Group Independent Component Analysis (gICA) is widely used to decompose high-dimensional functional MRI data into interpretable brain networks. However, conventional gICA primarily identifies components shared across subjects. This group-level assumption can limit the recovery of networks present only in individuals or subject subsets, reducing sensitivity to intersubject heterogeneity in clinical neuroimaging datasets. We introduce Copula-Linked Group ICA (CoLiG-ICA), an algorithm in the Group ICA 2.0 framework that jointly estimates template-linked, cohort-only, and subject-only brain networks within a unified model. CoLiG-ICA combines ICA-based spatial decomposition, copula-based dependence modeling, and deep learning optimization to preserve the consistency and interpretability of template-constrained ICA while enabling free components beyond the reference networks. By linking subject decompositions to shared templates and jointly estimating cohort-only and subject-only sources, CoLiG-ICA represents individual variability not captured by conventional group priors. We evaluate CoLiG-ICA using resting-state fMRI data from the UCLA-CNP dataset and compare it with conventional constrained ICA in estimating template-linked components, discovering additional free components, improving component independence, and capturing subject-level variability beyond the shared group prior. Compared with MOO-ICAR, CoLiG-ICA showed significantly lower intercomponent spatial dependence, indicating improved subject-level component independence, and significantly reduced motion-related variance in the template-linked components. Additionally, in a schizophrenia-only group analysis, CoLiG-ICA identified three additional resting-state networks beyond the 53 template-linked NeuroMark components: one sensorimotor and two visual networks.
Yiheng Liu, Chuhang Zheng, Peiliang Gong +3eess.IV cs.AI
EEG-based visual decoding provides a non-invasive pathway for interpreting visual semantics. However, existing methods often overlook the perceptual asymmetry between foreground and background in complex scenes, leading to background interference and semantic misalignment. EEG signals also exhibit rapid temporal dynamics and nonstationary spatial patterns, making it difficult to capture the time-varying brain connectivity associated with focal visual attention. To address these limitations, we propose FSDBN, a unified framework for robust EEG-visual decoding. FSDBN introduces Semantic-Consistent Saliency Alignment to separate semantically relevant foreground regions from background noise under joint saliency and semantic constraints. It further employs Semantic-Prior Dynamic Gating Foreground Fusion to adaptively regulate the contributions of foreground and background features. In parallel, EEG signals are modeled as adaptive spatiotemporal brain networks whose functional connectivity dynamically reorganizes to capture neural responses to salient foregrounds. Experiments on zero-shot brain-to-image retrieval demonstrate that FSDBN achieves 69.0 percent top-1 accuracy and 92.2 percent top-5 accuracy, outperforming previous state-of-the-art methods. Code is available at https://github.com/LiuYiheng1/FSDBN-EEG.
Functional brain networks exhibit a hierarchical organization across ROI, community, and whole-brain levels, supporting local processing, inter-community coordination, and global integration. Recent studies have demonstrated that brain community-aware modeling is beneficial for both diagnosis and biomarker identification of brain networks. However, existing brain graph modeling methods often struggle to model ROI-community interactions, thereby failing to fully exploit the hierarchy across ROI, community, and whole-brain network levels. To address this issue, inspired by deep hyperbolic learning in modeling hierarchical structures, we propose a novel framework, termed Hyperbolic Learning on Brain Graphs (HLBG), for brain network analysis. The core idea of HLBG is to exploit the inherent hierarchical geometry of hyperbolic space to model the hierarchical relationships among ROIs, functional communities, and the whole-brain network, thereby learning hierarchy-aware and highly discriminative representations for brain network data. Specifically, HLBG first projects representations from ROIs, communities, and the whole-brain network into Lorentzian hyperbolic space. Then, the multi-level hierarchy is imposed via two geometric entailment constraints. In addition, we introduce a new Graph-aware Mamba (GaMamba) model, which incorporates topology-derived structural prompts into Mamba to capture long-range dependencies while preserving graph topological information. Experiments on ABIDE-I and REST-MDD demonstrate that HLBG outperforms state-of-the-art methods and identifies disorder-relevant functional biomarkers.
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.
Vibhashree S H, Debanjali Bhattacharya, Vamshi Krishna Kancharla +1cs.CV q-bio.NC
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.
Multimodal neuroimaging, integrating functional connectivity from fMRI and structural connectivity from DTI, enables non-invasive analysis of brain networks using graph neural networks. However, demographic factors such as age and sex systematically confound the relationship between brain connectivity and clinical outcomes, causing GNNs to exploit spurious shortcuts rather than learning causally invariant representations. While recent causal GNN methods introduce causality at the graph-modeling level, their causal mechanisms remain domain-agnostic without accounting for the real-world confounders inherent in clinical neuroimaging data. Moreover, brain networks are constructed from atlas-based parcellations where each region exhibits distinct sensitivity to demographic factors, necessitating region-aware adjustment. We propose Artemis, a region-level causal framework that bridges this gap with causal intervention at each brain region independently by learning region-specific confounder representations with lightweight parameters. Our adjustment comprehensively utilized the multimodal functional and structural features for graph reasoning as a plug-in module compatible with arbitrary GNN backbones. Experiments on three benchmarks, ADNI for disease diagnosis, OASIS for dementia staging, and HCP for sex classification, demonstrate consistent improvements over representative GNN-based baselines. Multiple supporting experiments further demonstrate statistical significance and neuroscientific interpretability.
The graphical representation of the brain offers critical insights into diagnosing and prognosing neurodegenerative disease via relationships between regions of interest (ROIs). Despite recent emergence of various Graph Neural Networks (GNNs) to effectively capture the relational information, there remain inherent limitations in interpreting the brain networks. Specifically, convolutional approaches ineffectively aggregate information from distant neighborhoods, while attention-based methods exhibit deficiencies in capturing node-centric information, particularly in retaining critical characteristics from pivotal nodes. These shortcomings reveal challenges for identifying disease-specific variation from diverse features from different modalities. In this regard, we propose an integrated framework guiding diffusion process at each node by a downstream transformer where both short- and long-range properties of graphs are aggregated via diffusion-kernel and multi-head attention respectively. We demonstrate the superiority of our model by improving performance of pre-clinical Alzheimer's disease (AD) classification with various modalities. Also, our model adeptly identifies key ROIs that are closely associated with the preclinical stages of AD, marking a significant potential for early diagnosis and prevision of the disease.
Mario Severino, Manuela Moretto, Robert A. McCutcheon +1cs.LG
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.