Interpretable Hierarchical RNNs for rs-fMRI: Promise and Limits of Individualized Brain Dynamics

Abstract Modeling individual brain dynamics from resting-state fMRI (rs-fMRI) remains challenging due to substantial inter-subject variability, measurement noise, and limited data length per subject. Here, we systematically evaluate a hierarchical dynamical systems framework based on shallow piecewise-linear recurrent neural networks (shPLRNNs) for individualized modeling of rs-fMRI data, with a particular focus on reproducing subject-specific functional connectivity (FC). We applied the framework to 1,423 rs-fMRI samples from healthy participants of the Marburg-Münster Affective Disorders Cohort Study (MACS). Simulated rs-fMRI data robustly reproduced empirical FC patterns, with comparable reconstruction accuracy on training and independent validation sets. Generalization to unseen individuals was heterogeneous and strongly depended on how typical a subject’s connectivity pattern was relative to the training cohort, with template similarity explaining 37% of variance in reconstruction accuracy. Learned subject-specific parameters exhibited significant test-retest stability and higher within-subject than between-subject similarity on longitudinal data from two different timepoints, supporting their interpretation as individualized dynamical markers. Associations between individual parameters and demographic or cognitive variables were statistically significant but modest in effect size, and predictive performance remained below that obtained using empirical rs-fMRI features directly. Together, these results demonstrate that hierarchical shPLRNNs can extract meaningful and stable individual-specific dynamical structure from rs-fMRI data, while highlighting current limitations in capturing fine-grained individual differences. The findings delineate key trade-offs between model expressivity, generalization and subject specificity, and point to directions for future methodological refinement in individualized brain modeling.