Human Brain Networks

Multimodal large language models predict brain activity, but brain alignment has been a measurement, not a design tool. We propose the Platonic brain bridge hypothesis: omni models, multimodal large language models that process video, audio and text jointly, converge on brain-like representations usable in both directions. From model to brain, brain-likeness of seven omni models is stable across participants, rises with every input channel in three bases, and our encoders lead the Algonauts 2025 out-of-distribution leaderboard. From brain to model, Brain-MoE fixes the expert partition of a frozen base to the seven networks of human cortex, trains experts on network-labelled Brain-AVQA questions, raises held-out accuracy in all 15 model-benchmark pairs by 6.42 percentage points on average and exceeds capacity-matched random experts in 14. Brain-Scope localizes the correspondence to sparse features whose removal weakens brain prediction. Human brain organization is therefore a usable architectural prior for multimodal large language models.

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.

Photonic reservoir computing has attracted increasing attention as a fast and low-cost approach for time-series prediction. Photonic reservoir computing utilizes the high speed, broad bandwidth, and spatial parallelism of light. However, the effect of the internal connection structure (network topology) on the computing performance has not been investigated for large-scale photonic reservoirs. In this study, we experimentally and numerically demonstrate photonic reservoir computing using a spatial light modulator to systematically evaluate the relationship between the network topology and the performance of reservoir computing. We introduce complex network structures such as small-world and scale-free network topologies of the internal nodes in the reservoir. We perform the memory capacity measurement and the one-step-ahead prediction task of the chaotic time series to compare the performance. We found that the small-world network exhibits the maximum memory capacity and the best prediction performance. Our numerical calculations reveal that the performance of the time-series prediction can be optimized by changing the rewiring probability of the network and the leak rate of the reservoir. We also implement photonic human brain network as a reservoir, which is designed by the connectomes of human brain activities. We found that the network topology strongly affects the performance of reservoir computing, and the small-world network structure outperforms the other configurations.

Brain network analysis is crucial for understanding cognition and neurological disorders, yet existing deep learning methods mainly treat connectome analysis as a graph-to-logit classification problem, offering limited explanatory reasoning. Large language models (LLMs) provide a promising interface for knowledge-intensive scientific analysis, but directly applying general-purpose LLMs to brain networks remains challenging due to the structure-language gap, limited neuroscience grounding, and overconfident positive predictions. In this paper, we propose \textbf{BrainAgent}, an agentic LLM framework for knowledge-enhanced brain network analysis. BrainAgent reformulates connectome classification as an iterative process of topology-aware understanding, external retrieval, reasoning, and reflection. Specifically, it first converts raw brain networks into compact multi-level structural descriptions through brain-specific analysis tools, then retrieves relevant neuroscience knowledge and task-specific cases to ground the reasoning process, and finally generates structured predictions with reflective verification. Experiments on four public rs-fMRI datasets show that BrainAgent consistently improves different closed-source and open-source LLM backbones over direct prompting and standard reasoning baselines. Further ablation and interpretability analyses demonstrate the effectiveness of each component and show that BrainAgent produces more comprehensive, multi-level, and verifiable explanations.These results indicate that agentic LLMs provide a practical route toward interpretable and knowledge-grounded brain network analysis.

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.

Many complex systems such as brain networks, financial markets, and gene-regulatory circuits are described not by a fixed graph but by one that changes over time. A standard way to summarise such structure at each instant is the sparse precision (inverse-covariance) matrix, and the time-varying graphical lasso (TVGL) turns a multivariate signal into a smooth chain of these matrices. We introduce TVGL-CFM, a single model that learns the distribution of such chains and can both generate new, realistic time-varying network trajectories for a given class and forecast how an observed trajectory will continue. Each precision matrix lives on a curved space of positive-definite matrices, but a log-Euclidean chart flattens an entire trajectory into an ordinary vector space, so a simple conditional flow-matching model can be trained and sampled there while every decoded matrix is guaranteed to be a valid precision matrix. For forecasting we start the flow not from noise but from a rough extrapolation of the recent history, so the model only has to learn a small correction. Across EEG motor-imagery, chaotic systems, and gene-expression data, TVGL-CFM generates trajectories that keep the class-discriminative structure of real data, and it forecasts future connectivity more accurately than raw-signal baselines. Generating the structured precision trajectory directly is therefore more faithful than generating raw signals and estimating connectivity afterwards.

