arXiv subjects

Yu-Ping Wang

Publications and source records attributed to Yu-Ping Wang.

At least 19 recordsLinked to original sources

arXiv2026

High-Order Triadic Functional Connectivity in the Brain and Beyond

Here, we report high-order functional network connectivity as a promising way for studying the brain connectome. Traditional functional connectivity approaches capture only pairwise relationships between brain regions, overlooking complex multivariate dependencies that underlie cognition and behavior. First, we demonstrated that high-order interactions capture more information and can distinguish between resting-state and task-state brain activity. Second, we introduce a matrix-based entropy-functional method for estimating triadic interactions, which are statistical dependencies among triplets of brain regions, and apply it to large-scale functional brain networks. The resulting triadic networks revealed distinct community patterns that complement those observed in traditional pairwise functional connectivity analyses and simultaneously capture additional connection information. Despite the potential combinatorial explosion of triadic configurations, the networks exhibited constrained and hierarchical structures that allowed computation and interpretation. These findings position triadic connectivity as a promising next-step functional connectivity framework for probing brain network organization and high-order neural interactions, while also highlighting key biological and technical challenges that require careful consideration.

q-bio.NC↗

arXiv2026

DiagramRAG: A Lightweight Framework to Retrieve Scientific Diagram for Figure Generation

Scientific diagrams are essential for communicating complex methodologies in academic papers. A natural way for researchers to specify such diagrams is through rough sketches, where text labels, connectors, and spatial arrangements express early semantic and topological intentions. However, sketches are usually incomplete, making them insufficient for directly producing publication-quality diagrams. Existing sketch-based generation methods mainly reconstruct the sketch itself, while recent text-driven diagram generation frameworks rely on textual semantics and do not fully exploit the topological structure contained in sketches. In this paper, we introduce DiagramRAG, a lightweight retrieval-augmented framework for sketch-based scientific diagram completion. Given a user sketch, DiagramRAG retrieves reference diagrams that are both semantically relevant to the sketch content and topologically compatible with its structure, and uses them to guide downstream diagram generation. To enable efficient structure-aware retrieval, we represent diagrams as knowledge graphs, synthesize sketch variants at different simplification levels, and train an embedding model to align sketches with compatible diagrams in a shared space. The retrieved references further provide content, topology, and visual priors for completing and rendering the final diagram. Experiments show that DiagramRAG achieves F1-scores of 0.848 and 0.802 on DiagramBank and FigureBench, respectively, and improves generation quality with the best VLM-as-a-Judge score of 7.170, while reducing inference latency to 35.48 seconds per sample. Our code and data are available at https://anonymous.4open.science/r/DiagramRAG-A262 and https://huggingface.co/datasets/anonymous-review-a262/DiagramSketch.

cs.AI↗

arXiv2026

Gauss law constraint in A-theory branes

A-theory realizes U-duality symmetry by extending the string worldsheet to a higher dimensional brane worldvolume, in which the worldvolume and the spacetime belong to different representations of the exceptional group. The closure of the brane Virasoro algebra requires the Gauss law constraint. The Gauss law constraint promotes spacetime coordinates to gauge fields and extends the string worldsheet into the brane worldvolume. While the Virasoro constraint is used to reduce the spacetime coordinate, the Gauss law constraint is used to reduce both the worldvolume and the spacetime coordinates. As in conventional gauge theories, the treatment of the Gauss law constraint is a technically important aspect of the quantization of A-theory. We show that the string solution is only consistent solution of the Gauss law dimensional reduction condition for D=3 and 4 cases. This result implies that the physical symmetry of the theory is two-dimensional conformal symmetry, suggesting that the theory admits a string-like quantization. We further construct a string solution that is covariant under the exceptional group symmetry. The relation between this solution and the constant charge parameter appearing in the exceptional {\sigma}-model is also discussed.

hep-th↗

arXiv2026

BrainCast: A Spatio-Temporal Forecasting Model for Whole-Brain fMRI Time Series Prediction

