe Kong; Rui Jiao; Ziyang Yu 002; Tingyang Xu; Fandi Wu; Zihe Wang; Hongteng Xu; Zhewei Wei; et al. (Frontiers Comput. Sci., 2025)