Functional Connectivity

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10 papers in the last four weeks, against 2 the four weeks before. 0.1% of all new papers.

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Latest papers 28

Oct 7, 2026cs.LG

MovieSTAGE: Scene, Transition, and Global Encoding for Movie-fMRI ADHD Classification

Naturalistic movie-fMRI provides a shared, temporally structured probe of brain dynamics, yet predictive models commonly rely on whole-run functional connectivity (FC) or temporally generic representations that are not aligned with narrative events. We introduce MovieSTAGE (Scene, Transition, and Global Encoding), a multiscale framework that combines hypergraph-structured FC-profile organization within scenes, unsigned FC-profile differences across adjacent scenes, and whole-movie FC. We evaluated 260 participants from the CMI-HBN Despicable Me cohort on case-control, ADHD-subtype, and three-class classification using 10 repetitions of stratified five-fold cross-validation, complete out-of-fold (OOF) predictions, and paired subject-cluster bootstrap and permutation tests. MovieSTAGE achieved AUROCs of 0.69, 0.73, and 0.75 and balanced accuracies of 67.6%, 69.8%, and 58.3%, respectively, yielding the highest mean point estimates among the evaluated methods. On the three-class task, the full model outperformed all two-branch variants, the HGNN scene encoder outperformed MLP, GAT, and BNT alternatives under matched settings, and the human-annotated partition outperformed duration-matched random and fixed-count GSBS controls. These controlled results support incremental predictive value from event-aligned scene and transition representations when combined with whole-movie FC in this cohort. Post-hoc model-derived analyses generated network-level hypotheses involving frontoparietal and default-mode systems.

Boseong Kim, Haejun Chung, Ikbeom Jang

Hanyang University, Seoul, Republic of Korea · Hankuk University of Foreign Studies, Yongin, Republic of Korea

Neuroimaging Classification Functional Connectivity

Oct 5, 2026cs.LG

CoHyFuse: Condition-wise Hypergraph Fusion with Global Connectome in Task-fMRI

Task-fMRI connectomes reveal state-dependent neural reconfigurations, yet conventional methods marginalize these signals by aggregating distinct conditions into static pairwise graphs, thereby obscuring condition-specific multi-ROI organization. We introduce CoHyFuse, a condition-aware ROI-centered hypergraph framework that constructs a task-state-specific incidence matrix from condition-wise functional connectivity (FC)-profile embeddings, allowing the same ROI to form different multi-ROI hyperedges across task phases. Condition-specific neighborhood sizes

K_q

further adapt the hyperedge scale to each task state, and the resulting condition embeddings are fused with a complementary whole-session FC branch for prediction. In the AABC cohort (N=1,074), CoHyFuse achieved the best mean out-of-fold predictive performance among evaluated baselines on FACENAME Fluid Cognition Composite (FCC) prediction (7.83

\pm

0.10 MAE, 0.439

\pm

0.026

R^2

) and VISMOTOR age prediction (7.52

\pm

0.37 MAE, 0.592

\pm

0.022

R^2

). In an auxiliary CMI-HBN attention-deficit/hyperactivity disorder (ADHD) classification benchmark (N=223), CoHyFuse obtained 72.0

\pm

2.1% macro-AUC and 74.2

\pm

2.9% accuracy. Ablation studies support the contributions of condition-wise incidence construction and dual-view fusion, suggesting that state-resolved ROI-set structure provides complementary predictive information beyond whole-session FC alone. Occlusion analysis identifies the Distraction condition as the primary driver of model prediction, pointing toward the Salience/Ventral Attention Network (SAN)--FrontoParietal Network (FPN) and within-SAN hyperedge-defined ROI-set motifs as candidate model-relevant patterns. This framework provides an interpretable, state-resolved view of the connectome for downstream cohort analysis.

Boseong Kim, Haejun Chung, Ikbeom Jang

Hanyang University, Seoul, Republic of Korea · Hankuk University of Foreign Studies, Yongin, Republic of Korea

Functional Connectivity Neuroimaging Hypergraph Learning Feature Fusion Brain Network Analysis

Sep 29, 2026cs.AI

BrainNet Studio: A Unified Toolkit for Brain Network Construction, Intelligent Analysis, and Visualization

Brain networks characterize structural and functional relationships among brain regions and support research on cognition, brain disorders, and brain-computer interfaces. Their time-varying topology and higher-order spatiotemporal dependencies are not adequately represented by conventional static networks. Existing tools primarily focus on static connectomes and provide limited integration of dynamic network modeling with modern graph and sequence learning methods. We present BrainNet Studio, an integrated toolkit for static and dynamic brain network analysis. It provides a unified workflow encompassing network construction, feature extraction, predictive modeling, candidate biomarker identification, visualization, and assisted interpretation. The toolkit integrates 27 algorithms, including deep learning, graph neural networks, and spatiotemporal sequence models, to support classification and the identification of discriminative brain regions and connections. A large language model generates researcher-verifiable summaries of functional connectivity, structural connectivity, and structure-function coupling at individual and group levels. Within a consistent computational framework, users can configure analytical tasks, compare methods, inspect outputs, and extend functionality without repeatedly assembling application-specific pipelines. BrainNet Studio provides a practical and extensible platform for connectome analysis in cognitive neuroscience, exploratory studies of brain disorders, and brain-computer interfaces. The toolkit is publicly available at https://github.com/xbrainnet/Brainnet-Studio.

