ASDFormer: A Transformer with Mixtures of Pooling-Classifier Experts for Robust Autism Diagnosis and Biomarker Discovery

Abstract: Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition marked by disruptions in brain connectivity. Functional MRI (fMRI) offers a non-invasive window into large-scale neural dynamics by measuring blood-oxygen-level-dependent (BOLD) signals across the brain. These signals can be modeled as interactions among Regions of Interest (ROIs), which are grouped into functional communities based on their underlying roles in brain function. Emerging evidence suggests that connectivity patterns within and between these communities are particularly sensitive to ASD-related alterations. Effectively capturing these patterns and identifying interactions that deviate from typical development is essential for improving ASD diagnosis and enabling biomarker discovery. In this work, we introduce ASDFormer, a Transformer-based architecture that incorporates a Mixture of Pooling-Classifier Experts (MoE) to capture neural signatures associated with ASD. By integrating multiple specialized expert branches with attention mechanisms, ASDFormer adaptively emphasizes different brain regions and connectivity patterns relevant to autism. This enables both improved classification performance and more interpretable identification of disorder-related biomarkers. Applied to the ABIDE dataset, ASDFormer achieves state-of-the-art diagnostic accuracy and reveals robust insights into functional connectivity disruptions linked to ASD, highlighting its potential as a tool for biomarker discovery.