BrainCGT: A Brain Graph Transformer for Modeling Causal Connectivity in Neurological Disorder Diagnosis

Abstract

Brain connectivity analysis is a fundamental tool for identifying biomarkers and understanding of neurological disorders. Most existing approaches employ graph transformers over undirected functional connectivity networks, which are typically estimated using correlation statistics. Although effective for capturing statistical associations, these models do not represent directed interactions between brain regions that arise from causal relationships. As a result, direction-specific disease mechanisms are not explicitly modeled, and interpretability is often limited. To address this gap, we present BrainCGT, a brain graph transformer designed to model causal connectivity inferred from fMRI time-series data. In this framework, brain networks are modeled as directed graphs with a modular organization, where nodes correspond to individual brain regions and directed edges reflect causal flow of information between them. Direction-aware node representations together with direction-biased attention mechanisms allow the model to capture asymmetric interactions across regions. Experimental results on three large-scale fMRI datasets demonstrate that BrainCGT achieves consistently better performance than existing graph-based methods for neurological disorder classification. In addition, examination of the learned attention structures shows correspondence with established neurobiological pathways, suggesting improved interpretability. These results highlight the importance of incorporating causal directionality into brain graph transformer architectures for robust and interpretable neuroimaging analysis.