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cs.LG2025
ProteinAE: Protein Diffusion Autoencoders for Structure Encoding
Shaoning Li, Le Zhuo, Yusong Wang +5
Developing effective representations of protein structures is essential for advancing protein science, particularly for protein generative modeling. Current approaches often grappl…
cs.LG2024
Neural PM: A Long-Range Interaction Modeling Enhancer for Geometric GNNs
Yusong Wang, Chaoran Cheng, Shaoning Li +5
Geometric graph neural networks (GNNs) have emerged as powerful tools for modeling molecular geometry. However, they encounter limitations in effectively capturing long-range inter…
cs.LG2024
Improving AlphaFlow for Efficient Protein Ensembles Generation
Shaoning Li, Mingyu Li, Yusong Wang +4
Investigating conformational landscapes of proteins is a crucial way to understand their biological functions and properties. AlphaFlow stands out as a sequence-conditioned generat…