Functional magnetic resonance imaging (fMRI) enables noninvasive investigation of brain function, while short clinical scan durations, arising from human and non-human factors, usually lead to reduced data quality and limited statistical power for neuroimaging research. In this paper, we propose BrainCast, a novel spatio-temporal forecasting framework specifically tailored for whole-brain fMRI time series forecasting, to extend informative fMRI time series without additional data acquisition. It formulates fMRI time series forecasting as a multivariate time series prediction task and jointly models temporal dynamics within regions of interest (ROIs) and spatial interactions across ROIs. Specifically, BrainCast integrates a Spatial Interaction Awareness module to characterize inter-ROI dependencies via embedding every ROI time series as a token, a Temporal Feature Refinement module to capture intrinsic neural dynamics within each ROI by enhancing both low- and high-energy temporal components of fMRI time series at the ROI level, and a Spatio-temporal Pattern Alignment module to combine spatial and temporal representations for producing informative whole-brain features. Experimental results on resting-state and task fMRI datasets from the Human Connectome Project demonstrate the superiority of BrainCast over state-of-the-art time series forecasting baselines. Moreover, fMRI time series extended by BrainCast improve downstream cognitive ability prediction, highlighting the clinical and neuroscientific impact brought by whole-brain fMRI time series forecasting in scenarios with restricted scan durations.

cs.CV↗

arXiv2026

DDS-UDA: Dual-Domain Synergy for Unsupervised Domain Adaptation in Joint Segmentation of Optic Disc and Optic Cup

Convolutional neural networks (CNNs) have achieved exciting performance in joint segmentation of optic disc and optic cup on single-institution datasets. However, their clinical translation is hindered by two major challenges: limited availability of large-scale, high-quality annotations and performance degradation caused by domain shift during deployment across heterogeneous imaging protocols and acquisition platforms. While unsupervised domain adaptation (UDA) provides a way to mitigate these limitations, most existing approaches do not address cross-domain interference and intra-domain generalization within a unified framework. In this paper, we present the Dual-Domain Synergy UDA (DDS-UDA), a novel UDA framework that comprises two key modules. First, a bi-directional cross-domain consistency regularization module is enforced to mitigate cross-domain interference through feature-level semantic information exchange guided by a coarse-to-fine dynamic mask generator, suppressing noise propagation while preserving structural coherence. Second, a frequency-driven intra-domain pseudo label learning module is used to enhance intra-domain generalization by synthesizing spectral amplitude-mixed supervision signals, which ensures high-fidelity feature alignment across domains. Implemented within a teacher-student architecture, DDS-UDA disentangles domain-specific biases from domain-invariant feature-level representations, thereby achieving robust adaptation to heterogeneous imaging environments. We conduct a comprehensive evaluation of our proposed method on two multi-domain fundus image datasets, demonstrating that it outperforms several existing UDA based methods and therefore providing an effective way for optic disc and optic cup segmentation.

cs.CV↗

arXiv2026

Bridging Commutant and Polynomial Methods for Hilbert Space Fragmentation

A quantum model exhibits Hilbert space fragmentation (HSF) if its Hilbert space decomposes into exponentially many dynamically disconnected subspaces, known as Krylov subspaces. A model may however have different HSFs depending on the method for identifying them. Here we establish a connection between two vastly distinct methods recently proposed for identifying HSF: the commutant algebra (CA) method and integer characteristic polynomial factorization (ICPF) method. For a Hamiltonian consisting of operators admitting rational number matrix representations, we prove a theorem that, if its center of commutant algebra have all eigenvalues being rational, the HSF from the ICPF method must be equal to or finer than that from the CA method. We show that this condition is satisfied by most known models exhibiting HSF, for which we demonstrate the validity of our theorem. We further discuss representative models for which ICPF and CA methods yield different HSFs. Our results may facilitate the exploration of a unified definition of HSF.

cond-mat.stat-mech↗

arXiv2025

Unsupervised Anomaly Detection in Brain MRI via Disentangled Anatomy Learning

Detection of various lesions in brain MRI is clinically critical, but challenging due to the diversity of lesions and variability in imaging conditions. Current unsupervised learning methods detect anomalies mainly through reconstructing abnormal images into pseudo-healthy images (PHIs) by normal samples learning and then analyzing differences between images. However, these unsupervised models face two significant limitations: restricted generalizability to multi-modality and multi-center MRIs due to their reliance on the specific imaging information in normal training data, and constrained performance due to abnormal residuals propagated from input images to reconstructed PHIs. To address these limitations, two novel modules are proposed, forming a new PHI reconstruction framework. Firstly, the disentangled representation module is proposed to improve generalizability by decoupling brain MRI into imaging information and essential imaging-invariant anatomical images, ensuring that the reconstruction focuses on the anatomy. Specifically, brain anatomical priors and a differentiable one-hot encoding operator are introduced to constrain the disentanglement results and enhance the disentanglement stability. Secondly, the edge-to-image restoration module is designed to reconstruct high-quality PHIs by restoring the anatomical representation from the high-frequency edge information of anatomical images, and then recoupling the disentangled imaging information. This module not only suppresses abnormal residuals in PHI by reducing abnormal pixels input through edge-only input, but also effectively reconstructs normal regions using the preserved structural details in the edges. Evaluated on nine public datasets (4,443 patients' MRIs from multiple centers), our method outperforms 17 SOTA methods, achieving absolute improvements of +18.32% in AP and +13.64% in DSC.

