GNN-Guided Graph Coarsening and Adaptive QUBO Penalties for the Capacitated Vehicle Routing Problem with Time Windows on a Quantum Annealer

Graph coarsening reduces the large Quadratic Unconstrained Binary Optimization (QUBO) formulations arising when vehicle-routing problems are solved by quantum annealing. Nearby customers with compatible time windows are merged into super-nodes, the reduced problem is solved, and the solution is expanded to the original graph. For the Capacitated Vehicle Routing Problem with Time Windows (CVRPTW), existing coarsening heuristics require family-specific tuning and remain unreliable on random instances. We address these limitations on the Solomon benchmark using simulated annealing and a D-Wave Advantage2 processor. We first introduce adaptive penalty calibration. Uniform penalty scaling has little effect, whereas controlling the internal coefficient range substantially improves raw samples. Removing non-binding constraints, normalising binding ones, and scaling the remaining penalties reduces mean raw constraint violations from 33.0 to 0.06 at the same solver budget (p=3.7e-11, n=56). A variable-count-preserving control attributes this gain to conditioning rather than problem size. Second, we replace the hand-tuned merge score with a graph neural network (GNN) using one configuration across all families. At N=10, it achieves 100% feasibility across all Solomon families, including R-type (100% vs. 80% for the tuned heuristic). Across N=10,...,100, feasibility is 83% vs. 69%, with the GNN better or tied on 85/90 instance-size pairs. At N=80,100, the difference is significant (p=0.002; 25/25 pairs), while the QUBO remains approximately 5-6 times smaller. Finally, hardware experiments reproduce the conditioning effect at fixed logical variable count: feasible samples increase from 0.02% to 39% across 13 instances. Classical repair with local search remains a reference bound for end-to-end solution cost.