Graph Neural Networks for Supply Chain Management: A Framework and Real World Benchmark

Graph Neural Networks (GNNs) have emerged as a powerful, differentiable class of learning models for graph-structured systems. Their ability to generalize across topologies opens the prospect of a surrogate for combined structural and parametric optimization, which classical metamodels cannot offer. Supply chains are a natural target, yet the use of GNN surrogates for supply chain problems is largely unexplored. This paper lays the foundation, presents initial steps, and discusses key research directions. As a foundation, we formulate the problem and create a large public training dataset of programmatically generated supply chain graphs with input parameters and steady-state performance metrics obtained using our SupplyNetPy simulation library. As initial steps, we explore GNN architectures that work well as surrogates for node- and network-level predictions, and analyze their accuracy-compute trade-off against simulation. Most importantly, we outline the exciting directions this opens, namely gradient-based optimization over topology, fast design-space exploration, and sensitivity analysis.

Modern logistics networks generate rich operational data streams at every warehouse node and transportation lane -- from order timestamps and routing records to shipping manifests -- yet predicting delivery delays remains predominantly reactive. Existing predictive approaches typically treat this problem either as a tabular classification task, ignoring network topology, or as a time-series anomaly detection task, overlooking the spatial dependencies of the supply chain graph. To bridge this gap, we propose a hybrid deep learning framework for proactive supply chain risk management. The proposed method jointly models temporal order-flow dynamics via a lightweight Transformer patch encoder and inter-hub relational dependencies through an Edge-Aware Graph Attention Network (E-GAT), optimized via a multi-task learning objective. Evaluated on the real-world DataCo Smart Supply Chain dataset, our framework achieves consistent improvements over baseline methods, yielding an F1-score of 0.8762 and an AUC-ROC of 0.9773. Across four independent random seeds, the framework exhibits a cross-seed F1 standard deviation of only 0.0089 -- a 3.8 times improvement over the best ablated variant -- achieving the strongest balance of predictive accuracy and training stability among all evaluated models.

Inventory and distribution planning in Physical Internet networks requires coordinating factory-hub assignments, factory supply, lateral transshipment among collaborative hubs, retailer deliveries, and shortages. The problem combines discrete assignment decisions with interdependent continuous flows, while uncertain operating costs make robust planning more difficult. This study formulates deterministic and min-max regret models for a three-echelon network of factories, hubs, and retailers and develops a graph neural network-guided genetic algorithm (GNN-GA) for the assignment decisions. The GNN estimates hub-specific factory-selection probabilities that are used to construct the initial GA population and adapt mutation according to prediction uncertainty. Each previously unseen candidate assignment is evaluated by solving the remaining continuous-flow problem to LP optimality. Simulated annealing, a standard GA, and GNN-GA are compared on 15 instances using matched random seeds and fixed limits on distinct assignment evaluations. Because the evaluation budgets for test Instances 13-15 are smaller than the nominal population size, these experiments primarily assess the quality of learned initialization rather than multi-generation evolutionary search. A separate 400-evaluation experiment on exact test Instance 13 permits three complete offspring generations and a partial fourth pass, with GNN-GA outperforming GA in all 10 matched runs. Three independently generated exact-solvable instances provide a separate test of transfer. Ablation results show that learned initialization provides most of the improvement, while entropy-guided mutation has a smaller, instance-dependent effect. Per-instance solution times include GNN inference and search but exclude model training and one-time model setup.