Yuzhi Xu

EpiBench: Can LLMs Understand Epitopes for Antibody Drug Discovery?

The results show that current LLMs capture partial epitope-related signals but remain limited in antibody-specific sequence grounding, long-context residue localization, and biologically grounded reasoning, so EpiBench provides a diagnostic testbed for measuring and improving sequence-aware biomedical LLMs toward reliable LLM-assisted antibody discovery.

CatESO: Differentiable Enzyme Sequence Optimization Guided by Substrate-Aware kcat Prediction

NACraft: Programmatic nucleic-acid aptamer design via all-atom structure-model feedback

NACraft, a training-free and programmatic framework for all-atom nucleic-acid aptamer design based on backpropagation through structure-model feedback, is presented, demonstrating the effectiveness and versatility of NACraft and extending structure-model hallucination toward programmatic nucleic-acid aptamer design.