Graph neural networks (GNNs) are a class of neural networks suitable for learning on graph-structured data. Their application to spatial data is a natural extension, however its relatively unclear which message-passing operations, architectural configurations, and graph representation is best suited for classifying changes to objects in electronic navigational charts (ENCs)--geospatial vector datasets used for marine navigation. Maintaining these datasets is a challenge, and categorizing changes to objects in the ENC based on their significance to navigational safety is of particular importance. Here, we propose to represent these vector navigation datasets as a graph structure where the spatial objects serve as nodes and their spatial and semantic relationships form edges. We encode both the old ENC dataset and new ENC dataset into a pair of graphs and frame the task as a graph-pair classification problem. Building on this representation, we investigate the use of GNN architectures to classify whether the encoded graphs constitutes a critical or non-critical risk to navigational safety. We train and evaluate several GNN architectures and model configurations on ENC changes reviewed by maritime experts. Our results demonstrate that graph-based representations improve the classification of ENC updates, providing a scalable approach for automating or improving ENC maintenance workflows.

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