Generating Molecular Conformer Fields

Yuyang Wang, Ahmed A. A. Elhag, Navdeep Jaitly, Joshua M. Susskind, Miguel Ángel Bautista

Primary Area: applications to physical sciences (physics, chemistry, biology, etc.)

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Keywords: diffusion model, molecular conformations, fields

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TL;DR: A diffusion model of conformers as continuous functions on graphs

Abstract: In this paper we tackle the problem of generating conformers of a molecule in 3D space given its molecular graph. We parameterize these conformers as continuous functions that map elements from the molecular graph to points in 3D space. We then formulate the problem of learning to generate conformers as learning a distribution over these functions using a diffusion generative model, called Molecular Conformer Fields (MCF). Our approach is simple and scalable, and obtains results that are comparable or better than the previous state-of-the-art while making no assumptions about the explicit structure of molecules (\eg modeling torsional angles). MCF represents an advance in extending diffusion models to handle complex scientific problems in a conceptually simple, scalable and effective manner.

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Submission Number: 2805