A series of results from the NeuroAI over the past fifteen years have raised core questions both about how to compare Deep Neural Network (DNN) models to the brain, and about how much convergent evolution to expect between artificial networks and real brain networks. Here, we show that for any two minimal DNN solutions to a sufficiently hard task: (i) "weak" alignment of network representations based on affine mappings guarantees "strong" alignment of privileged axes, and (ii) alignment "zippers" up the network hierarchy, causing the emergence of privileged axes from end-to-end task optimization. These results formalize the notion of contravariance from Cao and Yamins [2024], and illustrate important consequences for the theory of NeuroAI: with sufficiently strong tasks, choice of metric for inter-network comparison is not all that sensitive, and that convergent evolution is probably inevitable.

Alzheimer's disease (AD) is a common neurodegenerative disorder, and early diagnosis is of great significance for delaying disease progression and enabling timely intervention. Mild cognitive impairment (MCI), which represents an intermediate clinical stage between cognitively normal aging and AD. Structural magnetic resonance imaging (sMRI) provides detailed characterization of anatomical structures and plays an important role in AD-related brain analysis. However, existing sMRI-based brain network methods typically rely on a single graph construction strategy, limiting their ability to jointly capture spatial relationships and morphological similarities between brain regions. To address these issues, this paper proposes an sMRI-based multi-view masked graph neural network model (MVMGNN) for AD diagnosis. A joint node-edge masking mechanism is proposed to simultaneously select radiomics feature dimensions and structural connections, reducing redundancy during graph learning. Furthermore, a patient-level cross-view gated fusion mechanism is proposed to integrate multi-view representations. Experimental results on the ADNI dataset demonstrate that MVMGNN outperforms several competing approaches in AD classification. Interpretability analysis further demonstrates that MVMGNN is able to identify key brain regions associated with AD, providing useful insights into discriminative patterns in sMRI-based brain networks.Our implementation is publicly available at https://github.com/chenzhao2023/MVMGNN_AD

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.

Large-scale, multi-subject widefield calcium imaging provides unprecedented access to brain-wide cortical dynamics. However, the high dimensionality, complex spatiotemporal structure, and substantial task-irrelevant activity in widefield recordings have largely restricted modeling efforts to single-session analyses, limiting scalability and generalization. While multi-subject pretrained models have been explored for some neural modalities, multi-subject models for widefield calcium imaging have not yet been demonstrated; further, subject-invariant zero-shot behavior decoding remains elusive for multi-subject models across neural modalities more broadly. As a first step toward foundation modeling of widefield data, we introduce WiCAT, a multi-subject model that leverages self-supervised pretraining to both outperform single-session models and enable zero-shot behavior decoding on unseen subjects. WiCAT introduces an atlas-grounded tokenization scheme without session-specific components and learns globally shared spatiotemporal representations. Across multiple widefield datasets, the pretrained model supports lightweight downstream decoding, transfers across subjects, tasks, and datasets, and outperforms baseline models. Notably, the model also achieves robust zero-shot continuous behavior decoding and left-out brain region reconstruction on unseen subjects.

Electroencephalography (EEG) offers a noninvasive approach for examining neurophysiological correlates of dimensional psychopathology, yet systematic evidence across EEG paradigms and feature granularities remains limited. Here, we develop a granularity-aware EEG feature pipeline that organizes multi-scale descriptors into global, regional, and channel levels. Using the Healthy Brain Network (HBN) cohort, we evaluate the prediction of four psychopathology dimensions: p-factor, internalizing, externalizing, and attention problems, across four EEG paradigms. Given the heterogeneity of pediatric psychopathology and the moderate reliability of questionnaire-derived scores, this setting represents a challenging feasibility test rather than a clinical screening scenario. Tree-based models and granularity-balanced feature selection showed promising improvements over conventional approaches in selected conditions, although effect sizes remained modest. Visualization of selected markers revealed dimension-specific spatial and spectral patterns that were broadly aligned with existing neurophysiological knowledge. An exploratory cross-dataset sanity check on the independent PEARL cohort suggested that the proposed selection principle remains technically feasible under protocol shifts, without claiming cross-dataset generalizability. Overall, multi-scale EEG features contain weak but detectable signals related to dimensional psychopathology, and granularity-aware selection may serve as a useful feature-reduction strategy for future EEG-based phenotyping studies.

