3 citations · 5 across the 6 of their papers we have counts for
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Deep Generative Models for Phylogenetic Inference with Complex Evolutionary Processes
Ethan Baron, Alan N. Amin, Andrew Gordon Wilson
Inference of phylogenetic trees from sequences plays a central role in understanding evolutionary relationships, with applications ranging from tracking pathogen spread to reconstr…
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…
A Diffusion Model to Shrink Proteins While Maintaining Their Function
Ethan Baron, Alan N. Amin, Ruben Weitzman +2
Many proteins useful in modern medicine or bioengineering are challenging to make in the lab, fuse with other proteins in cells, or deliver to tissues in the body, because their se…
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…
Why Masking Diffusion Works: Condition on the Jump Schedule for Improved Discrete Diffusion
Alan N. Amin, Nate Gruver, Andrew Gordon Wilson
Discrete diffusion models, like continuous diffusion models, generate high-quality samples by gradually undoing noise applied to datapoints with a Markov process. Gradual generatio…