The Topological Architecture of Brain Identity

Accurately identifying individuals from brain activity --functional fingerprinting-- is a powerful tool for understanding individual variability and detecting brain disorders. Most current approaches rely on functional connectivity (FC), which measures pairwise correlations between brain regions. However, FC is limited in capturing the higher-order, multiscale structure of brain organization. Here, we propose a novel fingerprinting method based on homological scaffolds, a topological representation derived from persistent homology of resting-state fMRI data. Using data from the Human Connectome Project (n= 100), we show that scaffold-based fingerprints achieve near-perfect identification accuracy (∼ 100%), outperforming FC-based methods (90%), and remain robust across preprocessing pipelines, atlas choices, and even with drastically shortened scan durations. Unlike FC, in which fingerprinting features localize within networks, scaffolds derive their discriminative power from inter-network connections, revealing the existence of individual mesoscale organizational signatures. Finally, we show that scaffolds act as bridges between redundancy and synergy, by balancing redundancy along high-FC border edges with high synergy across the topological voids that the cycles define. These findings establish topological scaffolds as a powerful tool for capturing individual variability, revealing that unique signatures of brain organization are encoded in the interplay between mesoscale network integration and information dynamics.