Objective: Recent studies demonstrate that functional connectomes contain subject-specific signatures, or \textit{fingerprints}, that can identify individuals across repeated sessions and tasks. Existing methods mostly rely on edge-level features that are sensitive to noise, difficult to interpret, and limited in their ability to generalize across tasks and datasets. Methods: We propose a multiscale community-based functional connectome fingerprinting framework that characterizes each individual by the mesoscale structure of their functional networks. We introduce a signed multilayer community detection framework that incorporates both correlated and anti-correlated brain activity to identify subject-specific community structures across tasks and sessions. Graph-theoretic metrics are then computed from the resulting joint community structures to derive low-dimensional community-level fingerprint representations. Results: The proposed framework is evaluated on 810 healthy control subjects from the Human Connectome Project (HCP). The results show that community-based fingerprints provide a reliable and interpretable substrate for individualized brain characterization across sessions and tasks. Conclusion: Mesoscale community structure provides meaningful and discriminative subject-specific fingerprints. Significance: The proposed framework offers a promising foundation for precision neuroimaging and personalized neuroscience applications.
Brain networks exhibit a modular community structure that varies across individuals and neurological conditions. However, existing self-supervised learning (SSL) methods often overlook this heterogeneity, relying on generic masking strategies that fail to capture subject-specific functional organization. We propose BrainPICM, a self-supervised framework for brain network analysis via progressive individualized community aware masking. BrainPICM formulates ROI-to-community mapping as a progressive unbalanced optimal transport process, yielding soft assignments and per-ROI confidence scores. Guided by these confidence estimates, a curriculum-style masking strategy gradually incorporates low-confidence, potentially pathological regions into training, enabling the model to learn both stable modular structures and individual variations. Additionally, a deviation-aware aggregation module quantifies functional reorganization by measuring mass redistribution relative to a population template, enhancing interpretability and downstream prediction. Experiments on three fMRI datasets (ABIDE-I, ADHD-200, ADNI) show that BrainPICM consistently outperforms state-of-the-art supervised and SSL methods in diagnostic accuracy, indicating that explicitly injecting modular community structure into masked modeling yields more functionally consistent and generalizable representations. The source code for this approach will be released at https://github.com/Hrychen7/BrainPICM.