Learning molecular dynamics with simple language model built upon long short-term memory neural network

Nat Commun. 2020 Oct 9;11(1):5115. doi: 10.1038/s41467-020-18959-8.

Abstract

Recurrent neural networks have led to breakthroughs in natural language processing and speech recognition. Here we show that recurrent networks, specifically long short-term memory networks can also capture the temporal evolution of chemical/biophysical trajectories. Our character-level language model learns a probabilistic model of 1-dimensional stochastic trajectories generated from higher-dimensional dynamics. The model captures Boltzmann statistics and also reproduces kinetics across a spectrum of timescales. We demonstrate how training the long short-term memory network is equivalent to learning a path entropy, and that its embedding layer, instead of representing contextual meaning of characters, here exhibits a nontrivial connectivity between different metastable states in the underlying physical system. We demonstrate our model's reliability through different benchmark systems and a force spectroscopy trajectory for multi-state riboswitch. We anticipate that our work represents a stepping stone in the understanding and use of recurrent neural networks for understanding the dynamics of complex stochastic molecular systems.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Artificial Intelligence
  • Dipeptides / chemistry
  • Kinetics
  • Language*
  • Markov Chains
  • Memory*
  • Models, Statistical*
  • Molecular Dynamics Simulation
  • Neural Networks, Computer*
  • Single Molecule Imaging

Substances

  • Dipeptides
  • alanylalanine