Dynamic Functional Connectivity

Forecasting time-varying functional connectivity from electroencephalography (EEG) requires modeling both history-dependent trends and structured variability across channels. Conditional flow matching provides a framework for distributional forecasting, yet it remains unclear whether graph-informed source distributions offer practical advantages over isotropic noise and strong deterministic predictors. We introduce a graph-structured residual flow framework that separates conditional mean prediction from stochastic residual transport. A history-only predictor estimates the future connectivity graph, while a graph Gaussian source encodes dependencies derived from past connectivity through a Laplacian-based covariance. A conditional velocity field transports source samples to future graph residuals, with transport time explicitly distinguished from physical EEG time. Our study identifies the conditions and controls needed to distinguish useful residual transport from improvements attributable to deterministic prediction, learned representations, and sampling effects.

High-resolution dynamic functional connectivity (DFC) can reveal rapidly evolving brain-network interactions, but short temporal windows yield noisy, often low-rank covariance estimates. Graph-Variate Dynamic (GVD) connectivity addresses this by modulating fast instantaneous interactions with stable trial-level support. This suppresses spurious fluctuations and emphasizes persistent, informative connections. We show that the Hadamard construction lifts low-rank instantaneous connectivity from the positive-semidefinite to the positive-definite cone, keeping high-resolution trajectories on the SPD manifold without ridge regularisation or post-hoc projection. We introduce GVD-CFM, a class-conditional generative model for high-resolution dynamic connectivity. Each trial is represented as SPD GVD matrices on a product Riemannian manifold, then mapped through a global log-Euclidean diffeomorphism and an invertible temporal DCT basis. A Transformer-based conditional flow models all spectral modes jointly and generates the full trajectory non-autoregressively in Euclidean coordinates while preserving exact correspondence with valid SPD sequences. Retaining the full DCT basis also enables decoding on denser temporal grids without retraining. Across multiple EEG motor-imagery datasets, GVD-CFM delivers the strongest overall results for held-out distributional fidelity, temporal-dynamics preservation, and synthetic-to-real classification. It also remains computationally efficient relative to strong raw-signal and direct GVD-space generative baselines. GVD-CFM therefore provides a practical framework for realistic, temporally coherent, high-resolution brain-network generation with preserved manifold structure and resolution-flexible decoding from a single trained model.

Multimodal fusion of structural MRI (sMRI) and dynamic functional network connectivity (dFNC) can reveal how brain structure relates to changing functional states. When the same structural latent representation is coupled with multiple states, applying independent vector analysis (IVA) separately to each state can produce unrelated structural decompositions, while forcing identical decompositions may suppress state-specific relationships. In addition, not every subject expresses every dynamic state. We propose masked structural residual IVA (MSR-IVA), a state-aware framework that combines a shared structural representation with state-specific residual adaptations and masks for incomplete state expression. On an Alzheimer's Disease Neuroimaging Initiative cohort, MSR-IVA improved matched source coupling by 6.5% and reduced unmatched dependence by 15.7% relative to the independent pairwise IVA baseline. Among subjects expressing both states, mean absolute cross-state structural source correlation was 0.9177 for MSR-IVA versus 0.2978 for no sharing, demonstrating controlled structural sharing that preserves source correspondence while allowing state-specific adaptation.

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.

Decoding emotional states from neural signals has been typically framed as a discrete, single-label classification task based on emotionally stable stimuli, a formulation that oversimplifies the continuous, fluid, and co-occurring nature of human affect. This study reconceptualizes emotion decoding by adopting a multi-target regression framework to track multiple overlapping emotional dimensions as continuous trajectories over time. Leveraging the robust generalization capabilities of Large Language Models (LLMs), we extracted fine-grained, continuous sentiment profiles from a naturalistic auditory narrative, Alice in Wonderland, to serve as scalable proxies for subjective affect from human fMRI dataset. Departing from standard classification paradigms or mass-univariate subtractive contrasts that filter out network dynamics, we leverage regularized and kernel-based machine learning algorithms as continuous estimators to track the magnitude of macroscale neural state variations. We demonstrate that models trained on temporal snapshots of Dynamic Functional Connectivity (DFC) significantly outperform static region-of-interest (ROI) amplitude representations, effectively capturing continuous emotional trajectories under rapidly fluctuating narrative input. Furthermore, by implementing graph-theoretical Explainable AI (XAI) techniques, we deconstruct the underlying predictive features to reveal highly interpretable, emotion-specific topological configurations. Collectively, these results highlight the utility of LLM-automated annotation in affective neuroscience and provide compelling empirical evidence for psychological constructionist frameworks, demonstrating that dynamic, distributed network interactions offer superior explanatory power over strictly locationist accounts of emotion.

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.

