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Poster
in
Workshop: Machine Learning for Drug Discovery (MLDD)

LEARNING PROTEIN FAMILY MANIFOLDS WITH SMOOTHED ENERGY-BASED MODELS

Nathan Frey · Dan Berenberg · Joseph Kleinhenz · Stephen Ra · Isidro Hotzel · Julien Lafrance-Vanasse · Ryan Kelly · Yan Wu · Arvind Rajpal · Richard Bonneau · Kyunghyun Cho · Andreas Loukas · Vladimir Gligorijevic · Saeed Saremi


Abstract:

We resolve difficulties in training and sampling from discrete energy-based models (EBMs) by learning a smoothed energy landscape, sampling the smoothed data manifold with Langevin Markov chain Monte Carlo, and projecting back to the true data manifold with one-step denoising. Our formalism combines the attractive properties of EBMs and improved sample quality of score-based models, while simplifying training and sampling by requiring only a single noise scale. We demonstrate the robustness of our approach on generative modeling of antibody proteins.

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