AgForce Enables Antigen-conditioned Generative Antibody Design
Antibody design methods condition on antigen structure to generate complementarity-determining regions (CDR), yet a systematic evaluation of baseline methods reveals that they largely ignore the antigen input. We identify three failure modes that explain this behavior. Antigen blindness arises because models derive predictions from antibody framework context rather than antigen information, producing nearly identical CDRs regardless of the target. Vocabulary collapse reduces predicted amino acids to three to five per position, far below the ground truth distribution in native sequences. The argmax bottleneck on the cross-entropy loss via greedy decoding acts as a null predictor that sees ...
| Authors | Mansoor Ahmed, Murray Patterson |
|---|---|
| Primary category | cs.LG |
| Published | 20 May 2026 |
| Last updated at source | 11 August 2026 |
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