Distilling Causal Signals for One-Shot Directed Evolution of Antibodies

Sai Pooja Mahajan, Natasa Tagasovska, Stefania Vasilaki, Arian Jamasb, Andrew Watkins, Rajesh Ranganath

International Conference on Learning Representations 2026 (ICLR 2026) Conference

Improving antibody binding to an antigen without antibody–antigen complex structures or antigen-specific training data is a central challenge in therapeutic protein design. We introduce AffinityEnhancer, a framework for one-shot antibody affinity improvement with strong generalization: given a single lead sequence, we propose variants that increase affinity without fine-tuning on the lead and without using antigen information, epitope/paratope labels, or the lead’s structure in complex with the antigen. During training, AffinityEnhancer leverages a pan-antigen dataset of diverse binding environments (antigens) and constructs paired examples of related sequences with higher vs. lower measured binding. A shared, structure-aware module learns to transform low-affinity sequences toward high-affinity ones, distilling consistent, causal features associated with improved binding across environments. By combining pretrained sequence–structure embeddings with a sequence decoder, AffinityEnhancer generalizes to entirely unseen antibody seeds. Across multiple held-out internal and public leads, AffinityEnhancer concentrates mutations on the rim of the paratope, outperforms existing structure-conditioned and inpainting baselines, and achieves substantial in silico affinity gains in true one-shot experiments, despite never observing antigen-specific data at test time.