Xiwei Zeng, Shengrong Li, Yiheng Liu +3

College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics, Nanjing, China · School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China

Functional Connectivity Neuroimaging Brain Network Analysis

Sep 29, 2026cs.AI

GRFBrain: Graph-Structured Rectified Flows for EEG Dynamic Modeling

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.

Haohui Jia, Zheng Chen, Jathurshan Pradeepkumar +4

Faculty of Information Science and Technology, Hokkaido University, Japan · SANKEN, The University of Osaka, Japan · Department of Computer Science, University of Illinois Urbana-Champaign, USA +1

Electroencephalography Functional Connectivity Conditional Flow Matching Rectified Flow Spatiotemporal Forecasting

Sep 29, 2026cs.AI

Flattening the Connectome Spectrum: A Spectral Filter for FC Induces a Pretraining Target for fMRI Encoders

Self-supervised pretraining reshaped prediction in language and vision, and brain foundation models (BFMs) inherited its promise. Representations learned from large unlabelled corpora should capture individual functional dynamics and generalise across cohorts. However, kernel ridge regression (KRR) fitted on functional connectivity (FC) matrices still predicts individual phenotypes more accurately than any BFM we tested. In this paper, we show that KRR is weighted by the eigenvalues of the FC which are miscalibrated for phenotype prediction. We apply an efficient spectral filter to recalibrate the eigenvalues of each subject's FC matrix, enabling the model to exploit more inter-individual variance. Across the 5 datasets, 11 parcellations and 6 prediction targets we tested, we match or exceed the KRR baseline. Based on this finding, we then pretrain a small encoder model on about 4,000 hours of fMRI from 162 open datasets, whereby we align the pairwise similarities between the embeddings of recording snippets with those between the recalibrated connectomes. Our model performs on par with the best of the 6 published BFMs we tested while having an order of magnitude fewer parameters. Our encoder performs better than FC on short scans and in smaller cohorts, especially in fingerprinting. We release the pretrained model weights, the code and the pretraining data, preprocessed and parcellated.

Giovanni Marraffini, Victoria Shevchenko, Carlo Alberto Barbano +1

UNITO · MIND

Kernel Ridge Regression Medical Imaging Foundation Models Functional Connectivity Self-Supervised Pre-Training fMRI Foundation Models Spectral Methods

Sep 28, 2026cs.CL

Deep Learning Methods in Neuroscience: From Modeling Molecular Mechanisms to Classifying States of Consciousness

A critical analysis of contemporary approaches to the study of conscious states. The review focuses on methods of classification, clustering, modeling of brain states under anesthesia and identification of measurable neurobiological characteristics of brain function. A comparative analysis was conducted in the following three major areas: automatic detection of states of consciousness using neural networks based on EEG and fMRI data; modeling of the structural-functional dynamics of the brain under the effects of anesthetics; and detection of neurophysiological indicators which correlate with the level of consciousness. The obtained conclusions demonstrate the growing effectiveness of deep neural models in the classification and prediction of brain states and the analysis of dynamic structural-functional connectivity. Nonetheless, significant limitations were also identified, including the limited interpretability of the models, the lack of standardized metrics, and the problem of the specificity of consciousness markers. Our findings support the need for developing hybrid, generalizible, physiologically grounded architectures. Furthermore, such approaches may improve the translational potential of computational models in clinical neuroscience. Diverse methods of machine and computational modeling have demonstrated their effectiveness in tasks of automatic clustering and classification of brain states, the development of multilevel models and the identification of connectivity patterns correlated with levels of consciousness. A larger-scale analysis and a larger dataset, as well as the implementation of model interpretability approaches are required for the practical application of the analyzed models. The models based on EEG and LFP are the most promising for clinical application due to their availability and the possibility of real-time monitoring.

Elena Benderskaya, Anastasiia Alifanova, Svetlana Batalova +2

Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya, 29, 195251 St.Petersburg, Russia

Functional Connectivity Brain Network Analysis

Sep 28, 2026cs.LG

Beyond Site Agreement: Re-estimation for Brain Network Generalization

Cross-site out-of-distribution (OOD) generalization in resting-state functional magnetic resonance imaging (rs-fMRI) often relies on learning task-discriminative representations from full-scan functional connectivity (FC) graphs and promoting invariance across source sites. However, FC graphs are estimated from finite, temporally correlated blood-oxygen-level-dependent (BOLD) sequences. Cross-site agreement therefore does not necessarily imply that predictive evidence remains supported under FC re-estimation within the same scan. In this paper, we propose Brain Network Re-estimation-Informed OOD Learning (BRIO), a framework that uses within-scan FC re-estimation to guide cross-site alignment. BRIO maps fullscan graphs and their re-estimates into consistently indexed connectome factors, enabling comparisons of their predictive contributions. It assesses re-estimation support from changes in these contributions relative to within-class subject variability and class separation. For each source-site pair and class, this task-calibrated support from both sites is combined with predictive relevance to form pairwise qualifications, which determine relative factor weights and overall alignment strength. Leave-one-site-out experiments on four real-world datasets (ABIDE, REST-metaMDD, SRPBS, and ABCD) show that BRIO consistently outperforms competitive baselines, with relative improvements of up to 3.8% in accuracy. These gains also persist under an alternative brain parcellation on ABIDE.

