3 papers
cs.LG2026
Conditional generation of antibody sequences with classifier-guided germline-absorbing discrete diffusion
Justin Sanders, Luca Giancardo, Lan Guo +4
Antibody therapeutics are among the most successful modern medicines, yet computationally designing antibodies with desirable binding and developability properties remains challeng…
q-bio.BM2025
Pi-SAGE: Permutation-invariant surface-aware graph encoder for binding affinity prediction
Sharmi Banerjee, Mostafa Karimi, Melih Yilmaz +4
Protein surface fingerprint encodes chemical and geometric features that govern protein-protein interactions and can be used to predict changes in binding affinity between two prot…
cs.LG2025
Foundation model for mass spectrometry proteomics
Justin Sanders, Melih Yilmaz, Jacob H. Russell +5
Mass spectrometry is the dominant technology in the field of proteomics, enabling high-throughput analysis of the protein content of complex biological samples. Due to the complexi…