arXiv subjects

Vince D. Calhoun

Publications and source records attributed to Vince D. Calhoun.

At least 19 recordsLinked to original sources

arXiv2026

MSR-IVA: Masked Structural Residual Independent Vector Analysis for State-Aware Fusion of Structural MRI and Dynamic Functional Network Connectivity

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

cs.LG↗

arXiv2026

Robust State-space Reconstruction of Brain Dynamics via Bootstrap Monte Carlo SSA

Reconstructing latent state-space geometry from time series provides a powerful route to studying nonlinear dynamics across complex systems. Delay-coordinate embedding provides the theoretical basis but assumes long, noise-free recordings, which many domains violate. In many real-world domains, recordings are short, noisy, and coarsely sampled; in neuroimaging, for example,fMRI additionally contains autocorrelated background structure that can obscure oscillatory components and destabilize embeddings. We propose bootstrap Monte Carlo singular spectrum analysis(BMC-SSA), which combines Monte Carlo SSA with bootstrap stability to retain oscillatory modes that are statistically supported and reproducible across resampled data. This produces reconstructions that emphasize reliable oscillatory structure, enhancing determinism and stabilizing subsequent embeddings. Our results show that BMC-SSA improves the reliability of functional measures and uncovers differences in state-space dynamics in fMRI, offering a general framework for robust embedding of noisy, finite signals.

q-bio.NC↗

arXiv2026

Bringing analytic rigor to agentic AI for science: The Brain Researcher platform for neuroimaging data analysis

AI agents can execute scientific analyses, but an analytic output becomes a defensible claim only after alternatives are weighed and the claim is limited to what the evidence supports. Agents may reproduce failures including selective analysis, premature declarations of success and optimization of imperfect criteria. We present Brain Researcher, an agentic research harness operating in a neuroimaging researcher's computational environment under rules for admissible analyses, required checks and claim scope. In benchmarks, Brain Researcher increased first-choice tool-selection accuracy across seven models by 70.2 percentage points (23.3% without it versus 93.6% with it) and verifiable grounding from 4.6% to 22.0%. In collaborator-led and self-evolving studies, multiverse analyses exposed analytic-choice sensitivity, and scientific review classified claims as accepted, qualified, revised, blocked, rejected or deferred. By linking decisions to evidence and provenance, Brain Researcher embeds methodological judgment within the workflow, not after it.

cs.AI↗

arXiv2026

AdaptICA: Data-Adaptive Transformation Learning for Independent Component Analysis

Independent component analysis (ICA) is widely used to recover latent structure from signal and imaging data, but standard ICA assumes that the observed measurement scale preserves a linear mixing structure. This assumption may fail for features produced through nonlinear preprocessing, such as band-specific power in motor-imagery EEG. We propose AdaptICA, an adaptive transformation-based framework that jointly learns grouped componentwise transformations and the demixing structure using a profiled mutual-information criterion. Because the transformation and demixing parameters may compensate for one another, their joint estimation introduces new identifiability and asymptotic challenges. We establish identifiability, consistency, and asymptotic normality of the transformation estimator, together with joint strong consistency of the transformation and demixing estimators. AdaptICA selects the transformation structure data-adaptively and includes the identity transformation as a candidate, thereby reducing to standard ICA when no scale adjustment is needed. Extensive simulations support the theoretical results. Applications demonstrate that AdaptICA can recover more independent and interpretable sources when transformation is beneficial while retaining standard ICA when the original measurement scale is adequate.

stat.ME↗

arXiv2026

ReMAP-PET: Beyond Visual Understanding -- Learning Region-Guided Metabolic Alignment Semantics from Brain PET

Positron Emission Tomography (PET) reveals brain metabolism and is clinically central to neurodegenerative disease assessment, yet existing 3D brain foundation models treat PET as generic volumetric data, missing the structured regional metabolic information that distinguishes it from structural neuroimaging. To address these limitations, we propose ReMAP-PET, a framework that moves beyond visual encoding by supervising a partially-tuned MedicalNet 3D ResNet-50 with brain regional standardized uptake value ratio (SUVR) profiles through joint regression and contrastive objectives, enabling the encoder to learn the metabolic semantics underlying PET modality. On 1015 paired PET--SUVR samples, ReMAP-PET achieves 0.070 SUVR MAE and 77.8% PET SUVR Recall@1, substantially outperforming five frozen pretrained baselines. We further connect the metabolic embedding to clinical language via contrastive alignment with frozen BioClinicalBERT and demonstrate end-to-end PET-to-report generation through SUVR-constrained verbalization. Linear probing on diagnostic classification and cognitive regression tasks confirms that the embeddings retain clinically relevant information without task-specific fine-tuning. Our results show that grounding PET encoders in regional metabolic semantics -- rather than treating PET as generic volumetric data -- yields representations that are structured, interpretable, and language-compatible, pointing to a new direction for metabolic-aware PET understanding.

