Abstract:Highlights•We propose a GNAS framework to build GNN model for disorder prediction.•We compare our model with other popular ML and DL models on multi-site datasets.•We use the GNNExplainer method to provide the explainability of the model.•The explainability results provide valuable insights for diagnosis and treatment.•The source code is available on GitHub at https://github.com/Shurun-Wang/EA-GNAS.