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Author

Zai-Qing Nie

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#artificial intelligence Preprint Sep 2026

Structure-aware Reinforcement Learning for Protein Directed Evolution

Protein optimization remains a longstanding goal in life sciences. Existing machine learning-assisted directed evolution (MLDE) methods primarily rely on sequence-only features, overlooking the critical spatial constraints and co-evolutionary interactions encoded in protein structures. However, directly integrating str...

Zi-Kun Nie, Su-Yuan Zhao, Yi-Zhen Luo et al. · 0 citations
#artificial intelligence Preprint Sep 2026

CellMSA: Context Modeling for Single-Cell Representation Learning

Single-cell transcriptomics enables profiling of cellular states at unprecedented resolution, but its high dimensionality, sparsity, and technical batch effects pose significant challenges for representation learning. Existing single-cell foundation models typically encode each cell independently or only model cells fr...

Su-Yuan Zhao, Ming-Hao Liu, Yi-Zhen Luo et al. · 0 citations
#artificial intelligence Preprint Sep 2026

AbGaze: Attentive Geometric Representation Learning for End-to-End Antibody Design

Computational antibody design requires representations that capture the geometric patterns underlying antigen--antibody interactions, yet existing approaches often rely on scalar distances or surface-intrinsic features, leaving cross-molecular geometry largely implicit. We present AbGaze, an end-to-end antibody design...

Jia-Shuo Wang, Si-Qi Fan, Yi-Zhen Luo et al. · 0 citations

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