3 papers
cs.LG2026
Higher-Order Modular Attention: Fusing Pairwise and Triadic Interactions for Protein Sequences
Shirin Amiraslani, Xin Gao
Transformer self-attention computes pairwise token interactions, yet protein sequence to phenotype relationships often involve cooperative dependencies among three or more residues…
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…