1 code implementation • NeurIPS 2023 • Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Lukas Jarosch, Daniel Berenberg, Ian Fisk, Andrew M. Watkins, Stephen Ra, Richard Bonneau, Mohammed AlQuraishi
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.
1 code implementation • 8 Jun 2023 • Nathan C. Frey, Daniel Berenberg, Karina Zadorozhny, Joseph Kleinhenz, Julien Lafrance-Vanasse, Isidro Hotzel, Yan Wu, Stephen Ra, Richard Bonneau, Kyunghyun Cho, Andreas Loukas, Vladimir Gligorijevic, Saeed Saremi
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.
no code implementations • 17 May 2018 • James P. Bagrow, Daniel Berenberg, Joshua Bongard
Many research fields codify their findings in standard formats, often by reporting correlations between quantities of interest.
no code implementations • 14 Dec 2018 • Daniel Berenberg, James P. Bagrow
Further, the total size of the collective causal attribution network held by humans is currently unknown, making it challenging to assess the progress of these surveys.
no code implementations • 9 May 2022 • Daniel Berenberg, Jae Hyeon Lee, Simon Kelow, Ji Won Park, Andrew Watkins, Vladimir Gligorijević, Richard Bonneau, Stephen Ra, Kyunghyun Cho
We introduce an alternative approach to this guided sampling procedure, multi-segment preserving sampling, that enables the direct inclusion of domain-specific knowledge by designating preserved and non-preserved segments along the input sequence, thereby restricting variation to only select regions.