cs.CV↗

arXiv2025

A Deep Spatio-Temporal Architecture for Dynamic Effective Connectivity Network Analysis Based on Dynamic Causal Discovery

Dynamic effective connectivity networks (dECNs) reveal the changing directed brain activity and the dynamic causal influences among brain regions, which facilitate the identification of individual differences and enhance the understanding of human brain. Although the existing causal discovery methods have shown promising results in effective connectivity network analysis, they often overlook the dynamics of causality, in addition to the incorporation of spatio-temporal information in brain activity data. To address these issues, we propose a deep spatio-temporal fusion architecture, which employs a dynamic causal deep encoder to incorporate spatio-temporal information into dynamic causality modeling, and a dynamic causal deep decoder to verify the discovered causality. The effectiveness of the proposed method is first illustrated with simulated data. Then, experimental results from Philadelphia Neurodevelopmental Cohort (PNC) demonstrate the superiority of the proposed method in inferring dECNs, which reveal the dynamic evolution of directed flow between brain regions. The analysis shows the difference of dECNs between young adults and children. Specifically, the directed brain functional networks transit from fluctuating undifferentiated systems to more stable specialized networks as one grows. This observation provides further evidence on the modularization and adaptation of brain networks during development, leading to higher cognitive abilities observed in young adults.

cs.LG↗

arXiv2024

Strings and membranes from $\mathcal{A}$-theory five brane

The $\mathcal{A}$-theory takes U-duality symmetry as a guiding principle, with the SL(5) U-duality symmetry being described as the world-volume theory of a 5-brane. Furthermore, by unifying the 6-dimensional world-volume Lorentz symmetry with the SL(5) spacetime symmetry, it extends to SL(6) U-duality symmetry. The SL(5) spacetime vielbein fields and the 5-brane world-volume vielbein fields are mixed under the SL(6) U-duality transformation. We demonstrate that consistent sectionings of the SL(6) $\mathcal{A}$5-brane world-volume Lagrangian yield Lagrangians of the ${\cal T}$-string with O(D,D) T-duality symmetry, the conventional string, the $\mathcal{M}$5-brane with GL(4) duality symmetry, and the non-perturbative M2-brane in supergravity theory. The GL(4) covariant Lagrangian of the $\mathcal{M}$5-brane derived in this manner is a new, perturbatively quantizable theory.

hep-th↗

arXiv2024

Triple Product Amplitude from Chiral String

In this paper, we proposed a worldsheet construction of a subset of triple product amplitudes proposed by Huang and Remmen (2022). We start with closed bosonic strings but left and right-moving momenta are not necessarily equal. Instead, they satisfy certain conditions. We called them section conditions. These conditions are generalizations of the section condition in double field theory. The vertex operators of chiral strings have nontrivial monodromy, so we interpret them as attached to the end of defects. In the calculation of the amplitude, we not only have to integrate over the moduli space, we also have to sum over different defect configurations. Unitarity and other consistency conditions for chiral string amplitudes are checked. We found the graviton amplitude, the Virasoro amplitude, and also a special kind of amplitude that has one infinite spin tower. Similar kinds of amplitude have appeared in bootstrap literature. The more general $N$-point amplitude could be obtained from a modified KLT relation. The five-point chiral string amplitude is also explicitly calculated.

hep-th↗

arXiv2024

Integrated Brain Connectivity Analysis with fMRI, DTI, and sMRI Powered by Interpretable Graph Neural Networks

Multimodal neuroimaging modeling has becomes a widely used approach but confronts considerable challenges due to heterogeneity, which encompasses variability in data types, scales, and formats across modalities. This variability necessitates the deployment of advanced computational methods to integrate and interpret these diverse datasets within a cohesive analytical framework. In our research, we amalgamate functional magnetic resonance imaging, diffusion tensor imaging, and structural MRI into a cohesive framework. This integration capitalizes on the unique strengths of each modality and their inherent interconnections, aiming for a comprehensive understanding of the brain's connectivity and anatomical characteristics. Utilizing the Glasser atlas for parcellation, we integrate imaging derived features from various modalities: functional connectivity from fMRI, structural connectivity from DTI, and anatomical features from sMRI within consistent regions. Our approach incorporates a masking strategy to differentially weight neural connections, thereby facilitating a holistic amalgamation of multimodal imaging data. This technique enhances interpretability at connectivity level, transcending traditional analyses centered on singular regional attributes. The model is applied to the Human Connectome Project's Development study to elucidate the associations between multimodal imaging and cognitive functions throughout youth. The analysis demonstrates improved predictive accuracy and uncovers crucial anatomical features and essential neural connections, deepening our understanding of brain structure and function.

