Fusion Learning from Dynamic Functional Connectivity: Combining the Amplitude and Phase of fMRI Signals to Identify Brain Disorders

Major depressive disorder (MDD) is a common neuropsychiatric condition whose accurate diagnosis from resting-state functional magnetic resonance imaging (rs-fMRI) remains difficult. Dynamic functional connectivity (DFC) captures time-varying interactions among brain regions and provides rich spatio-temporal information, yet current DFC-based methods face three limitations: sliding-window Pearson correlation yields noisy estimates sensitive to window length and motion artifacts; correlation-derived node features do not fully exploit frequency-domain properties of blood-oxygen-level-dependent (BOLD) signals; and most spatio-temporal graph models handle spatial structure and temporal dynamics in separate stages, restricting their ability to represent coupled brain network evolution. To overcome these issues, we reformulate DFC learning as joint spatio-temporal graph representation learning under a Hawkes-process-inspired temporal dependency prior and propose HWSTCL, a two-stage framework built on a reliability-refined joint spatio-temporal graph with a kernel-weighted pretraining objective. Within each temporal window, BOLD signals are encoded as spectral node descriptors and functional edges are refined by an exponential distance-decay prior that down-weights less reliable long-range connections. The joint graph is then formed by linking each region to itself across future windows through a Hawkes-inspired exponential kernel, allowing spatial and temporal information to be propagated together during message passing. A kernel-weighted contrastive objective further promotes temporal consistency for each region across windows while reducing redundant similarity between different regions. Experiments on a benchmark rs-fMRI dataset show that HWSTCL outperforms recent baselines and yields coherent spatio-temporal representations for MDD diagnosis.

Functional Magnetic Resonance Imaging ( fMRI ) data are often pooled into collaborative multi-site consortia, as deep learning models for analyses require large datasets to generalize well. While Federated Learning (FL) offers a privacy-preserving paradigm for collaborative training, standard approaches continue to struggle with statistical heterogeneity. In particular, site differences pose a key challenge in multi-site data settings. Additionally, existing FL approaches for fMRI rely on static Functional Connectivity ( FC), omitting dynamic information in brain networks. To address this, we propose FedDOSE, a novel framework that explicitly decomposes site differences for analysis of dynamic FC (dFC). FedDOSE introduces a Modularity-Guided Tucker Decomposition block to encode high-dimensional dFC tensors and capture modular-level spatio-temporal patterns efficiently. Class-specific prototypes are generated across all sites and subsequently aligned at the global level by using a combination of Optimal Transport (OT) barycenter formulation and Procrustes analysis. Extensive experiments for diagnosing Autism Spectrum Disorder (ASD) and Attention-Deficit Hyperactivity Disorder (ADHD) on three multi-site resting-state fMRI datasets: ABIDE-I, ABIDE-II, and ADHD-200, demonstrate that FedDOSE outperforms state-of-the-art methods in ASD and ADHD detection. Our results highlight its effectiveness in learning robust representations from multi-site datasets for reliable analysis.

Functional magnetic resonance imaging (fMRI) commonly characterizes large-scale brain organization through functional connectivity (FC). However, an observed FC matrix is not a fixed brain graph but a statistical estimate determined by the finite BOLD frames used to compute it. Conventional FC-based approaches typically represent each scan with a single Pearson-correlation matrix, leaving frame-resolved variations in regional interactions unexploited. To address this limitation, we introduce CoFlu-Brain, which organizes framewise cofluctuation observations into multiple retained and dropped views, each summarized as an FC matrix. The model learns connectivity structure reproducible across retained views and predicts the representations of the corresponding dropped views, while adopting SIGReg from LeJEPA to prevent representation collapse. We pretrained CoFlu-Brain on 13,444 subjects from eight dataset groups and evaluated its representations via frozen-encoder linear probing on seven classification and two age-prediction tasks across seven datasets. CoFlu-Brain showed strong transfer across demographic, developmental, and clinical prediction tasks, outperforming the evaluated released models on most tasks. Random frame partitioning improved aggregate transfer, while the complete objective achieved the strongest overall performance. Code is available.