David M Miller

This paper evaluates projected gradient descent (PGD) for hallucination-based protein binder design, finding it improves design efficiency and diversity compared to softmax-based methods.

ContrasTED improves homology classification by using contrastive learning to assign domains to superfamilies with high accuracy, outperforming existing methods.

ProFam is an open-source protein family language model that improves fitness prediction and design by leveraging evolutionary context through homologous sequences.