Visualizing functional network connectivity differences using an explainable machine-learning method

<i>Objective</i>. Functional network connectivity (FNC) estimated from resting-state functional magnetic resonance imaging showed great information about the neural mechanism in different brain disorders. But previous research has mainly focused on standard statistical learning approaches to find FNC features separating patients from control. While machine learning models can improve classification accuracy, they often lack interpretability, making it difficult to understand how they arrive at their decisions.<i>Approach</i>. Explainable machine learning helps address this issue by identifying which features contribute most to the model's predictions. In this study, we introduce a novel framework leveraging SHapley Additive exPlanations (SHAPs) to identify crucial FNC features distinguishing between two distinct population classes.<i>Main results</i>. Initially, we validate our approach using synthetic data. Subsequently, applying our framework, we ascertain FNC biomarkers distinguishing between, controls and schizophrenia (SZ) patients with accuracy of 81.04% as well as middle aged adults and old aged adults with accuracy 71.38%, respectively, employing random forest, XGBoost, and CATBoost models.<i>Significance</i>. Our analysis underscores the pivotal role of the cognitive control network (CCN), subcortical network (SCN), and somatomotor network in discerning individuals with SZ from controls. In addition, our platform found CCN and SCN as the most important networks separating young adults from older.