Efficient simulation of Darcy flow in highly heterogeneous porous media requires iterative solvers that remain robust under large permeability contrasts and mixed boundary conditions. Spectral coarse spaces in two-level overlapping Schwarz methods provide such robustness, but their practical use is often limited by an expensive setup phase dominated by many local generalized eigenvalue solves. We propose a purely algebraic, coarse-space approximation that avoids these repeated local eigensolves by using a graph neural network operating on the system-matrix graph. On the analysis side, we introduce a coefficient-weighted subspace-distance measure to quantify the discrepancy between the approximated and target local multiscale coarse spaces, and we derive a condition-number bound for the resulting preconditioned operator in terms of this distance. This bound yields a principled supervised-training objective and links learning error to solver performance. Numerical experiments on 2D and 3D high-contrast Darcy systems with varying mixed boundary conditions demonstrate that the proposed approach substantially reduces setup cost and improves end-to-end time-to-solution, while preserving robust convergence across the tested contrasts and boundary configurations.

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