A Generative Model for Molecular Distance Geometry

Anonymous

Sep 25, 2019 ICLR 2020 Conference Blind Submission readers: everyone Show Bibtex
  • Keywords: graph neural networks, variational autoencoders, distance geometry, molecular conformation
  • TL;DR: Neural network based generative model for molecular conformations utilizing Euclidean distance geometry.
  • Abstract: Computing equilibrium states for many-body systems, such as molecules, is a long-standing challenge. In the absence of methods for generating statistically independent samples, great computational effort is invested in simulating these systems using, for example, Markov chain Monte Carlo. We present a probabilistic model that generates such samples for molecules from their graph representations. Our model learns a low-dimensional manifold that preserves the geometry of local atomic neighborhoods through a principled learning representation that is based on Euclidean distance geometry. We create a new dataset for molecular conformation generation with which we show experimentally that our generative model achieves state-of-the-art accuracy. Finally, we show how to use our model as a proposal distribution in an importance sampling scheme to compute molecular properties.
  • Code: https://figshare.com/s/1b42bf865bd78c457354
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