cs.CV↗

arXiv2026

Batch Effects In Brain Foundation Model Embeddings

Foundation models show strong potential for large-scale, high-dimensional biomedical applications, yet their ability to capture relevant neurobiological characteristics remains underexplored. We systematically evaluate embeddings from two neuroimaging foundation models, BrainLM and SwiFT, across multi-site fMRI datasets using a comprehensive evaluation framework. Our results show that foundation model embeddings encode substantial batch-related variability, often dominating diagnosis-related information across heterogeneous datasets. We further investigate how harmonization, applied to reduce batch effects, influences these embeddings. In addition, we find that BrainLM prefers to capture fine-grained regional activity, whereas SwiFT tends to represent interactions between regions, consistent with their respective model architectures. Our study highlights the importance of accounting for batch effects in foundation models and motivates future work on disentangling biologically meaningful signals from acquisition-related variability.

eess.SP↗

arXiv2026

Sparse Deep Additive Model with Interactions: Enhancing Interpretability and Predictability

Recent advances in deep learning highlight the need for personalized models that can learn from small samples, handle high-dimensional features, and remain interpretable. To address this, we propose the Sparse Deep Additive Model with Interactions (SDAMI), a framework that combines sparsity-driven feature selection with deep subnetworks for flexible function approximation. Central to SDAMI is the Effect Footprint principle, which posits that higher-order interactions leave detectable marginal traces on constituent variables, enabling their discovery without exhaustive search. SDAMI executes this principle through a three-stage strategy: (1) screening for footprint variables, (2) disentangling main effects from interactions via group lasso, and (3) modeling components with dedicated deep subnetworks. Theoretical analysis confirms that footprints vanish only under measure-zero symmetry conditions that are rare in practice, ensuring consistent interaction recovery. Extensive simulations demonstrate that SDAMI successfully identifies pure interactions that heredity-based baselines fundamentally miss, recovering complex effect structures with near-zero false positive rates. Together, these results position SDAMI as a principled framework for interpretable high-dimensional regression.

stat.ML↗

arXiv2026

Isolating Nonlinear Independent Sources in fMRI with $β$-TCVAE Models

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.

cs.LG↗

arXiv2026

fMRI-LM: Towards a Universal Foundation Model for Language-Aligned fMRI Understanding

Recent advances in multimodal large language models (LLMs) have enabled unified reasoning across images, audio, and video, but extending such capability to brain imaging remains largely unexplored. Bridging this gap is essential to link neural activity with semantic cognition and to develop cross-modal brain representations. To this end, we present fMRI-LM, a foundational model that bridges functional MRI (fMRI) and language through a three-stage framework. In Stage 1, we learn a neural tokenizer that maps fMRI into discrete tokens embedded in a language-consistent space. In Stage 2, a pretrained LLM is adapted to jointly model fMRI tokens and text, treating brain activity as a sequence that can be temporally predicted and linguistically described. To overcome the lack of natural fMRI-text pairs, we construct a large descriptive corpus that translates diverse imaging-based features into structured textual descriptors, capturing the low-level organization of fMRI signals. In Stage 3, we perform multi-task, multi-paradigm instruction tuning to endow fMRI-LM with high-level semantic understanding, supporting diverse downstream applications. Across various benchmarks, fMRI-LM achieves strong zero-shot and few-shot performance, and adapts efficiently with parameter-efficient tuning (LoRA), establishing a scalable pathway toward a language-aligned, universal model for structural and semantic understanding of fMRI.

cs.CL↗

arXiv2026

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 $O$-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.

cs.LG↗

arXiv2026

NeuroBRIDGE: Behavior-Conditioned Koopman Dynamics with Riemannian Alignment for Early Substance Use Initiation Prediction from Longitudinal Functional Connectome

