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The multi-scale nature of gaseous flows poses tremendous difficulties for theoretical and numerical analysis. The Boltzmann equation, while possessing a wider applicability than hydrodynamic equations, requires significantly more computational resources due to the increased degrees of freedom in the model. The success of a hybrid fluid-kinetic flow solver for the study of multi-scale flows relies on accurate prediction of flow regimes. In this paper, we draw on binary classification in machine learning and propose the first neural network classifier to detect near-equilibrium and non-equilibrium flow regimes based on local flow conditions. Compared with classical semi-empirical criteria of continuum breakdown, the current method provides a data-driven alternative where the parameterized implicit function is trained by solutions of the Boltzmann equation. The ground-truth labels are derived rigorously from the deviation of particle distribution functions and the approximations based on the Chapman-Enskog ansatz. Therefore, no tunable parameter is needed in the criterion. Following the entropy closure of the Boltzmann moment system, a data generation strategy is developed to produce training and test sets. Numerical analysis shows its superiority over simulation-based samplings. A hybrid Boltzmann-Navier-Stokes flow solver is built correspondingly with adaptive partition of local flow regimes. Numerical experiments including one-dimensional Riemann problem, shear flow layer and hypersonic flow around circular cylinder are presented to validate the current scheme for simulating cross-scale and non-equilibrium flow physics. The quantitative comparison with a semi-empirical criterion and benchmark results demonstrates the capability of the current neural classifier to accurately predict continuum breakdown.