Graph Neural Networks (GNNs) have been widely used to capture spatial functional connectivity patterns to improve electroencephalography (EEG)-based depression recognition performance. However, the functional connectivity of brain networks in patients with depression exhibits an inherent hierarchical structure, making it difficult to capture accurate connection patterns. To address these issues, this paper proposes a novel model named Sample-Adaptive Hyperbolic Graph Neural Network (SA-HGNN), which aims to accurately extract the authentic hierarchical structure of depression-affected brain networks. Specifically, the proposed model comprises three core modules. First, a Sample-Adaptive Graph Construction module dynamically constructs personalized brain network topologies to capture more complex spatial relationships within the brain network. Second, hyperbolic graph convolution is employed to overcome the representation bottlenecks of Euclidean space, leveraging hyperbolic geometry to precisely capture latent hierarchical relationships within the brain network. Finally, an Attention Pooling module adaptively filters out highly redundant noise channels in EEG signals, effectively mitigating the interference of inherent noise on the authentic hierarchical topology. Extensive experiments on public EEG datasets demonstrate the superior performance of our method across resting-state and task-related paradigms, validating its robustness to noise and efficacy in capturing abnormal functional connectivity patterns in brain networks of patients with depression.

Effective brain disease diagnosis requires the synergy of brain connectivity patterns and high-level semantic knowledge. Existing methods, however, largely treat semantics from large language models (LLMs) as auxiliary features or supervision, limiting their direct role in decision-making and constraining classification stability and robustness. To overcome this, we propose a semantic-aligned brain network framework that actively integrates LLM-derived semantics into the prediction process. Specifically, ROI-level semantics are first incorporated via global self-attention to enrich node representations and provide whole-brain context. Multi-scale hypergraphs are then constructed to explicitly model functional subnetworks and multi-ROI interactions, addressing the locality limitations of traditional GNNs and capturing high-order dependencies. Finally, a decision-level semantic alignment mechanism selectively injects patient-specific textual embeddings into graph representations, enabling semantics to directly guide predictions without perturbing the underlying network structure. Experiments on public brain network datasets ABIDE and ADHD-200 demonstrate state-of-the-art performance, enhanced stability, and improved interpretability, particularly in small-sample settings.

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.

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.

Whole-brain 4D fMRI generation is valuable for modeling functional brain dynamics, yet existing fMRI foundation models mainly target representation learning and downstream prediction rather than conditional predictive generation. We introduce BrainWorld, a structural-prior-conditioned generative model for whole-brain 4D fMRI dynamics. BrainWorld uses sMRI as subject-level anatomical context to guide future fMRI generation, integrating structural information into the denoising process rather than treating it as a parallel modality. Evaluated on 22 datasets spanning diverse cohorts and brain states, BrainWorld generates stable 4D fMRI trajectories up to 400 frames, improves downstream performance through generated-example augmentation, and learns transferable multimodal representations that outperform baselines. Together, these results establish BrainWorld as a condition-aware generative framework for long-horizon brain dynamics modeling and multimodal representation learning.

Post-traumatic epilepsy (PTE) is a severe complication of traumatic brain injury (TBI). Yet, early identification remains challenging due to the complex structural and functional alterations it induces in the brain. To address this, we propose a dynamic multimodal Mixture-of-Experts (MoE) framework that integrates functional and structural connectivity through time-aware functional-structural encoding and class-conditioned expert routing. Within this framework, modality-specific and cross-modal experts learn complementary representations, while a Modality-Class MoE (MCoE) module dynamically adjusts expert weights according to each classification objective. Experimental results across three binary classification tasks demonstrate that the framework consistently outperforms static fusion baselines, and high-interpretability analyses further reveal meaningful regions of interest (ROIs) interactions. This dynamic multimodal expert framework effectively captures class-dependent brain interaction patterns and provides an interpretable approach for PTE diagnosis and risk stratification.

Flow matching is a powerful generative modeling framework, valued for its simplicity and strong empirical performance. However, its standard formulation treats signals on structured spaces, such as fMRI data on brain graphs, as points in Euclidean space, overlooking the rich topological features of their domains. To address this, we introduce topological flow matching, a topology-aware generalization of flow matching. We interpret flow matching as a framework for solving a degenerate Schrödinger bridge problem and inject topological information by augmenting the reference process with a Laplacian-derived drift. This principled modification captures the structure of the underlying domain while preserving the desirable properties of flow matching: a stable, simulation-free objective and deterministic sample paths. As a result, our framework serves as a drop-in replacement for standard flow matching. We demonstrate its effectiveness on diverse structured datasets, including brain fMRIs, ocean currents, seismic events, and traffic flows.

