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State predictive information bottleneck
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AI
DOI：10.1063/5.0038198.png)
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摘要
En 中文
The ability to make sense of the massive amounts of high-dimensional data generated from molecular dynamics simulations is heavily dependent on the knowledge of a low-dimensional manifold (parameterized by a reaction coordinate or RC) that typically distinguishes between relevant metastable states, and which captures the relevant slow dynamics of interest. Methods based on machine learning and artificial intelligence have been proposed over the years to deal with learning such low-dimensional manifolds, but they are often criticized for a disconnect from more traditional and physically interpretable approaches. To deal with such concerns, in this work we propose a deep learning based state predictive information bottleneck approach to learn the RC from high-dimensional molecular simulation trajectories. We demonstrate analytically and numerically how the RC learnt in this approach is connected to the committor in chemical physics and can be used to accurately identify transition states. A crucial hyperparameter in this approach is the time delay or how far into the future the algorithm should make predictions about. Through careful comparisons for benchmark systems, we demonstrate that this hyperparameter choice gives useful control over how coarse-grained we want the metastable state classification of the system to be. We thus believe that this work represents a step forward in systematic application of deep learning based ideas to molecular simulations.
Keyword:
DIFFUSION MAPS
DYNAMICS
REPRESENTATION
KINETICS
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期刊
IF:
3.1
论文数:
7.2W
被引数:
23.2W
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Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories马尔可夫状态模型揭示了超长MD轨迹中的折叠和功能动力学
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