From the 1 of 16 linked papers with an AI index.
16 papers
Latent-Kernel Discrete Flow Maps for Few-Step Generation
Mansoor Ahmed, Yue-Tsz Fan, Hemanth Venkateswara +1
The paper proposes Latent‑Kernel Discrete Flow Maps, a flow‑based model that uses a shared latent variable to tie together multiple factorized components, enabling correlated updat…
ConTact: Contact-First Antibody CDR Design via Explicit Interface Reasoning
Mansoor Ahmed, Spencer VonBank, Nadeem Taj +3
Computational antibody CDR design methods condition on antigen structure to generate binding loops. Yet, the existing architectures conflate two fundamentally distinct sub-problems…
CHIMERA-Bench: A Benchmark Dataset for Epitope-Specific Antibody Design
Mansoor Ahmed, Nadeem Taj, Imdad Ullah Khan +2
Computational antibody design has seen rapid methodological progress, with dozens of deep generative methods proposed in the past three years, yet the field lacks a standardized be…
EpiFormer: Learning Antigen-Antibody Interactions for Epitope Prediction via Geometric Deep Learning
Mansoor Ahmed, Huirong Chai, Haoxin Wang +2
Antibodies neutralize foreign antigens by binding to specific surface regions called epitopes. Computational epitope prediction is critical for understanding immune recognition and…
AgForce Enables Antigen-conditioned Generative Antibody Design
Mansoor Ahmed, Murray Patterson
Antibody design methods condition on antigen structure to generate complementarity-determining regions (CDR), yet a systematic evaluation of baseline methods reveals that they larg…
EvoStruct: Bridging Evolutionary and Structural Priors for Antibody CDR Design via Protein Language Model Adaptation
Mansoor Ahmed, Sujin Lee, Umar Khayaz +1
Equivariant graph neural network (GNN) methods for antibody complementarity-determining region (CDR) design achieve the highest sequence recovery but suffer from severe vocabulary…