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that affects millions of older adults, with prevalence expected to rise significantly in the coming years. Early diagnosis, particularly during the mild cognitive impairment (MCI) stage, is critical for timely intervention. Structural Magnetic Resonance Imaging (sMRI) has emerged as a key modality for detecting AD-related brain changes, but traditional graph-based approaches often struggle with modality and inter-site heterogeneity, limiting diagnostic performance. In this paper, we propose Graph Matching Network for Alzheimer's Disease Diagnosis (GMN4AD), designed to model interactions between heterogeneous brain graphs derived from neuroimaging data. Unlike conventional methods that treat each brain graph independently, GMN4AD leverages graph matching to capture cross-graph relationships, enhancing diagnostic precision. Furthermore, we introduce a test-time domain adaptation strategy that combines contrastive learning to mitigate domain shifts during inference. Extensive experiments on three public AD datasets demonstrate that GMN4AD achieves superior performance compared to state-of-the-art methods, offering a robust and generalizable solution for AD diagnosis.

Flow matching and diffusion models enable conditional generation across domains ranging from images to proteins, with recent extensions to out-of-distribution contexts. Yet generative models of neural time series have largely remained restricted to categorical conditioning, precluding compositional and zero-shot generalization. In this work, we propose a per-timestep conditioned diffusion transformer for generating realistic fMRI brain dynamics during unseen cognitive tasks by injecting both compositional language and optional spatial priors in-context. Such zero-shot generation could enable counterfactual neuroscience by supporting in-silico design and evaluation of novel cognitive experiments before empirical validation. Leveraging this model, we evaluate across hundreds of held-out task conditions and characterize predictive performance in relation to the training manifold. From language alone, the model recovers region-specific recruitment across tasks and held-out spatial activation patterns. Spatial priors, when available, complement the text pathway by anchoring generation in regions of task space where language alone degrades, while retaining the compositional structure needed for counterfactual task specification. To our knowledge this is the first generative model of whole-cortex fMRI dynamics for unseen cognitive tasks, advancing counterfactual neuroscience and data-driven experimental design.

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.

Recent developments in brain recording are driving a demand for machine learning tools capable of decoding the latent structure of large populations of neurons. In this paper, we provide a comprehensive survey that outlines the trajectory of Latent Variable Models (LVMs) from early state-space models to more recent deep generative models. We organize the literature into three closely related domains: (1) Single-Region Latent Dynamics, which includes models such as linear dynamical systems to more complex dynamics represented by Recurrent Neural Networks (RNNs) and Neural Ordinary Differential Equations (ODEs); (2) Multi-Region Communication, which employs probabilistic as well as subspace methods to study how information is transferred across different brain areas considering synaptic propagation delays and network connectivity; and (3) Behavior-Aligned Modeling, which seeks to disentangle neural activity related to task performance from other internal states via supervised or contrastive learning. This survey also includes large-scale neural foundation models, such as Transformers and diffusion models, that rely on large-scale pre-training for optimal performance across subjects. Finally, we conclude and discuss benchmarks, evaluation criteria, and open challenges, such as the ability to identify causal links or directionality of communication, to facilitate future research for bridging interpretable brain dynamics with reliable neural decoding.

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.

Understanding complex interactions between brain regions is critical for early neurodegenerative disease classification such as Alzheimer's Disease (AD) and Parkinson's Disease (PD). While graph-based models are widely used to analyze brain networks, most existing approaches primarily focus on pairwise interactions between directly connected nodes, limiting their ability to capture higher-order dependencies across multiple regions. Although hypergraph-based methods have been proposed to model higher-order relations, many rely on predefined hyperedges or restrict learning to hyperedge weights, reducing flexibility and limiting their capacity to capture multi-resolution structural patterns. In this regard, we introduce an adaptive multi-scale hyperedge learning framework, i.e., MuHL, which constructs hierarchical node features and dynamically learns high-order interactions through continuous hyperedge construction over multi-resolution graph signals. Extensive experiments on multiple brain network benchmarks demonstrate that MuHL consistently improves disease classification performance across different stages, and further identifies key regions of interest (ROIs) and their group-wise interactions from the learned hyperedges that are associated with disease progression, highlighting its potential as a powerful tool for brain network analysis in neurodegenerative disorders.

EEG-based emotion recognition holds significant promise for objective diagnosis of mood disorders. Graph neural networks (GNNs) have emerged as the dominant paradigm for modeling inter-channel dependencies in EEG, yet existing approaches rely on symmetric adjacency matrices derived from spatial proximity or functional correlations that fundamentally capture statistical associations rather than directed causal influences, which conflicts with the inherently asymmetric, causally-driven nature of neural information flow. To bridge this gap, we propose GL-LFGNN, a Global-Local Dual-branch Causal Graph Neural Network grounded in Liang-Kleeman information flow theory. Unlike Granger causality that merely assesses temporal precedence, our approach rigorously quantifies causal strength from a dynamical systems perspective, yielding neurophysiologically interpretable directed graphs. A dual-branch architecture further integrates whole-brain connectivity with region-specific processing aligned to established functional neuroanatomy. On the MEEG dataset, GL-LFGNN achieves 86.17% (Arousal) and 86.71% (Valence) accuracy with only 37K parameters -- approximately 10% of the current state-of-the-art -- demonstrating that principled causal modeling can simultaneously enhance interpretability, generalization, and computational efficiency. Code will be released.