Yingxu Wang, Kunyu Zhang, Yanwu Yang3 +4

Mohamed bin Zayed University of Artificial Intelligence · Zhengzhou University · University Hospital Tübingen +3

Functional Connectivity OOD Generalization Brain Network Analysis

Sep 28, 2026cs.LG

FAST-Brain: A Flow-Aligned Spatio-Temporal Surrogate Brain Model

Modeling resting-state functional magnetic resonance imaging (rs-fMRI) data is crucial for understanding brain-wide neural activity. However, traditional methods struggle to capture complex temporal dynamics over long horizons, to account for the brain's anatomical spatial structure, and to model high-dimensional ambient signals that lie on a low-dimensional intrinsic subspace. We propose FAST-Brain, a unified flow-aligned spatio-temporal surrogate brain model that addresses all three challenges. At its core is a flow-aligned generative framework that directly predicts the clean blood-oxygen-level-dependent (BOLD) signal, paired with a graph convolutional network that captures spatial structural constraints and a Transformer that models long-range temporal dependencies. Theoretically, we show that under a low-dimensional subspace assumption, the approximation error of our model scales with the intrinsic dimension rather than the ambient dimension, which justifies our direct modeling of the BOLD signal. Extensive experiments on synthetic and Human Connectome Project datasets demonstrate that FAST-Brain achieves state-of-the-art performance in recovering functional connectivity, effective connectivity, and the implicit low-dimensional signal subspace.

Shucheng Liu, Changchun Shi, Kai Zhang +1

University of North Carolina at Chapel Hill · London School of Economics and Political Science

Neural Surrogate Modeling Functional Connectivity Generative Modeling Flow-Based Generative Modeling Neuroimaging Spatiotemporal GNNs+1

Sep 27, 2026q-bio.NC

Explainable Deep Learning of Resting-State Functional Connectomes Reveals Network Biomarkers of Adolescent Intelligence

Mapping resting-state brain organization to individual differences in cognitive ability remains a major challenge in population neuroinformatics. Although deep learning enables flexible modeling of brain connectivity, limited interpretability restricts its scientific and clinical utility. To address this objective, we developed an explainable deep learning framework based on sparse projected residual networks to predict fluid, crystallized, and total intelligence from resting-state functional magnetic resonance imaging in 5,285 participants from the Adolescent Brain Cognitive Development study. We incorporated three complementary explainability methods (Integrated Gradients, Gradient Shapley Additive Explanations, and Occlusion) to interpret model behavior. The framework outperformed existing approaches, achieving Pearson correlations of 0.44, 0.58, and 0.56 for fluid, crystallized, and total intelligence, respectively, corresponding to predictive improvements of 6 to 9 percent. All three explainability methods produced near-identical feature rankings (pairwise rank correlations greater than 0.99). Consensus maps revealed a dual-layered functional architecture where primary predictive hubs localized within canonical systems, while the strongest global predictive pathways frequently bypassed these hubs through distributed, long-range relay connections. These findings suggest that intelligence emerges from the interaction between localized computational hubs and distributed communication pathways. Ultimately, these normative network architectures provide clinical reference maps to detect individual deviations, supporting earlier diagnosis, cognitive subtype stratification, and treatment monitoring in atypical neurodevelopment.

Md. Tanvir Rahman, Nabil Anan Orka, Asaduzzaman Khan +1

School of Health and Rehabilitation Sciences, The University of Queensland, QLD 4072, Australia · Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Tangail 1902, Bangladesh

Explainable Artificial Intelligence Functional Connectivity Neuroimaging Brain Network Analysis

Sep 24, 2026cs.CG

It's the Geometry, Not the Model: Effective Rank and Subspace Alignment in Functional Connectivity Classification

Resting-state functional connectivity (FC) is widely used to classify brain phenotypes and disorders. Most pipelines use the full connectome and seek gains through model design. We instead examine how FC geometry constrains classification and cross-site transfer. Across-subject FC variation concentrates in a small effective subspace, suggesting substantial redundancy in nominal dimensions. Across cohorts, these subspaces may differ in orientation even when their effective ranks are comparable, potentially limiting transfer. Across 2,330 subjects from HCP, ABIDE, and ADHD-200, effective-rank analysis reveals strong spectral concentration. Projection onto leading components at the effective-rank scale recovers most of the full-FC classification performance. In ABIDE, site-specific effective subspaces are weakly aligned, and their principal-angle overlap predicts pairwise transfer after covariate adjustment despite comparable per-site effective ranks. Controlled rotations that alter subspace orientation while preserving the mean and covariance spectrum drive transfer toward chance, whereas displacement-matched label-orthogonal rotations do not. These results identify subspace orientation as a key factor in transfer degradation under controlled perturbations. This study offers a geometric diagnostic of FC generalization and suggests evaluating cross-site harmonization by its ability to align effective subspaces alongside classification accuracy.

