Graph-structured optimization with linear constraints is fundamental to critical infrastructure but faces scalability limits due to massive strict hard constraints and high dimensionality. While recent projection-based methods such as Trainable Sampling Kaczmarz-Motzkin Net (T-SKM-Net) guarantee feasibility, they face high computational costs in dynamic environments by processing the entire constraint set and requiring expensive matrix factorizations. To bridge this gap, we propose the Accelerated Trainable-SKM (AT-SKM) Net framework. To concentrate computation on the active constraints and eliminate redundant calculations, we introduce a hybrid sampling strategy guided by a topology-aware heterogeneous GNN model. To efficiently handle topological shifts in graph-based constraints, we employ a Cholesky Update mechanism that theoretically reduces the equality projection complexity from O(N^3) to O(N^2) under low-rank perturbations. Experiments on random geometric graphs, N-1 Security-Constrained DC-OPF, and minimum-cost gas transport problem demonstrate that AT-SKM reduces iteration counts by up to 85% and achieves 2.95x-7.29x SKM layer speedups, while maintaining zero constraint violations.

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