Early identification of adolescents at risk for substance use initiation (SUI) is vital yet difficult, as most predictors treat connectivity as static or cross-sectional and miss how brain networks change over time and with behavior. We proposed NeuroBRIDGE (Behavior conditioned RIemannian Koopman Dynamics on lonGitudinal connEctomes), a novel graph neural network-based framework that aligns longitudinal functional connectome in a Riemannian tangent space and couples dual-time attention with behavioral-conditioned Koopman dynamics to capture temporal change. Evaluated on ABCD, NeuroBRIDGE improved future SUI prediction over relevant baselines while offering interpretable insights into neural pathways, refining our understanding of neurodevelopmental risk and informing targeted prevention.

cs.CV↗

arXiv2026

Learning Structural-Functional Brain Representations through Multi-Scale Adaptive Graph Attention for Cognitive Insight

Understanding how brain structure and function interact is key to explaining intelligence yet modeling them jointly is challenging as the structural and functional connectome capture complementary aspects of organization. We introduced Multi-scale Adaptive Graph Network (MAGNet), a Transformer-style graph neural network framework that adaptively learns structure-function interactions. MAGNet leverages source-based morphometry from structural MRI to extract inter-regional morphological features and fuses them with functional network connectivity from resting-state fMRI. A hybrid graph integrates direct and indirect pathways, while local-global attention refines connectivity importance and a joint loss simultaneously enforces cross-modal coherence and optimizes the prediction objective end-to-end. On the ABCD dataset, MAGNet outperformed relevant baselines, demonstrating effective multimodal integration for advancing our understanding of cognitive function.

cs.CV↗

arXiv2026

Time-Varying Directed Interactions in Functional Brain Networks: Modeling and Validation

Understanding the dynamic nature of brain connectivity is critical for elucidating neural processing, behavior, and brain disorders. Traditional approaches such as sliding-window correlation (SWC) characterize time-varying undirected associations but do not resolve directional interactions, limiting inference about time-resolved information flow in brain networks. We introduce sliding-window prediction correlation (SWpC), which embeds a directional linear time-invariant (LTI) model within each sliding window to estimate time-varying directed functional connectivity (FC). SWpC yields two complementary descriptors of directed interactions: a strength measure (prediction correlation) and a duration measure (window-wise duration of information transfer). Using concurrent local field potential (LFP) and fMRI BOLD recordings from rat somatosensory cortices, we demonstrate stable directionality estimates in both LFP band-limited power and BOLD. Using Human Connectome Project (HCP) motor task fMRI, SWpC detects significant task-evoked changes in directed FC strength and duration and shows higher sensitivity than SWC for identifying task-evoked connectivity differences. Finally, in post-concussion vestibular dysfunction (PCVD), SWpC reveals reproducible vestibular-multisensory brain-state shifts and improves healthy-control vs subacute patient (HC-ST) discrimination using state-derived features. Together, these results show that SWpC provides biologically interpretable, time-resolved directed connectivity patterns across multimodal validation and clinical application settings, supporting both basic and translational neuroscience.

q-bio.NC↗

arXiv2026

Algebraic Connectivity Reveals Modulated High-Order Functional Networks in Alzheimer's Disease

Functional MRI is a neuroimaging technique that analyzes the functional activity of the brain by measuring blood-oxygen-level-dependent signals throughout the brain. The derived functional features can be used for investigating brain alterations in neurological and psychiatric disorders. In this work, we employed a hypergraph to model high-order functional relations across brain regions, introducing algebraic connectivity (a(G)) for estimating the hyperedge weights. The hypergraph structure was derived from healthy controls to build a common topology across individuals. The considered cohort for subsequent analyses included subjects covering the Alzheimer's disease (AD) continuum, encompassing both mild cognitive impairment and AD patients. Statistical analysis and three classification tasks: HC vs AD, MCI vs AD, and HC vs MCI, were performed to assess differences across the three groups and the potential of the hyperedge weights as functional features. Furthermore, a mediation analysis was performed to evaluate the reliability of the a(G) values, representing functional information as the mediator between tau-PET levels, a key biomarker of AD, and cognitive scores. The proposed approach identified a larger number of hyperedges statistically different across groups compared to state-of-the-art methods. The a(G) hyperedge weights also demonstrated a higher discriminative power in all three binary classifications. Finally, two hyperedges belonging to salience/ventral attention and somatomotor networks showed a partial mediation effect between the tau biomarker and cognitive decline. These results suggested that a(G) can be an effective approach for extracting the hyperedge weights, including important functional information that resides in the brain areas forming the hyperedges.

