3 papers
q-bio.QM2025
UniOTalign: A Global Matching Framework for Protein Alignment via Optimal Transport
Yue Hu, Zanxia Cao, Yingchao Liu
Protein sequence alignment is a cornerstone of bioinformatics, traditionally approached using dynamic programming (DP) algorithms that find an optimal sequential path. This paper i…
q-bio.QM2025
Lie-RMSD: A Gradient-Based Framework for Protein Structural Alignment using Lie Algebra
Yue Hu, Zanxia Cao, Yingchao Liu
The comparison of protein structures is a fundamental task in computational biology, crucial for understanding protein function, evolution, and for drug design. While analytical me…
cs.LG2025
Dimer-Enhanced Optimization: A First-Order Approach to Escaping Saddle Points in Neural Network Training
Yue Hu, Zanxia Cao, Yingchao Liu
First-order optimization methods, such as SGD and Adam, are widely used for training large-scale deep neural networks due to their computational efficiency and robust performance.…