4 papers
How to make the most of your masked language model for protein engineering
Calvin McCarter, Nick Bhattacharya, Sebastian W. Ober +1
A plethora of protein language models have been released in recent years. Yet comparatively little work has addressed how to best sample from them to optimize desired biological pr…
A Unification of Discrete, Gaussian, and Simplicial Diffusion
Nuria Alina Chandra, Yucen Lily Li, Alan N. Amin +5
To model discrete sequences such as DNA, proteins, and language using diffusion, practitioners must choose between three major methods: diffusion in discrete space, Gaussian diffus…
Is Sequence Information All You Need for Bayesian Optimization of Antibodies?
Sebastian W. Ober, Calvin McCarter, Aniruddh Raghu +4
Bayesian optimization is a natural candidate for the engineering of antibody therapeutic properties, which is often iterative and expensive. However, finding the optimal choice of…
Guided Sequence-Structure Generative Modeling for Iterative Antibody Optimization
Aniruddh Raghu, Sebastian Ober, Maxwell Kazman +1
Therapeutic antibody candidates often require extensive engineering to improve key functional and developability properties before clinical development. This can be achieved throug…