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Dan Berenberg

2 accepted papers

2024

Protein Discovery with Discrete Walk-Jump Sampling

ICLR 2024oral

We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the true data manifold with one-step denoising. Our $\textit{Discre…

2023

OpenProteinSet: Training data for structural biology at scale

NeurIPS 2023poster

Multiple sequence alignments (MSAs) of proteins encode rich biological information and have been workhorses in bioinformatic methods for tasks like protein design and protein structure prediction for decades. Recent breakthroughs like AlphaFold2 that use transformers to attend directly over large qu…