Xiao Fan, Jingyuan Li, Yubo Han +6

Intrinsic Dimensionality Functional Connectivity Cross-Domain Transfer Learning Representation Alignment Latent Space Alignment

Sep 21, 2026cs.LG

Artificial Structure Function Search: Preserving Artificial Functional Connectivity for Structured Pruning

Structured pruning is a model compression technique that is used to reduce the computational cost of deploying deep neural networks on resource-constrained devices. Popular methods of pruning rely on opaque heuristics or weight-based criteria that give no indication as to the structural dependencies in the network. To address these limitations we present Artificial Structure Function Search (ASF-S): a novel structured pruning framework. ASF-S utilizes Principle Gradient Importance (PGI): a novel prune-candidate selection criteria that is inspired by structure-function relationships in the brain. By ensuring the pruned structure of the model respects topographical organization of the output layer, we define Artificial Functional Connectivity (AFC) for artificial neural networks. AFC provides evidence to demonstrate that accurate smaller networks can be found using careful prune candidate selection criteria. We present results for PGI as a selection criterion and for ASF-S as a pruning framework against recent benchmarks, demonstrating that our method yields model variants with 70% parameter reduction, that can recover baseline accuracy without re-training the pruned layers.

Mindula Illeperuma, Rafael Pina, Charuka Herath +2

Intitute for Digital Technologies, Loughborough University London · Center for Neuromorphic Intelligence, Aston University

Model Compression Functional Connectivity Neural Network Pruning

Sep 8, 2026cs.LG

XAI-Refine: An Automated Explanation-Knowledge Loop for Brain-Age Prediction

Brain-age prediction models are commonly evaluated by predictive accuracy, yet accurate predictions alone do not establish that a model relies on reproducible or neurobiologically supported mechanisms. Post-hoc explanation methods can expose these mechanisms, but existing workflows typically stop at diagnosis or require correction targets to be specified before model analysis. We propose XAI-Refine, an automated explanation-knowledge loop for brain-age prediction from resting-state functional connectivity. At each iteration, XAI-Refine consolidates complementary post-hoc analyses across repeated training runs into reliable, structured model explanations. It converts each reliable explanation into a neutral neurobiological question, retrieves and verifies relevant literature, and compiles the verified evidence into an admissible set in the same typed explanation space. The target for refinement is defined as the minimal projection of the current model explanation onto the admissible set induced by applicable verified knowledge. This revised explanation is then translated into a differentiable constraint while preserving the originating model variable, measurement operator, and applicable scope. Candidate updates are promoted only when multi-seed validation confirms target-directed explanatory movement, predictive performance remains within a prespecified guardrail, and non-target explanatory drift remains bounded. Experiments on functional-connectivity-based brain-age prediction evaluate predictive performance, explanation reliability, literature alignment, and target-specific model revision, illustrating a structured route from post-hoc analysis to evidence-guided model refinement.

Yang Qiao, Junjie Wu, Deqiang Qiu +2

Department of Computer Science Emory University Atlanta, Georgia, USA · Department of Radiology and Imaging Sciences Computational NeuroImaging & Neuroscience Lab, Emory University Atlanta, Georgia, USA · Department of Neurology Emory University School of Medicine Atlanta, Georgia, USA

Explainable Artificial Intelligence Functional Connectivity Brain Age Prediction Neuroimaging Explainability Evaluation

Aug 31, 2026eess.SP

Benchmarking External Generalization of SPD Matrix Learning for Resting-State fMRI Connectome Prediction

Resting-state functional magnetic resonance imaging (rs-fMRI) functional connectivity (FC) matrices are widely used for individual-level prediction, but strong performance within one cohort may not generalize to a new cohort. We ask whether within-dataset performance remains when the test data come from an entirely held-out rs-fMRI dataset. Each scan is represented as a regularized symmetric positive definite (SPD) correlation connectome, which allows methods to use the geometry of the SPD manifold. We introduce a reproducible age-prediction benchmark across six rs-fMRI datasets: COBRE, ADNIDOD, Cam-CAN, ABIDE, OASIS-3, and ADNI. The benchmark compares a vectorized correlation baseline, Tangent-Space Ridge, SPDNet, and split-wise Riemannian harmonization under within-dataset GroupKFold, pooled GroupKFold, and leave-one-dataset-out (LODO) evaluation. Within-dataset and pooled GroupKFold results are substantially more favorable than LODO results. When an entire dataset is held out, prediction error increases, differences among methods narrow, and performance is strongly affected by age-range mismatch and cohort heterogeneity. The benchmark provides common inputs, model settings, data splits, and analysis scripts so that future SPD matrix learning methods can be evaluated under the same external-validation protocol.

Ce Ju, Antoine Collas, Florent Bouchard +1

Inria, CEA, Universit´e Paris-Saclay, Palaiseau, France · Universit´e Paris-Saclay, CNRS, CentraleSup´elec, L2S, France

Functional Connectivity Brain Age Prediction Neuroimaging Cross-Dataset Generalization Brain Network Analysis

Aug 12, 2026q-bio.NC

Beyond Local Power: Functional Connectivity Analysis for Subject-Independent Learning Style Recognition

Identifying individual learning styles optimizes pedagogical efficacy. While traditional questionnaires are structured, behavioral tracking methods require prolonged interaction log accumulation. To overcome these temporal constraints, this paper proposes an objective Electroencephalography (EEG) approach evaluating Phase Locking Value (PLV) connectivity against localized features across the Active-Reflective (AR) and Verbal-Visual (VV) Felder-Silverman dimensions. EEG signals were recorded from 28 participants during Raven's Advanced Progressive Matrices tasks. Support Vector Machine classification used Leave-One-Subject-Out Cross-Validation (LOSO-CV) alongside a 70:30 intra-subject split. The VV dimension achieved 70.00% subject-level accuracy driven by distinct fronto-occipital polarization. Conversely, the AR dimension yielded lower cross-subject generalizability (55.56%) due to overlapping executive networks and a "Systematic Neural Inversion" phenomenon, where stable individual connectivity signatures operated diametrically opposed to global boundaries (up to 20-0 voting margins). Ultimately, these outcomes demonstrate that rigid "one-size-fits-all" classifiers are bounded by biological diversity, emphasizing the need for future adaptive feature transformation techniques to bridge the cross-subject generalization gap.

