protein language models

2 items

RESEARCHarXiv CS.LG·29d ago

Conditional generation of antibody sequences with classifier-guided germline-absorbing discrete diffusion

This research introduces a novel approach for conditional generation of antibody sequences, addressing limitations in current protein language models by better modeling somatic variation and enabling flexible classifier-guided generation. It proposes discrete diffusion fine-tuning and germline absorbing diffusion for improved antibody design.

Antibody Design Diffusion Models computational biology protein language models

RESEARCHarXiv CS.LG·27d ago

Structural Interpretations of Protein Language Model Representations via Differentiable Graph Partitioning

This research proposes a framework to interpret protein language model representations by projecting them onto protein contact graphs and applying SoftBlobGIN, a Graph Isomorphism Network. This method performs structure-aware message passing to learn functional substructures, achieving 92.8% accuracy in enzyme classification and providing auditable structural explanations.

AI interpretation protein language models structural biology Graph Neural Networks