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

Sun-Ting Tsai, En-Jui Kuo and Pratyush Tiwary ()
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Sun-Ting Tsai: University of Maryland
En-Jui Kuo: University of Maryland
Pratyush Tiwary: University of Maryland

Nature Communications, 2020, vol. 11, issue 1, 1-11

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-18959-8

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