Wiga Maulana Baihaqi, Indriana Hidayah, Sri Kusrohmaniah +1

Dept. of Electrical and Information Engineering, Faculty of Engineering, Universitas Gadjah Mada, Yogyakarta, Indonesia · Department of Psychology, Faculty of Psychology, Universitas Gadjah Mada, Yogyakarta, Indonesia

Cross-Subject EEG Decoding Functional Connectivity

Aug 7, 2026cs.LG

FedDOSE: Federated Learning Framework Decomposing Site Effects for Modeling Brain Dynamic Functional Connectivity

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.

Deepank Girish, Yi Hao Chan, Yubin Zheng +2

Nanyang Technological University · Shanghai Jiao Tong University · Indian Institute of Technology Ropar

Functional Connectivity Medical Diagnosis Neuroimaging Federated Learning Heterogeneous Federated Learning Brain Network Analysis

Jul 29, 2026eess.IV

An Attention-Based Framework for Alzheimers Disease Classification Using Resting-State fMRI

Accurate identification of Alzheimers disease (AD) using resting-state functional magnetic resonance imaging (rs-fMRI) remains challenging due to the high dimensionality, noise, and complex inter-regional dependencies inherent in functional brain connectivity, which limit the effectiveness of traditional approaches based on handcrafted connectivity features or conventional machine learning models. In this work, we present an attention-based deep learning framework for Alzheimers disease classification that operates directly on rs-fMRI functional connectivity matrices by treating brain regions as tokens and employing a Transformer-inspired self-attention mechanism to model long-range and global functional dependencies across distributed brain networks. The proposed framework learns discriminative functional representations without reliance on manual feature engineering and is evaluated on a longitudinal cohort from the Alzheimers Disease Neuroimaging Initiative (ADNI) comprising cognitively normal and Alzheimers disease subjects with multiple visits. A subject-wise evaluation protocol is adopted to prevent information leakage across visits, and class-weighted optimization is incorporated to address mild class imbalance. Experimental results for binary AD versus cognitively normal classification demonstrate that the proposed attention- based rs-fMRI model achieves an accuracy of 88.95% and a ROC-AUC of 0.90, along with a favorable precision-recall balance, highlighting the effectiveness of self-attention-driven functional connectivity modeling as a robust and interpretable approach for Alzheimers disease detection using resting-state fMRI.

Harshiddhi Pathak, Gowtham Reddy N, Mrinal Acharya +1

School of Medical Science and Technology · Department of Computer Science and Engineering at the Indian Institute of Technology Gandhinagar · Dr B C Roy Multi Speciality Medical Research Centre, Indian Institute of Technology Kharagpur, India

Alzheimer's Disease Functional Connectivity Medical Image Classification Alzheimer's Disease Classification Neuroimaging

Jun 28, 2026cs.LG

BrainRiem: Riemannian Prototype Learning for Source-Free Cross-Site Brain Network Diagnosis

Multi-site functional MRI (fMRI) studies are essential for robust neuropsychiatric diagnosis yet suffer severe domain shifts from scanner heterogeneity, demographics, and site-specific acquisition protocols. Traditional domain adaptation requires concurrent source and target data access, violating clinical privacy regulations. Moreover, functional connectivity matrices lie on the Symmetric Positive Definite (SPD) manifold, where Euclidean operations cause geometric distortions corrupting diagnostic patterns. We propose BrainRiem, a source-free domain adaptation framework learning compact Riemannian brain prototypes via manifold-aware bi-level optimization. It employs the Log-Euclidean Metric to ensure prototypes remain valid SPD matrices, while Dirichlet Energy spectral calibration aligns their frequency characteristics with real brain networks. Only anonymized prototypes are transmitted to target sites, serving as stable anchors for training local models without source data access and reducing leakage under the evaluated attacks. Comprehensive experiments on ABIDE and REST-meta-MDD show BrainRiem consistently outperforms state-of-the-art source-free, traditional, and graph domain adaptation methods across diverse scanners and demographics. Notably, learned prototypes exhibit biologically interpretable connectivity patterns aligning with established neuroscience findings, validating the necessity of Riemannian geometry for brain network analysis.

Kunyu Zhang, Tianxiang Xu

Zhengzhou University, Zhengzhou 450000, China · Peking University, Beijing 102600, China

Source-Free Domain Adaptation Functional Connectivity Neuroimaging

Jun 15, 2026cs.CV

Sex-based Network-Specific Differences in Connectomes: A Krakencoder-Based Analysis

This study examines how deficiencies in one brain connectome modality propagate to the other, using the Krakencoder as a simulation framework. Structural and functional connectomes from 702 healthy participants in the Human Connectome Project were analyzed, with the impact of each of the Yeo-7 functional networks assessed separately. Seven scenarios were considered, each involving the removal of a single network while the remaining networks were preserved. The resulting perturbations in cross-modal predictions were quantified using three complementary metrics: KL divergence on eigenvalue spectra, Frobenius norm, and Wasserstein distance. In addition, the persistence of sex-specific information within the predicted connectomes was evaluated. Across all metrics and both prediction directions, the Default Mode Network produced the largest perturbations, whereas the Somatomotor network yielded the smallest. Sex differences in network-level perturbation signatures were subtle, with the best result being an accuracy of 66.09% from connectomes predicted under network-removal conditions. In contrast, connectomes predicted from intact inputs achieved substantially higher sex classification accuracy, reaching up to 84.76%. These findings confirm that full predicted connectomes retain considerably more sex-discriminative information than perturbation-derived signatures alone.