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.

Efficient neural network models that generate brain-like dynamic activity can be a valuable resource for generating synthetic data, analyzing differences in brain transients under conditions such as testing perturbation activity or inferring the underlying generative dynamics. However, large language models (LLMs) or standard recurrent neural networks (RNNs) ignore the anatomical organization and therefore do not produce components that align with brain regions. On the other hand, graph-based networks often have very simple message passing rules that are not sufficiently expressive for brain-like dynamics. To address this, we introduce BrainDyn, a sheaf neural ordinary differential equation (neural ODE) model for continuous-time dynamics on structured brain graphs. BrainDyn encodes the recent activity history of each brain region using a long short-term memory (LSTM) model over a sliding temporal window to produce hidden states, or stalks, that are projected through learnable restriction maps into edge-specific shared spaces. Discrepancies between neighboring nodes in these shared spaces are characterized by a sheaf Laplacian that can facilitate message passing between neuronal units. The output of these messages is then fed to a neural ODE that governs the continuous-time evolution of neuronal activity. We evaluated BrainDyn on resting-state fMRI (PNC dataset), scalp EEG with focal epilepsy (TUSZ dataset), and simulated activity from the NEST spiking network simulator. BrainDyn achieves strong forecasting ability across modalities, and the resulting representations support downstream tasks including in silico perturbation prediction.

Visual image reconstruction from functional Magnetic Resonance Imaging (fMRI) is a fundamental task in brain decoding, providing a crucial pathway for understanding human perceptual mechanisms and developing advanced brain-computer interfaces (BCIs). However, most current methods simply flatten fMRI signals from localized visual cortices into one-dimensional (1D) vectors, mapping them directly into latent spaces such as that of Contrastive Language-Image Pre-training (CLIP). This paradigm not only disrupts the inherent network topology of the brain-leading to limited neuroscientific interpretability-but also overlooks the synergistic contributions of other distributed functional networks in processing high-level visual semantics. To address these limitations, we propose FPED, a Functional-Network Prior-Guided Mixture of Experts (MoE) framework for interpretable brain decoding. FPED explicitly models different functional brain networks as specialized experts and employs adaptive routing to capture their complementary contributions to visual semantic understanding. Unlike conventional homogeneous decoding paradigms, our framework incorporates neurobiologically grounded priors to enable structured and interpretable network-level representation learning. Experimental results demonstrate that FPED achieves highly competitive semantic reconstruction performance with only 0.68B parameters. The learned routing dynamics reveal biologically meaningful correspondence between functional brain networks and modality-specific semantic processing, providing transparent neuroscientific interpretability. This suggests that brain network-aware expert modeling is a promising direction for bridging neural decoding and biologically inspired artificial intelligence.

Learning meaningful latent representations from nonlinear fMRI data remains a fundamental challenge in neuroimaging analysis. Traditional independent component analysis, widely used due to its ability to estimate interpretable functional brain networks, relies on a linear mixing assumption for latent sources, limiting its ability to capture the inherently nonlinear and complex organization of brain dynamics. More recently, deep representation learning methods have emerged as promising alternatives for modeling nonlinear latent structure. However, many of these approaches have been evaluated primarily on simulated datasets or natural image benchmarks, with comparatively limited validation on real-world neuroimaging data such as fMRI. In this work, we are motivated by the $β$-TCVAE (Total Correlation Variational Autoencoder), a refinement of the $β$-VAE framework for learning latent representations without introducing additional hyperparameters during training. We adapt and modify this model to fMRI data for nonlinear source disentanglement, aiming to separate mixed spatial and temporal brain signals into interpretable components. We show that the $β$-TCVAE framework can recover meaningful nonlinear spatial components with biological relevance, including well-established intrinsic connectivity networks such as the default mode network. Furthermore, we evaluate the learned representations using functional network connectivity, showing that the latent structure captures coherent and interpretable brain organization patterns. This study provides a pilot investigation that bridges nonlinear representation learning and fMRI analysis.

