Multivariate Time-Series (MTS) analysis is crucial across various domains. Considering the spatial and temporal consistency of MTS, existing methods leverage graph structures with temporal augmentation and contrastive learning to achieve robust learning of spatial dependencies and temporal patterns. Given the inherent high-order correlations in MTS, hypergraphs present a promising approach. However, two key challenges limit their further development: 1) Feature-based perspectives capture limited spatial information, while structural perspectives encode richer spatial consistency and evolution dependency; 2) Various semantic patterns (e.g., synergy, inhibition) entangle in sensor correlations, leading to semantic ambiguity. The underlying reason is that conventional hypergraph structures cannot distinguish specific semantic roles within or across hyperedges. Thus, we propose Role Hypergraph Contrastive Learning for MTS analysis. Specifically, we introduce the concept of role to generalize hypergraphs to Role Hypergraphs, enabling precise modeling of sensor correlations by assigning each vertex-hyperedge pair with a semantic role. Building on this structure, we design a role hypergraph contrastive learning paradigm to comprehensively capture the spatial and temporal dependencies: From a structural perspective, role hypergraph structural contrasting captures spatial short-term consistency and long-term evolution; from a feature perspective, alignment of complementary role information ensures sensor-level temporal consistency. Experiments on classification and forecasting tasks demonstrate the effectiveness and interpretability of our method.

Hypergraph neural networks (HGNNs) effectively model complex high-order relationships in domains like protein interactions and social networks by connecting multiple vertices through hyperedges, enhancing modeling capabilities, and reducing information loss. Developing foundation models for hypergraphs is challenging due to their distinct data, which includes both vertex features and intricate structural information. We present Hyper-FM, a Hypergraph Foundation Model for multi-domain knowledge extraction, featuring Hierarchical High-Order Neighbor Guided Vertex Knowledge Embedding for vertex feature representation and Hierarchical Multi-Hypergraph Guided Structural Knowledge Extraction for structural information. Additionally, we curate 11 text-attributed hypergraph datasets to advance research between HGNNs and LLMs. Experiments on these datasets show that Hyper-FM outperforms baseline methods by approximately 13.4%, validating our approach. Furthermore, we propose the first scaling law for hypergraph foundation models, demonstrating that increasing domain diversity significantly enhances performance, unlike merely augmenting vertex and hyperedge counts. This underscores the critical role of domain diversity in scaling hypergraph models.

Hypergraph neural networks (HGNNs) are widely used models for analyzing higher-order relational data. HGNNs suffer from the rapid performance degradation with increasing layers. Hypergraph dynamic system (HDS) is a potential way to deal with this challenge. However, hypergraph dynamic system is confined to a time-continuous isotropic model, lacking positional information in the structural space of the hypergraph. In contrast, anisotropic diffusion can capture structural space differences among vertices, providing a more precise representation of the information propagation process in hypergraph structures than isotropic diffusion. In this paper, we introduce HGNNv2, a stable hypergraph neural network, which is built as a hypergraph dynamic system with partial differential equation (PDE). This model incorporates a position-aware anisotropic diffusion term and an external control term. We further present the vertex-rooted subtree method to determine anisotropic diffusion intensity. HGNNv2 has properties that vertices occupying equivalent positions in the structural space share equivalent structural labels and positional features. Experiments on 6 hypergraph datasets and 3 graph datasets reveal that HGNNv2 outperforms all 12 compared methods. HGNNv2 is capable of achieving stable final representations and task accuracy even under noisy conditions. HGNNv2 achieves stable performance with fewer layers than hypergraph dynamic systems employing isotropic diffusion. We provide feature visualizations to illustrate the evolution of representations.

High-order correlations, which capture complex interactions among multiple entities, extend beyond traditional graph representations and support a wider range of applications. However, existing neural network models for high-order correlations encounter scalability issues on large datasets due to the substantial computational complexity involved in processing large-scale structures. In addition, long-tailed distributions, which are common in real-world data, result in underrepresented categories and hinder the model's ability to learn effective high-order interaction patterns for rare instances. To address these issues, we introduce a novel framework known as HyperGraph-based High-order Correlation analysis (HGHC) for large-scale long-tailed data classification. Firstly, to tackle the long-tailed distribution problem, HGHC generates synthetic vertices and computes their attributed high-order correlations using an oversampling module inspired by SMOTE, termed HSMOTE, to enhance the representation of tail categories. Secondly, for efficient computational scaling, we treat the data as having two modalities: the structural modality capturing high-order relationships and the feature modality representing individual attributes. We perform computations on both CPU and GPU separately and then fuse the results to achieve a lightweight vertex transformation and aggregation scheme for high-order correlation data. Additionally, we contribute the first benchmark for large-scale long-tailed datasets involving high-order correlations, known as Amazon-LT, which includes multiple datasets with varying imbalance ratios. Our experimental results demonstrate that HGHC achieves state-of-the-art performance in handling high-order correlation analysis issues for large-scale, long-tailed data.