Vibhashree S H, Debanjali Bhattacharya, Vamshi Krishna Kancharla +1

Centre for Brain Research, Indian Institute of Science, Bengaluru 560012, India · Dept. of Artificial Intelligence, Amrita School of Artificial Intelligence, Amrita Vishwa Vidyapeetham, Bengaluru 560035, India

Functional Connectivity Neuroimaging Brain Network Analysis

May 31, 2026cs.CV

NeuroAlign: Hierarchical Multimodal Fusion of Dynamic and Structural Neuroimaging for MCI Analysis

Multimodal neuroimaging fusion of functional MRI (fMRI) and diffusion tensor imaging (DTI) provides complementary information for cognitive impairment analysis, but remains challenged by heterogeneous feature spaces and misaligned representations. We propose \textit{NeuroAlign}, a hierarchical framework for structured multimodal fusion. It introduces (1) \textit{Dual-Modal Hierarchical Alignment} (DMHA), which models multi-scale dynamic connectivity and aligns dynamic-static and functional-structural embeddings; and (2) \textit{Dual-Domain Hierarchical Interaction} (DDHI), which enables fine-grained modulation and global interaction between connectivity- and region-level features. To support feature-level inspection, we design \textit{Synergistic Activation Mapping} (SAM), a gradient-free, marker-oriented attribution method for DFC, SFC, ALFF, and FA. Evaluated on GUTCM, ADNI, and OASIS under five-fold validation, NeuroAlign achieves competitive MCI/SCD detection and preliminary cross-dataset transferability. Attribution analyses reveal modality-specific and partially consistent brain patterns, providing model-derived evidence for multimodal representation analysis.

Xiongri Shen, Zhenxi Song, Jiaqi wang +13

Department of Computer Science and Technology, Harbin Institute of Technology (Shenzhen), Shenzhen, 518055, China · School of Intelligence Science and Engineering, College of Artificial Intelligence, Harbin Institute of Technology, Shenzhen, 518055, China · School of Artificial Intelligence, Beijing University of Posts and Telecommunications, Beijing, China +5

Feature Attribution Functional Connectivity Cross-Modal Alignment Neuroimaging Multimodal Fusion

May 29, 2026q-bio.NC

The Variance Brain Foundation Models Forgot: Third-Order Statistics Predict Cognition Where Billion-Parameter Models Fail

Brain foundation models (BFMs) are self-supervised Transformers pretrained on fMRI data. We posit that these models should capture each subject's cognitive performance from their fMRI signal. Yet across three state-of-the-art BFMs and every readout we test, they predict cognition worse than a linear regression from the

\sim

80K parameters of the functional connectivity matrix (FC). The gap widens with scale: BrainLM's 650M model predicts cognition worse than its 111M. We attribute this to a \textbf{variance allocation problem}: BFM pretraining captures the variance components that dominate fMRI but not the higher-order structure that predicts cognition. Our per-cumulant analysis of the reconstructed signal shows that the second-order covariance is partially preserved, while the third-order co-skewness tensor is largely destroyed. To recover what BFMs lose, we design a linear pipeline that projects the fMRI signal into the subspace that best preserves its co-skewness and computes FC there. This \textbf{exceeds raw FC and every pretrained BFM} on every dataset and parcellation we test, outperforming prior state-of-the-art under controlled evaluation \textbf{with no pretraining and no GPU}. We \textbf{recover the raw-FC ceiling on BrainLM's forward pass} by finetuning with a loss targeted at this same subspace. This shows that the bottleneck is the pretraining objective, not the architecture or the model size.

Giovanni Marraffini, Gabriel Mahuas, Trinidad Borrell +2

Inria Saclay Île-de-France, CEA, Université Paris-Saclay, Palaiseau, France · Sigma Nova · Sorbonne Université, Institut du Cerveau - Paris Brain Institute - ICM +1

Medical Imaging Foundation Models Functional Connectivity fMRI Foundation Models Neuroimaging

May 22, 2026cs.CV

Distance-Aware Joint Spatio-Temporal Graph Contrastive Learning for Major Depressive Disorder Diagnosis

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.