Several brain foundation models (FM) have recently been proposed to predict brain disorders by modelling dynamic functional connectivity (FC). While they demonstrate remarkable model performance and zero- or few-shot generalization, the salient features identified as potential biomarkers are yet to be thoroughly evaluated. We propose RE-CONFIRM, a framework for evaluating the robustness of potential biomarker candidates elucidated by deep learning (DL) models including FMs. From experiments on five large datasets of Autism Spectrum Disorder (ASD), Attention-deficit Hyperactivity Disorder (ADHD), and Alzheimer's Disease (AD), we found that although commonly used performance metrics provide an intuitive assessment of model predictions, they are insufficient for evaluating the robustness of biomarkers identified by these models. RE-CONFIRM metrics revealed that simply finetuning FMs leads to models that fail to capture regional hubs effectively, even in disorders where hubs are known to be implicated, such as ASD and ADHD. In view of this, we propose Hub-LoRA (Low-Rank Adaptation) as a fine-tuning technique that enables FMs to not only outperform customised DL models but also produce neurobiologically faithful biomarkers supported by meta-analyses. RE-CONFIRM is generalizable and can be easily applied to ascertain the robustness of DL models trained on functional MRI datasets. Code is available at: https://github.com/SCSE-Biomedical-Computing-Group/RE-CONFIRM.

Attention Deficit Hyperactivity Disorder (ADHD) is a prevalent neurodevelopmental disorder whose neuroimaging-based diagnosis remains challenging due to complex time-varying disruptions in brain connectivity. Functional MRI (fMRI) provides a powerful non-invasive modality for identifying functional alterations. Existing deep learning (DL) studies employ diverse neuroimaging features; however, static functional connectivity remains widely used, whereas dynamic connectivity modeling is comparatively underexplored. Moreover, many DL models lack interpretability. In this work, we propose D-GATNet, an interpretable temporal graph-based framework for automated ADHD classification using dynamic functional connectivity (dFC). Sliding-window Pearson correlation constructs sequences of functional brain graphs with regions of interest as nodes and connectivity strengths as edges. Spatial dependencies are learned via a multi-layer Graph Attention Network, while temporal dynamics are modeled using 1D convolution followed by temporal attention. Interpretability is achieved through graph attention weights revealing dominant ROI interactions, ROI importance scores identifying influential regions, and temporal attention emphasizing informative connectivity segments. Experiments on the Peking University site of the ADHD-200 dataset using stratified 10-fold cross-validation with a 5-seed ensemble achieved 85.18% +_5.64 balanced accuracy and 0.881 AUC, outperforming state-of-the-art methods. Attention analysis reveals cerebellar and default mode network disruptions, indicating potential neuroimaging biomarkers.

Dynamic functional connectivity (dFC) derived from resting-state functional magnetic resonance imaging (fMRI) has been extensively utilized in brain science research. The sliding window correlation (SWC) method is a widely used approach for constructing dFC by computing correlation coefficients between amplitude time series of signals from pairs of brain regions. In this study, we propose an integrated approach that incorporates both amplitude and phase information of fMRI signals to improve the detection of brain disorders. Specifically, we introduce a multi-scale fusion learning framework, namely MSFL, which leverages two complementary dFC features derived from SWC and phase synchronization (PS). Here, SWC captures amplitude correlations, while PS measures phase coherence within dFC. We evaluated the efficacy of MSFL in classifying autism spectrum disorder and major depressive disorder using two publicly available datasets: ABIDE I and REST-meta-MDD, respectively. The results indicate that MSFL significantly outperforms existing comparative models. Moreover, we performed model explanation analysis using the SHAP framework, which showed that both types of dFC features from SWC and PS contribute to detecting brain disorders.

Dynamic functional connectivity captures time-varying brain states for better neuropsychiatric diagnosis and spatio-temporal interpretability, i.e., identifying when discriminative disease signatures emerge and where they reside in the connectivity topology. Reliable interpretability faces major challenges: diagnostic signals are often subtle and sparsely distributed across both time and topology, while nuisance fluctuations and non-diagnostic connectivities are pervasive. To address these issues, we propose BrainSTR, a spatio-temporal contrastive learning framework for interpretable dynamic brain network modeling. BrainSTR learns state-consistent phase boundaries via a data-driven Adaptive Phase Partition module, identifies diagnostically critical phases with attention, and extracts disease-related connectivity within each phase using an Incremental Graph Structure Generator regularized by binarization, temporal smoothness, and sparsity. Then, we introduce a spatio-temporal supervised contrastive learning approach that leverages diagnosis-relevant spatio-temporal patterns to refine the similarity metric between samples and capture more discriminative spatio-temporal features, thereby constructing a well-structured semantic space for coherent and interpretable representations. Experiments on ASD, BD, and MDD validate the effectiveness of BrainSTR, and the discovered critical phases and subnetworks provide interpretable evidence consistent with prior neuroimaging findings. Our code: https://anonymous.4open.science/r/BrainSTR1.

The white matter of the brain is organised into axonal bundles that support long-range neural communication. Although diffusion MRI (dMRI) enables detailed mapping of these pathways through tractography, how white matter pathways directly facilitate large-scale neural synchronisation remains poorly understood. We developed a data-driven framework that integrates dMRI and functional MRI (fMRI) to model the dynamic coupling supported by white matter tracks. Specifically, we employed track dynamic functional connectivity (Track-DFC) to characterise functional coupling of remote grey matter connected by individual white matter tracks. Using independent component analysis followed by k-medoids clustering, we derived functionally-coherent clusters of white matter tracks from the Human Connectome Project young adult cohort. When applied to the HCP ageing cohort, these clusters exhibited widespread age-related declines in both functional coupling strength and temporal variability. Importantly, specific clusters encompassing pathways linking control, default mode, attention, and visual systems significantly mediated the relationship between age and cognitive performance. Together, these findings depict the functional organisation of white matter tracks and provide a powerful tool to study brain ageing and cognitive decline.