Deep learning of committor and explainable artificial intelligence analysis for identifying reaction coordinates

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Abstract
In complex molecular systems, the reaction coordinate (RC) that characterizes transition pathways is essential to understand underlying molecular mechanisms. This review surveys a framework for identifying the RC by applying deep learning to the committor, which provides the most reliable measure of the progress along a transition path. The inputs to the neural network are collective variables (CVs) expressed as functions of atomic coordinates of the system, and the corresponding RC is predicted as the output by training the network on the committor as the learning target. Because deep-learning models typically operate in a black-box manner, it is difficult to determine which input variables govern the predictions. The incorporation of explainable artificial intelligence techniques enables quantitative assessment of the contributions of individual input variables to the predictions. This approach allows the identification of CVs that play dominant roles and demonstrates that the committor distribution on the surface using important CVs is separated by well-defined boundaries. The framework provides an explainable deep learning strategy for assigning a molecular mechanism from the RC and is applicable to a wide range of complex molecular systems.
Funding Information
  • Japan Society for the Promotion of Science (JP23K23858)
  • Japan Society for the Promotion of Science (JP25H02299)
  • Japan Society for the Promotion of Science (JP23K23303)
  • Japan Society for the Promotion of Science (JP23KK0254)
  • Japan Society for the Promotion of Science (JP24K21756)
  • Japan Society for the Promotion of Science (JP25H02464)
  • Japan Society for the Promotion of Science (JP25K02235)
  • Japan Society for the Promotion of Science (JP25K00968 JP24H01719)
  • Japan Society for the Promotion of Science (JP22K03550)
  • Japan Society for the Promotion of Science (JP23H02622)
  • Fugaku Supercomputing (JPMXP1020230325)
  • Fugaku Supercomputing (JPMXP1020230327)
  • Data-Driven Material Research (JPMXP1122714694)
  • National Institutes of Natural Sciences (25-IMS-C052)
  • National Institutes of Natural Sciences (25-IMS-C105)
  • National Institutes of Natural Sciences (25-IMS-C227)
  • National Institutes of Natural Sciences (26-IMS-C019)
  • National Institutes of Natural Sciences (26-IMSC051)
  • National Institutes of Natural Sciences (26-IMS-C239)

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