We present Supervised Deep Multimodal Matrix Factorization (SD3MF), an interpretable framework for integrative brain network analysis that generalizes Symmetric Nonnegative Matrix Tri-Factorization (SNMTF) from unsupervised single-graph clustering to supervised prediction over populations of multimodal graphs. SD3MF learns deep hierarchical factorizations for each modality together with a shared latent representation that aligns subjects across views. An encoder-decoder formulation jointly optimizes graph reconstruction and supervised prediction, while adaptive weights enable data-driven multimodal fusion. By representing each subject through community-level interaction matrices, the model yields interpretable and discriminative features. Experiments on multimodal connectome datasets show that SD3MF consistently outperforms strong deep learning baselines such as CNNs and GNNs, while enabling biologically interpretable insights. Code for reproducibility is available at: https://github.com/amjadseyedi/SD3MF.

Recent advances in neuroimaging have deepened our understanding of the brain's complex functional and structural organization. Among these, functional Magnetic Resonance Imaging (fMRI) - particularly resting-state fMRI (rs-fMRI) - has emerged as a tool for identifying biomarkers of intrinsic brain connectivity and delineating large-scale neural networks. These networks are typically represented as volumetric spatial maps that capture functionally coherent brain regions and reflect individual differences in brain activity and structure. The spatial resolution of these maps plays an important role, as it determines the ability to localize functional units with precision, perform reliable brain parcellation, and detect subtle, spatially specific neurobiological alterations associated with development, aging, or disease. Therefore, improving the effective resolution of neuroimaging-derived maps holds significant promise for enabling more detailed insights into brain architecture and its relationship to behavior and pathology. To address this need, we propose NeuroGAN-3D, a novel 3D generative super-resolution model tailored to the computational demands of volumetric neuroimaging. Our model leverages a generative adversarial network architecture to enhance the spatial resolution of rs-fMRI spatial maps, significantly outperforming a conventional baseline.

Graph-based learning on functional magnetic resonance imaging (fMRI) has shown strong potential for brain network analysis. However, existing methods degrade under cross-site out-of-distribution (OOD) settings because site-conditioned confounders induce non-pathological shortcuts, while functional connectivity constructed by temporal averaging obscures transient neurodynamics, limiting generalization to unseen sites. In this paper, we propose Cross-site OOD Robust brain nEtwork (CORE), a unified framework for brain network learning across unseen sites. CORE first performs site-aware confounder decoupling to mitigate site-conditioned bias and extract a cross-site population scaffold of reproducible diagnostic connectivity edges. It then profiles transient pathway dynamics over this scaffold using lightweight temporal descriptors and organizes scaffold edges into a line graph for transferable pathway-level modeling. Finally, CORE introduces a prior-guided subject-adaptive gating mechanism that leverages scaffold-derived population priors while preserving subject-specific connectivity variability. Extensive experiments under leave-one-site-out evaluation on real-world datasets (ABIDE, REST-meta-MDD, SRPBS, and ABCD) show that CORE consistently outperforms state-of-the-art baselines, with up to 6.7% relative gain. Furthermore, CORE remains robust to atlas variations, maintaining performance gains across different brain parcellation schemes.

Cognitive neuroscience is fragmented into specialized models, each tailored to specific experimental paradigms, hence preventing a unified model of cognition in the human brain. Here, we introduce TRIBE v2, a tri-modal (video, audio and language) foundation model capable of predicting human brain activity in a variety of naturalistic and experimental conditions. Leveraging a unified dataset of over 1,000 hours of fMRI across 720 subjects, we demonstrate that our model accurately predicts high-resolution brain responses for novel stimuli, tasks and subjects, superseding traditional linear encoding models, delivering several-fold improvements in accuracy. Critically, TRIBE v2 enables in silico experimentation: tested on seminal visual and neuro-linguistic paradigms, it recovers a variety of results established by decades of empirical research. Finally, by extracting interpretable latent features, TRIBE v2 reveals the fine-grained topography of multisensory integration. These results establish artificial intelligence as a unifying framework for exploring the functional organization of the human brain.

Representing dynamical systems through data-driven universal spaces has proven effective; however, achieving this universality for human brain activity remains a significant challenge, further aggravated by diverse cognitive states and individual subjects. Recognizing that spatial properties reflect physical wiring while temporal properties reflect brain function, we develop Universal Brain Dynamics (UBD) to construct a universal space tailored to brain activity and quantify corresponding dynamics using a model-derived Jacobian matrix. Crucially, we validate UBD's universality by accurately predicting functional magnetic resonance imaging (fMRI) signals (Pearson's r > 0.9) across eight states and 963 subjects in the Human Connectome Project (HCP). Through evaluating resting-state fMRI represented within UBD, we gain insight into how infra-slow fluctuation (ISF) underpins brain activity. Furthermore, we reveal a new perspective on structure-function coupling (SFC) by analyzing the temporal sequence of brain dynamics. Extending UBD to task-evoked states, we derive brain dynamics across various cognitive conditions, elucidating the neural mechanisms driving cognitive transitions at a finer granularity. For individual differences, we compare brain dynamics across subjects to identify the neural underpinnings of these variations. Our findings suggest that synergistically integrating spatial and temporal properties of brain activity establishes a universal space for its unfolding, enabling the precise numerical analysis of underlying neural mechanisms across varying conditions.