Muhammad Asif Hasan, Yanming Zhu, Xuefei Yin +1

School of Information Technology and Communication, Griffith University, Australia

Functional Connectivity Depression Detection Graph Contrastive Learning Neuroimaging Spatiotemporal GNNs

May 21, 2026cs.NE

Rare Events, Real Signals: Functional Ensembles as Units of Computation in Deep Spiking Networks

We investigate how internal representations emerge across hierarchical processing systems by introducing a neuroscience-inspired framework for analyzing deep spiking neural networks (SNN) through the lens of functional connectivity. Drawing on concepts from systems neuroscience and information theory, we form the first-order functionally-connected (1FC) group of a neuron based on its statistically significant pairwise correlations with neurons from the previous layer of a trained SNN architecture. We then track its response properties during inference under various conditions. Our analysis shows that several principles of functional connectivity previously observed in biological cortex are preserved in spiking ResNet architectures. These 1FC ensembles display interesting properties: their aggregate cofiring reliably predicts downstream neuronal responses through a robust, ReLU-like input-output relationship, whose gain scales systematically with ensemble size. Reliable encoding of the presented class emerges only during high 1FC cofiring events, which themselves occur infrequently, indicating that informative representations are concentrated in rare but highly coordinated activity patterns. Under uniform random noise or adversarial perturbations, these response profiles are disrupted, particularly in early and intermediate layers. This enables a targeted high-resolution interrogation at specific nodes and pathways. We showed that the functional connectivity structure is shaped by learning and this structure breaks under weight permutation. These establish 1FC ensembles as a functionally meaningful substrate for input encoding and information transfer, with potential implications in designing targeted fine-grained diagnostics on the information flow.

Aditi Aravind, Konstantinos Ladakis, Mario Alexios Savaglio +2

University of Crete, Greece · 2Foundation of Research & Technology - Hellas (FORTH), Greece · 4Harvard Medical School, USA +2

Functional Connectivity Neural Network Interpretability Spiking Neural Networks Neural Encoding

May 21, 2026cs.LG

Riemannian geometry meets fMRI: the advantages of modeling correlation manifolds and eigenvector subspaces

Correlation matrices are fundamental summaries of functional brain networks, yet standard analyses often treat entries independently, ignoring the curved geometry of correlation space. Existing geometric methods frequently lack closed-form operations or depend on arbitrary region ordering, limiting scalability. We introduce a scalable geometric framework with two components: (i) the Off-log metric, a smooth transformation mapping correlation matrices to symmetric zero-diagonal matrices. This enables closed-form expressions for distances, Frechet means, and linear models, allowing standard statistical modeling without complex manifold optimization. (ii) Grassmannian subspace discrimination, which compares subjects via principal-angle distances between eigenvector subspaces, resolving inherent sign and basis ambiguities. Both components integrate into standard machine-learning workflows for inference, regression, and classification. Validated across two clinical cohorts (Parkinson's and psychosis) and three ageing fMRI datasets, the Off-log metric increased sensitivity in permutation tests and matched or exceeded Riemannian and Euclidean baselines in classification. Brain-age prediction performance was comparable, with Riemannian metrics excelling in two of three cohorts. The Grassmannian method consistently outperformed Euclidean baselines, highlighting disease-relevant networks. Overall, geometry-aware representations improve sensitivity and predictive performance while remaining straightforward to deploy at scale.

Mario Severino, Manuela Moretto, Robert A. McCutcheon +1

Department of Information Engineering, University of Padova, Padova, Italy · Department of Neuroimaging, Institute of Psychiatry, Psychology and Neuroscience (IoPPN), King’s College London, London, United Kingdom · Department of Psychiatry, University of Oxford, Warneford Hospital, Warneford Ln, Headington, Oxford OX3 7JX, United Kingdom +2

Functional Connectivity Neuroimaging Riemannian Geometry

May 13, 2026cs.AI

Network-Aware Bilinear Tokenization for Brain Functional Connectivity Representation Learning

Masked autoencoders (MAEs) have recently shown promise for self-supervised representation learning of resting-state brain functional connectivity (FC). However, a fundamental question remains unresolved: how should FC matrices be tokenized to align with the intrinsic modular organization of large-scale brain networks? Existing approaches typically adopt region-centric or graph-based schemes that treat FC as structurally homogeneous elements and overlook the large-scale network brain organization. We introduce NERVE (Network-Aware Representations of Brain Functional Connectivity via Bilinear Tokenization), a self-supervised learning framework that redefines FC tokenization by partitioning FC matrices into patches of intra- and inter-network connectivity blocks. Unlike image-based MAE, where fixed-size patches share a common tokenizer, FC patches defined by network pairs are heterogeneous in size and correspond to distinct functional roles. To resolve this problem, NERVE embeds FC patches through a novel structured bilinear factorization. This formulation preserves network identity and reduces parameter complexity from quadratic to linear scaling in the number of networks. We evaluate NERVE across three large-scale developmental cohorts (ABCD, PNC, and CCNP) for behavior and psychopathology prediction. Compared to structurally agnostic MAE variants and graph-based self-supervised baselines, the proposed network-aware formulation yields more stable and transferable representations, particularly in cross-cohort evaluation. Ablation studies confirm that the proposed bilinear network embedding and anatomically grounded parcellation are critical for performance. These findings highlight the importance of incorporating domain-specific structural priors into self-supervised learning for functional connectomics. Code is available at: https://github.com/leomlck/NERVE.

Leo Milecki, Qingyu Hu, Bahram Jafrasteh +2

Department of Radiology, Weill Cornell Medicine, New York, NY, USA. · School of Electrical and Computer Engineering, Cornell University and Cornell Tech, New York, NY, USA.