q-bio.NC↗

arXiv2024

DSAM: A Deep Learning Framework for Analyzing Temporal and Spatial Dynamics in Brain Networks

Resting-state functional magnetic resonance imaging (rs-fMRI) is a noninvasive technique pivotal for understanding human neural mechanisms of intricate cognitive processes. Most rs-fMRI studies compute a single static functional connectivity matrix across brain regions of interest, or dynamic functional connectivity matrices with a sliding window approach. These approaches are at risk of oversimplifying brain dynamics and lack proper consideration of the goal at hand. While deep learning has gained substantial popularity for modeling complex relational data, its application to uncovering the spatiotemporal dynamics of the brain is still limited. We propose a novel interpretable deep learning framework that learns goal-specific functional connectivity matrix directly from time series and employs a specialized graph neural network for the final classification. Our model, DSAM, leverages temporal causal convolutional networks to capture the temporal dynamics in both low- and high-level feature representations, a temporal attention unit to identify important time points, a self-attention unit to construct the goal-specific connectivity matrix, and a novel variant of graph neural network to capture the spatial dynamics for downstream classification. To validate our approach, we conducted experiments on the Human Connectome Project dataset with 1075 samples to build and interpret the model for the classification of sex group, and the Adolescent Brain Cognitive Development Dataset with 8520 samples for independent testing. Compared our proposed framework with other state-of-art models, results suggested this novel approach goes beyond the assumption of a fixed connectivity matrix and provides evidence of goal-specific brain connectivity patterns, which opens up the potential to gain deeper insights into how the human brain adapts its functional connectivity specific to the task at hand.

q-bio.NC↗

arXiv2024

A Demographic-Conditioned Variational Autoencoder for fMRI Distribution Sampling and Removal of Confounds

Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging. Methods: We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP). Results: We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity. Conclusion: Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics. Significance: Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

q-bio.QM↗

arXiv2024

Counting Cohesive Subgraphs with Hereditary Properties

Counting small cohesive subgraphs in a graph is a fundamental operation with numerous applications in graph analysis. Previous studies on cohesive subgraph counting are mainly based on the clique model, which aim to count the number of $k$-cliques in a graph with a small $k$. However, the clique model often proves too restrictive for practical use. To address this issue, we investigate a new problem of counting cohesive subgraphs that adhere to the hereditary property. Here the hereditary property means that if a graph $G$ has a property $\mathcal{P}$, then any induced subgraph of $G$ also has a property $\mathcal{P}$. To count these hereditary cohesive subgraphs (\hcss), we propose a new listing-based framework called \hcslist, which employs a backtracking enumeration procedure to count all \hcss. A notable limitation of \hcslist is that it requires enumerating all \hcss, making it intractable for large and dense graphs due to the exponential growth in the number of \hcss with respect to graph size. To overcome this limitation, we propose a novel pivot-based framework called \hcspivot, which can count most \hcss in a combinatorial manner without explicitly listing them. Two additional noteworthy features of \hcspivot is its ability to (1) simultaneously count \hcss of any size and (2) simultaneously count \hcss for each vertex or each edge, while \hcslist is only capable of counting a specific size of \hcs and obtaining a total count of \hcss in a graph. We focus specifically on two \hcs: $s$-defective clique and $s$-plex, with several non-trivial pruning techniques to enhance the efficiency. We conduct extensive experiments on 8 large real-world graphs, and the results demonstrate the high efficiency and effectiveness of our solutions.

cs.DS↗

arXiv2024

An Interpretable Cross-Attentive Multi-modal MRI Fusion Framework for Schizophrenia Diagnosis

Both functional and structural magnetic resonance imaging (fMRI and sMRI) are widely used for the diagnosis of mental disorder. However, combining complementary information from these two modalities is challenging due to their heterogeneity. Many existing methods fall short of capturing the interaction between these modalities, frequently defaulting to a simple combination of latent features. In this paper, we propose a novel Cross-Attentive Multi-modal Fusion framework (CAMF), which aims to capture both intra-modal and inter-modal relationships between fMRI and sMRI, enhancing multi-modal data representation. Specifically, our CAMF framework employs self-attention modules to identify interactions within each modality while cross-attention modules identify interactions between modalities. Subsequently, our approach optimizes the integration of latent features from both modalities. This approach significantly improves classification accuracy, as demonstrated by our evaluations on two extensive multi-modal brain imaging datasets, where CAMF consistently outperforms existing methods. Furthermore, the gradient-guided Score-CAM is applied to interpret critical functional networks and brain regions involved in schizophrenia. The bio-markers identified by CAMF align with established research, potentially offering new insights into the diagnosis and pathological endophenotypes of schizophrenia.

