Time-Sensitive Networking (TSN) is critical to deterministic communication in safety-critical domains, with formal verification such as Network Calculus (NC) serving as the cornerstone for schedulability guarantees. However, during automated configuration-space exploration, repeated schedulability analysis consumes over 90% of the total configuration time, becoming the primary bottleneck for large-scale TSN configurations. To address this challenge, we propose DeepNC, a novel pre-verification surrogate module that pioneers the structural fusion of NC principles into a Graph Neural Network (GNN) for TSN configuration-space exploration. Rather than replacing formal verification, DeepNC acts as a high-speed pre-verification filter, reserving computationally expensive formal verification only for promising candidates. Extensive evaluations demonstrate that DeepNC significantly improves worst-case delay prediction accuracy over state-of-the-art learning-based methods, increasing the average $R^2$ by 55.8% and reducing the average MAPE by 65.3%. More importantly, its high-fidelity regression substantially reduces the number of formal verification calls during configuration-space exploration by 93.25%, while accelerating NC-based verification by more than two orders of magnitude.

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