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 $O$-information, a signed measure that characterizes the informational nature of HOIs, and integrate third- and fourth-order $O$-information into a unified multi-view information bottleneck framework for fMRI-based psychiatric diagnosis. To enable scalable $O$-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.

Whether artificial neural networks organize information comparably to the human brain remains unclear. Prior brain--AI alignment studies are constrained by specific inputs and tasks, limiting cross-modal comparison. Here we introduce a brain--model topological alignment space, mapping Transformer attention topology onto human intrinsic connectivity networks (ICNs) to enable task-free, modality-agnostic comparison. Analyzing 151 Transformer-based models with 62,480 attention head graphs, we observe a continuous arc-shaped distribution reflecting varying alignment. Models optimized for global semantics aligned with higher-order ICNs, while local-detail models aligned with sensory ICNs. Non-intuitive findings include reduced alignment in DINOv2 compared to its predecessors and a counterintuitive scaling inversion in distilled DeiT models, while fine-tuning and instruction tuning had limited effect. Alignment scores showed no significant correlation with ImageNet accuracy (r = 0.266, p = 0.156). This work offers a quantitative framework for comparing the organizational principles of artificial and biological systems.

Dementia disorders such as Alzheimer's disease (AD) and frontotemporal dementia (FTD) exhibit overlapping electrophysiological signatures in EEG that challenge accurate diagnosis. Existing EEG-based methods are limited by full-band frequency analysis, which hinders the precise differentiation of dementia subtypes and severity stages. To address this limitation, we propose a Variational Mixture of Graph Neural Experts (VMoGE) framework that integrates multi-band EEG analysis with variational graph neural networks and a mixture-of-experts architecture. Each expert specializes in a specific EEG frequency band and models brain connectivity using a Gaussian Markov random field prior, while a variational gating mechanism adaptively integrates the expert outputs. This design enables the model to learn frequency-specific brain network representations while modeling latent uncertainty through variational inference. Experimental results on two EEG dementia datasets show that VMoGE achieves strong performance, with an AUC of 0.89 for HC vs. AD classification in the main comparison and competitive results across dementia subtyping and CDR staging tasks. Clinically, VMoGE offers three key translational values: the expert gating weights correlate with MMSE scores and CDR severity; slow-wave $δ$- and $θ$-band contributions are associated with AD-related EEG slowing and disease progression; and spatially localized activation maps reveal posterior $θ$- and $α$-band alterations and region-specific $β$-band changes, providing neurophysiologically interpretable markers aligned with known AD neuropathology.

Effective analysis in neuroscience benefits significantly from robust conceptual frameworks. Traditional metrics of interbrain synchrony in social neuroscience typically depend on fixed, correlation-based approaches, restricting their explanatory capacity to descriptive observations. Inspired by the successful integration of geometric insights in network science, we propose leveraging discrete geometry to examine the dynamic reconfigurations in neural interactions during social exchanges. Unlike conventional synchrony approaches, our method interprets inter-brain connectivity changes through the evolving geometric structures of neural networks. This geometric framework is realized through a pipeline that identifies critical transitions in network connectivity using entropy metrics derived from curvature distributions. By doing so, we significantly enhance the capacity of hyperscanning methodologies to uncover underlying neural mechanisms in interactive social behavior.

Dementia affects over 55 million people worldwide, projected to reach 139 million by 2050, with Alzheimer's disease (AD) accounting for 60-70% of cases. AD is associated with disruptions in metabolic brain connectivity. Detecting these disruptions early is crucial for AD management. FDG-PET is a useful tool for identifying such impairments. However, most studies rely on group-level analyses or thresholding, potentially masking individual differences and overlooking weaker yet biologically critical brain connections. Moreover, AD prediction largely focuses on univariate rather than multivariate outcomes. To address this, we introduce explainable graph-theoretical machine learning (XGML), a framework for constructing individual metabolic brain graphs and identifying subgraphs most predictive of multivariate disease-related outcomes. Using Alzheimer's Disease Neuroimaging Initiative (ADNI) FDG-PET data, we compared six graph representations against three non-graph baselines, each with six machine learning models using repeated stratified 3-fold cross-validation (10 repeats). The best configuration combined kernel density estimation with Hellinger distance and random forest. Across eight cognitive scores, it reached an overall Fisher-z-averaged Pearson correlation of r=0.595, with strongest performance for ADAS13 (r=0.67), ADAS11 (r=0.65), and ADASQ4 (r=0.62). We identified key edges that were jointly but differentially predictive across outcomes, suggesting their potential as network biomarkers of cognitive decline. Preliminary external feasibility validation on an OASIS3 cohort yielded weak predictive performance for CDRSB (r=0.26) and MMSE (r=0.18), likely reflecting cohort, protocol, and diagnostic differences. Overall, our results suggest the promise of graph-theoretical machine learning for biomarker discovery, disease prediction, and understanding the neural mechanisms underlying AD.