eess.IV↗

arXiv2024

Exploring General Intelligence via Gated Graph Transformer in Functional Connectivity Studies

Functional connectivity (FC) as derived from fMRI has emerged as a pivotal tool in elucidating the intricacies of various psychiatric disorders and delineating the neural pathways that underpin cognitive and behavioral dynamics inherent to the human brain. While Graph Neural Networks (GNNs) offer a structured approach to represent neuroimaging data, they are limited by their need for a predefined graph structure to depict associations between brain regions, a detail not solely provided by FCs. To bridge this gap, we introduce the Gated Graph Transformer (GGT) framework, designed to predict cognitive metrics based on FCs. Empirical validation on the Philadelphia Neurodevelopmental Cohort (PNC) underscores the superior predictive prowess of our model, further accentuating its potential in identifying pivotal neural connectivities that correlate with human cognitive processes.

q-bio.NC↗

arXiv2023

ImageNomer: description of a functional connectivity and omics analysis tool and case study identifying a race confound

Most packages for the analysis of fMRI-based functional connectivity (FC) and genomic data are used with a programming language interface, lacking an easy-to-navigate GUI frontend. This exacerbates two problems found in these types of data: demographic confounds and quality control in the face of high dimensionality of features. The reason is that it is too slow and cumbersome to use a programming interface to create all the necessary visualizations required to identify all correlations, confounding effects, or quality control problems in a dataset. To remedy this situation, we have developed ImageNomer, a data visualization and analysis tool that allows inspection of both subject-level and cohort-level demographic, genomic, and imaging features. The software is Python-based, runs in a self-contained Docker image, and contains a browser-based GUI frontend. We demonstrate the usefulness of ImageNomer by identifying an unexpected race confound when predicting achievement scores in the Philadelphia Neurodevelopmental Cohort (PNC) dataset. In the past, many studies have attempted to use FC to identify achievement-related features in fMRI. Using ImageNomer, we find a clear potential for confounding effects of race. Using correlation analysis in the ImageNomer software, we show that FCs correlated with Wide Range Achievement Test (WRAT) score are in fact more highly correlated with race. Investigating further, we find that whereas both FC and SNP (genomic) features can account for 10-15\% of WRAT score variation, this predictive ability disappears when controlling for race. In this work, we demonstrate the advantage of our ImageNomer GUI tool in data exploration and confound detection. Additionally, this work identifies race as a strong confound in FC data and casts doubt on the possibility of finding unbiased achievement-related features in fMRI and SNP data of healthy adolescents.

q-bio.PE↗

arXiv2023

Somatomotor-Visual Resting State Functional Connectivity Increases After Two Years in the UK Biobank Longitudinal Cohort

Purpose: Functional magnetic resonance imaging (fMRI) and functional connectivity (FC) have been used to follow aging in both children and older adults. Robust changes have been observed in children, where high connectivity among all brain regions changes to a more modular structure with maturation. In this work, we examine changes in FC in older adults after two years of aging in the UK Biobank longitudinal cohort. Approach: We process data using the Power264 atlas, then test whether FC changes in the 2,722-subject longitudinal cohort are statistically significant using a Bonferroni-corrected t-test. We also compare the ability of Power264 and UKB-provided, ICA-based FC to determine which of a longitudinal scan pair is older. Results: We find a 6.8\% average increase in SMT-VIS connectivity from younger to older scan (from $ρ=0.39$ to $ρ=0.42$) that occurs in male, female, older subject ($>65$ years old), and younger subject ($<55$ years old) groups. Among all inter-network connections, this average SMT-VIS connectivity is the best predictor of relative scan age, accurately predicting which scan is older 57\% of the time. Using the full FC and a training set of 2,000 subjects, one is able to predict which scan is older 82.5\% of the time using either the full Power264 FC or the UKB-provided ICA-based FC. Conclusions: We conclude that SMT-VIS connectivity increases in the longitudinal cohort, while resting state FC increases generally with age in the cross-sectional cohort. However, we consider the possibility of a change in resting state scanner task between UKB longitudinal data acquisitions.

q-bio.NC↗