Learning Neural Generative Dynamics for Molecular Conformation GenerationDownload PDF


28 Sep 2020 (modified: 17 Nov 2020)ICLR 2021 Conference Blind SubmissionReaders: Everyone
  • Keywords: Molecular conformation generation, deep generative models, continuous normalizing flow, energy-based models
  • Abstract: We study how to generate molecule conformations (\textit{i.e.}, 3D structures) from a molecular graph. Traditional methods, such as molecular dynamics, sample conformations via computationally expensive simulations. Recently, machine learning methods have shown great potential by training on a large collection of conformation data. Challenges arise from the limited model capacity for capturing complex distributions of conformations and the difficulty in modeling long-range dependencies between atoms. Inspired by the recent progress in deep generative models, in this paper, we propose a novel probabilistic framework to generate valid and diverse conformations given a molecular graph. We propose a method combining the advantages of both flow-based and energy-based models, enjoying: (1) a high model capacity to estimate the multimodal conformation distribution; (2) explicitly capturing the complex long-range dependencies between atoms in both hidden and observation space. Extensive experiments demonstrate the superior performance of the proposed method on several benchmarks, including conformation generation and distance modeling tasks, with a significant improvement over existing generative models for molecular conformation sampling.
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  • One-sentence Summary: A novel probabilistic framework to generate valid and diverse molecular conformations. Reaching state-of-the-art results on conformation generation and inter-atomic distance modeling.
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