q-bio.NC↗

arXiv2026

KOCOBrain: Kuramoto-Guided Graph Network for Uncovering Structure-Function Coupling in Adolescent Prenatal Drug Exposure

Exposure to psychoactive substances during pregnancy, such as cannabis, can disrupt neurodevelopment and alter large-scale brain networks, yet identifying their neural signatures remains challenging. We introduced KOCOBrain: KuramotO COupled Brain Graph Network; a unified graph neural network framework that integrates structural and functional connectomes via Kuramoto-based phase dynamics and cognition-aware attention. The Kuramoto layer models neural synchronization over anatomical connections, generating phase-informed embeddings that capture structure-function coupling, while cognitive scores modulate information routing in a subject-specific manner followed by a joint objective enhancing robustness under class imbalance scenario. Applied to the ABCD cohort, KOCOBrain improved prenatal drug exposure prediction over relevant baselines and revealed interpretable structure-function patterns that reflect disrupted brain network coordination associated with early exposure.

q-bio.NC↗

arXiv2026

Physics-Guided Multi-View Graph Neural Network for Schizophrenia Classification via Structural-Functional Coupling

Clinical studies reveal disruptions in brain structural connectivity (SC) and functional connectivity (FC) in neuropsychiatric disorders such as schizophrenia (SZ). Traditional approaches might rely solely on SC due to limited functional data availability, hindering comprehension of cognitive and behavioral impairments in individuals with SZ by neglecting the intricate SC-FC interrelationship. To tackle the challenge, we propose a novel physics-guided deep learning framework that leverages a neural oscillation model to describe the dynamics of a collection of interconnected neural oscillators, which operate via nerve fibers dispersed across the brain's structure. Our proposed framework utilizes SC to simultaneously generate FC by learning SC-FC coupling from a system dynamics perspective. Additionally, it employs a novel multi-view graph neural network (GNN) with a joint loss to perform correlation-based SC-FC fusion and classification of individuals with SZ. Experiments conducted on a clinical dataset exhibited improved performance, demonstrating the robustness of our proposed approach.

eess.IV↗

arXiv2026

Unified Cross-Modal Attention-Mixer Based Structural-Functional Connectomics Fusion for Neuropsychiatric Disorder Diagnosis

Gaining insights into the structural and functional mechanisms of the brain has been a longstanding focus in neuroscience research, particularly in the context of understanding and treating neuropsychiatric disorders such as Schizophrenia (SZ). Nevertheless, most of the traditional multimodal deep learning approaches fail to fully leverage the complementary characteristics of structural and functional connectomics data to enhance diagnostic performance. To address this issue, we proposed ConneX, a multimodal fusion method that integrates cross-attention mechanism and multilayer perceptron (MLP)-Mixer for refined feature fusion. Modality-specific backbone graph neural networks (GNNs) were firstly employed to obtain feature representation for each modality. A unified cross-modal attention network was then introduced to fuse these embeddings by capturing intra- and inter-modal interactions, while MLP-Mixer layers refined global and local features, leveraging higher-order dependencies for end-to-end classification with a multi-head joint loss. Extensive evaluations demonstrated improved performance on two distinct clinical datasets, highlighting the robustness of our proposed framework.

cs.CV↗

arXiv2026

NeuroKoop: Neural Koopman Fusion of Structural-Functional Connectomes for Identifying Prenatal Drug Exposure in Adolescents

Understanding how prenatal exposure to psychoactive substances such as cannabis shapes adolescent brain organization remains a critical challenge, complicated by the complexity of multimodal neuroimaging data and the limitations of conventional analytic methods. Existing approaches often fail to fully capture the complementary features embedded within structural and functional connectomes, constraining both biological insight and predictive performance. To address this, we introduced NeuroKoop, a novel graph neural network-based framework that integrates structural and functional brain networks utilizing neural Koopman operator-driven latent space fusion. By leveraging Koopman theory, NeuroKoop unifies node embeddings derived from source-based morphometry (SBM) and functional network connectivity (FNC) based brain graphs, resulting in enhanced representation learning and more robust classification of prenatal drug exposure (PDE) status. Applied to a large adolescent cohort from the ABCD dataset, NeuroKoop outperformed relevant baselines and revealed salient structural-functional connections, advancing our understanding of the neurodevelopmental impact of PDE.

q-bio.NC↗