3 papers
cs.LG2026
Beyond Pairwise Attention: Higher-Order Modular Attention for Efficient Sequence Learning
Shirin Amiraslani, Xin Gao
Sequence modeling tasks can involve intrinsic higher-order dependencies, while standard self-attention assigns scores to token pairs and does not explicitly parameterize such inter…
q-bio.BM2025
NS-Pep: De novo Peptide Design with Non-Standard Amino Acids
Tao Guo, Junbo Yin, Yu Wang +1
Peptide drugs incorporating non-standard amino acids (NSAAs) offer improved binding affinity and improved pharmacological properties. However, existing peptide design methods are l…
cs.CV2025
CFP-Gen: Combinatorial Functional Protein Generation via Diffusion Language Models
Junbo Yin, Chao Zha, Wenjia He +2
Existing PLMs generate protein sequences based on a single-condition constraint from a specific modality, struggling to simultaneously satisfy multiple constraints across different…