Representation Learning Masked Autoencoders Functional Connectivity Self-Supervised Learning Neuroimaging Brain Network Analysis

May 7, 2026q-bio.NC

Learning Cross-Atlas Consistent Brain Disorder Representations via Disentangled Multi-Atlas Functional Connectivity Learning

Functional connectivity (FC) derived from resting-state fMRI is widely used to characterize large-scale brain network alterations in neurological and psychiatric disorders. However, FC construction critically depends on the choice of brain atlas, and different parcellations may emphasize distinct organizational features, leading to heterogeneous and sometimes inconsistent representations. Existing multi-atlas approaches partially alleviate this issue but often fuse atlas-derived features or predictions at a relatively shallow level, while single-atlas disentanglement methods do not explicitly address cross-atlas heterogeneity. We propose Multi-Atlas Disentangled Connectivity LEarning (MADCLE), a multi-branch representation learning framework that jointly encodes FC matrices derived from different brain atlases. Rather than introducing a single explicitly shared latent variable across parcellations, MADCLE learns atlas-wise disease-related representations and encourages them to be cross-atlas consistent through distributional alignment. Meanwhile, covariate-related and atlas-dependent residual factors are modeled separately using covariate similarity supervision, atlas-specific reconstruction, and decorrelation constraints, thereby reducing the leakage of non-disease and parcellation-dependent information into the disease-related embeddings. Experiments on the ADNI and ADHD-200 datasets suggest that MADCLE achieves competitive or improved performance compared with single-atlas baselines, multi-atlas GNN/Transformer models, and recent multi-atlas consistency frameworks. These results support the potential value of structured disentanglement for FC-based disorder identification under heterogeneous parcellation schemes.

Minheng Chen, Chao Cao, Jing Zhang +2

Department of Computer Science and Engineering, University of Texas at Arlington, United States · School of Computing, University of Georgia, United States

Multi-View Consistency Disentangled Representation Learning Functional Connectivity Medical Diagnosis Neuroimaging

May 7, 2026cs.LG

Learning beyond Site Bias for OOD Generalization in Brain Networks

Graph-based learning from functional magnetic resonance imaging (fMRI) has shown strong potential for brain network analysis. However, existing methods often degrade under cross-site out-of-distribution (OOD) settings, as site-dependent confounder effects can obscure disease-related connectivity patterns and static functional connectivity (FC) does not explicitly capture informative within-scan variations. In this paper, we propose Cross-site OOD Robust brain nEtwork (CORE), a unified framework for brain network learning across unseen sites. First, CORE estimates site-specific confounder effects and aggregates the resulting deconfounders by cross-source reliability for unseen-site correction, while extracting a population scaffold of reproducible label-associated connections from site-wise residualized FC. It then summarizes temporal variations on scaffold edges into compact descriptors for line-graph modeling. Finally, prior-guided subject-adaptive gating modulates message passing, balancing population priors with individual variability. Extensive leave-one-site-out experiments on ABIDE, REST-meta-MDD, SRPBS, and ABCD demonstrate that CORE consistently outperforms competitive baselines, with up to a 10.3% relative improvement in accuracy. These gains also persist across different brain parcellation schemes on ABIDE.

Yingxu Wang, Kunyu Zhang, Yanwu Yang +5

Zhengzhou University · City University of Hong Kong

Functional Connectivity Domain Generalization OOD Generalization Neuroimaging Spatiotemporal GNNs Brain Network Analysis

Apr 23, 2026q-bio.NC

Foundation models for discovering robust biomarkers of neurological disorders from dynamic functional connectivity

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.

Deepank Girish, Yi Hao Chan, Sukrit Gupta +2

College of Computing and Data Science, Nanyang Technological University, Singapore

Medical Imaging Foundation Models Functional Connectivity fMRI Foundation Models Scientific Discovery Low-Rank Adaptation Neural Network Interpretability+2

Apr 20, 2026cs.LG

Modeling Higher-Order Brain Interactions via a Multi-View Information Bottleneck Framework for fMRI-based Psychiatric Diagnosis

Resting-state functional magnetic resonance imaging (fMRI) has emerged as a cornerstone for psychiatric diagnosis, yet most approaches rely on pairwise brain cortical or sub-cortical connectivities that overlooks higher-order interactions (HOIs) central to complex brain dynamics. While hypergraph methods encode HOIs through predefined hyperedges, their construction typically relies on heuristic similarity metrics and does not explicitly characterize whether interactions are synergy- or redundancy-dominated. In this paper, we introduce

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-information, a signed measure that characterizes the informational nature of HOIs, and integrate third- and fourth-order

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-information into a unified multi-view information bottleneck framework for fMRI-based psychiatric diagnosis. To enable scalable

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-information estimation, we further develop two independent acceleration strategies: a Gaussian analytical approximation and a randomized matrix-based Rényi entropy estimator, achieving over a 30-fold computational speedup compared with conventional estimators. Our tri-view architecture systematically fuses pairwise, triadic, and tetradic brain interactions, capturing comprehensive brain connectivity while explicitly penalizing redundancy. Extensive evaluation across four benchmark datasets (REST-meta-MDD, ABIDE, UCLA, ADNI) demonstrates consistent improvements, outperforming 11 baseline methods including state-of-the-art graph neural network (GNN) and hypergraph based approaches. Moreover, our method reveals interpretable region-level synergy-redundancy patterns which are not explicitly characterized by conventional hypergraph formulations.

Kunyu Zhang, Qiang Li, Vince D. Calhoun +1

Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV, The Netherlands · Tri-Institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, and Emory University, Atlanta, GA, 30303, USA · Department of Physics and Technology, UiT - The Arctic University of Norway, Tromsø, 9019, Norway

Functional Connectivity Multi-View Learning Information Bottleneck Neuroimaging Brain Network Analysis