Alignment between human brain networks and artificial models has become an active research area in vision science and machine learning. A widely adopted approach is identifying "metamers," stimuli physically different yet perceptually equivalent within a system. However, conventional methods lack a direct approach to searching for the human metameric space. Instead, researchers first develop biologically inspired models and then infer about human metamers indirectly by testing whether model metamers also appear as metamers to humans. Here, we propose the Multidimensional Adaptive Metamer Exploration (MAME) framework, enabling direct, high-dimensional exploration of human metameric spaces through online image generation guided by human perceptual feedback. MAME modulates reference images across multiple dimensions based on hierarchical neural network responses, adaptively updating generation parameters according to participants' perceptual discriminability. Using MAME, we successfully measured multidimensional human metameric spaces within a single psychophysical experiment. Experimental results using a biologically plausible CNN model showed that human discrimination sensitivity was lower for metameric images based on Gram-matrix representations derived from low-level CNN features than for those derived from high-level CNN features. The finding suggests a relatively worse alignment between the metameric spaces of humans and the CNN model for low-level processing compared to high-level processing. Counterintuitively, given recent discussions on alignment at higher representational levels, our results highlight the importance of early visual computations in shaping biologically plausible models. Our MAME framework can serve as a future scientific tool for directly investigating the functional organization of human vision.

Functional near-infrared spectroscopy (fNIRS) is employed as a non-invasive method to monitor functional brain activation by capturing changes in the concentrations of oxygenated haemoglobin (HbO) and deoxygenated haemo-globin (HbR). Various machine learning classification techniques have been utilized to distinguish cognitive states. However, conventional machine learning methods, although simpler to implement, undergo a complex pre-processing phase before network training and demonstrate reduced accuracy due to inadequate data preprocessing. Additionally, previous research in cog-nitive load assessment using fNIRS has predominantly focused on differ-sizeentiating between two levels of mental workload. These studies mainly aim to classify low and high levels of cognitive load or distinguish between easy and difficult tasks. To address these limitations associated with conven-tional methods, this paper conducts a comprehensive exploration of the im-pact of Long Short-Term Memory (LSTM) layers on the effectiveness of Convolutional Neural Networks (CNNs) within deep learning models. This is to address the issues related to spatial features overfitting and lack of tem-poral dependencies in CNN in the previous studies. By integrating LSTM layers, the model can capture temporal dependencies in the fNIRS data, al-lowing for a more comprehensive understanding of cognitive states. The primary objective is to assess how incorporating LSTM layers enhances the performance of CNNs. The experimental results presented in this paper demonstrate that the integration of LSTM layers with Convolutional layers results in an increase in the accuracy of deep learning models from 97.40% to 97.92%.

Psychiatry research seeks to understand the manifestations of psychopathology in behavior, as measured in questionnaire data, by identifying a small number of latent factors that explain them. While factor analysis is the canonical tool for this purpose, the resulting factors may not be interpretable, and may also be subject to confounding variables. Moreover, missing data are common, and explicit imputation is often required. To overcome these limitations, we introduce Interpretability Constrained Questionnaire Factorization (ICQF), a non-negative matrix factorization method with regularization tailored for questionnaire data. Our method aims to promote factor interpretability and solution stability. We provide an optimization procedure with theoretical convergence guarantees, and an automated procedure to determine latent dimensionality accurately. We validate these procedures using realistic synthetic data. We demonstrate the effectiveness of our method in a widely used general-purpose questionnaire, in two independent datasets (the Healthy Brain Network and Adolescent Brain Cognitive Development studies). Specifically, we show that ICQF preserves diagnostic information across a range of disorders, outperforming competing methods for smaller dataset sizes, and improves interpretability, as assessed by our clinical research collaborators and co-authors. This suggests that the regularization in our method matches domain characteristics, in addition to satisfying qualitative desiderata.