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Alzheimer&#x2019;s disease (AD) is the leading form of dementia worldwide. AD disrupts neuronal pathways and thus is commonly viewed as a network disorder. Many studies demonstrate the power of functional connectivity (FC) graph-based biomarkers for automated diagnosis of AD using electroencephalography (EEG). However, various FC measures are commonly utilised, as each aims to quantify a unique aspect of brain coupling. Graph neural networks (GNN) provide a powerful framework for learning on graphs. While a growing number of studies use GNN to classify EEG brain graphs, it is unclear which method should be utilised to estimate the brain graph. We use eight FC measures to estimate FC brain graphs from sensor-level EEG signals. GNN models are trained in order to compare the performance of the selected FC measures. Additionally, three baseline models based on literature are trained for comparison. We show that GNN models perform significantly better than the other baseline models. Moreover, using FC measures to estimate brain graphs improves the performance of GNN compared to models trained using a fixed graph based on the spatial distance between the EEG sensors. However, no FC measure performs consistently better than the other measures. The best GNN reaches 0.984 area under sensitivity-specificity curve (AUC) and 92&#x0025; accuracy, whereas the best baseline model, a convolutional neural network, has 0.924 AUC and 84.7&#x0025; accuracy.

EEG-Based Graph Neural Network Classification of Alzheimer’s Disease: An Empirical Evaluation of Functional Connectivity Methods