Performing unsupervised anomaly detection in retinal optical coherence tomography (OCT) images involves training a model solely on anomaly-free samples and detecting anomalies during inference, which reduces the cost of collecting large-scale annotated anomalous data. However, retinal OCT images exhibit significant variations in shape, thickness, and orientation, and lesions often have similar reflectance signals as normal tissues, making anomaly localization highly challenging. Existing methods address these challenges by flattening retinal layers, normalizing thickness, or leveraging reflectance priors, but their reliance on complex pre- and post-processing introduces uncertainties and limits end-to-end clinical applicability. To overcome these issues, we propose a novel semantic augmentation variational autoencoder (SeAugVAE) for unsupervised anomaly detection in retinal OCT images. Specifically, to capture the anatomical variability of normal retinas and thereby enhance anomaly sensitivity, we introduce a self-supervised semantic data augmentation strategy that enforces dual distribution consistency in both image and feature spaces during VAE training. For precise anomaly localization, we develop structural-semantic anomaly attention maps in the inference phase to detect anomalies from both local and global perspectives, and combine them to calculate anomaly score maps as the metric for localizing anomalous regions in images. Extensive experiments on multiple publicly and privately collected Cirrus and Spectralis OCT datasets demonstrate the effectiveness of SeAugVAE in pixel-wise unsupervised anomaly detection across multiple retinal diseases. Our codes are available at https://github.com/xyzhou1121/SeAugVAE.

Semantic labels are inherently tied to geometry and luminance reconstruction, as entities with similar shapes and appearances often share categories. Traditional methods use synthesis-analysis, NeRF, or 3D Gaussian representations to encode semantics and geometry separately. However, 2D methods lack view consistency, NeRF extensions are slow, and faster 3D Gaussian methods risk spatial and channel inconsistencies between semantic and RGB. Moreover, these methods require costly manual dense semantic labels. To alleviate resource demands and achieve effective semantic reconstruction with sparse inputs while enhancing RGB rendering quality, we build upon 3D Gaussian by integrating semantic features from pre-trained models-requiring no additional ground truth input-into Gaussian features, and construct a hypergraph neural network to capture higher-order correlations across RGB and semantic information as well as between different frames. Hypergraphs use hyperedges to link multiple vertices, capturing complex relationships essential for cross-modal tasks. This higher-order structure addresses the limitations of NeRF and Gaussian methods, which lack the capacity for such advanced associations. This framework enables precise novel view synthesis and 2D semantic reconstruction without manual annotations, achieving state-of-the-art results for RGB and semantic tasks on room-scale scenes in the ScanNet and Replica datasets, while supporting real-time rendering speeds of 34 FPS.

Single-template-based brain functional network analysis methods can provide limited functional connectivity information, which constrains the performance of brain disease diagnosis. Previous works have explored multi-template functional network analysis but failed to integrate the high-order correlation information within templates and the complementary information between templates into a unified relationship strength between nodes, and we extract the high-order correlation information within each template through hypergraph convolution. Secondly, for the analysis of functional connectivity between templates, we propose a cross-template Transformer to capture long-range dependencies between templates. A cross-template mask is applied to focus the model’s attention on important connections between templates, thereby enhancing model robustness. Finally, we progressively fuse the high-order information captured within templates with the global information across templates for downstream classification tasks. The proposed method has been validated on the public ABIDE dataset, and it outperforms existing methods in the ASD diagnosis task.

Existing methods for whole-slide histopathological image analysis commonly depend on patch-level sampling and deep feature extraction based on ImageNet pre-trained models. However, this strategy frequently fails to fully capture the diversity and complex associations within the tissue microenvironment. To address this problem, we propose a HyperGraph Self-supervised Learning (HGSL) method to utilize both local and global information in whole-slide images. Specifically, HGSL consists of two key modules: a Transformer-based self-supervised pretraining (TranSSL) module and a pathology hypergraph neural network (PathHGNN) module. TranSSL uses a mask reconstruction task to mine latent structures and patterns from unlabeled data, thus yielding pathology semantic deep representations. PathHGNN builds a hypergraph structure based on these representations to describe high-order relationships among patches, enabling multi-level feature aggregation and propagation to integrate local microenvironmental information with the overall topological correlations. The proposed HGSL was validated on the TCGA-GBM and TCGA-KIRC datasets, and the experimental results show that HGSL significantly outperforms all existing comparative methods in survival prediction tasks. Furthermore, the KM curve demonstrates that the proposed HGSL significantly distinguishes between high-and low-risk groups, indicating its potential for future clinical applications.

Survival prediction on histopathology whole slide images (WSIs) involves the analysis of multi-level complex correlations, such as inter-correlations among patients and intra-correlations within gigapixel histopathology images. However, the current graph-based methods for WSI analysis mainly focus on the exploration of pairwise correlations, resulting in the loss of high-order correlations. Hypergraph-based methods can handle such high-order correlations, while existing hypergraph-based methods fail to integrate multi-level high-order correlations into a unified framework, which limits the representation capability of WSIs. In this work, we propose an inter-intra hypergraph computation (I$^{2}$2HGC) framework to address this issue. The I$^{2}$2HGC framework implements multi-level hypergraph computation for survival prediction on WSIs, namely intra-hypergraph computation and inter-hypergraph computation. Specifically, the intra-hypergraph computation considers each patch sampled from the histopathology WSI as a vertex of the intra-hypergraph and models the high-order correlations among all patches of an individual WSI in both topology and semantic feature spaces using a hypergraph structure. Then, the intra-hypergraph module generates the intra-embedding and intra-risk for each patient. Subsequently, the inter-hypergraph computation employs these intra-embeddings as features for each patient to form the population-level high-order correlations using data- and knowledge-driven hypergraph modeling strategies. Finally, the intra-risks and the inter-risks are fused for the final survival prediction of each patient. Extensive experimental results on four widely used TCGA carcinoma datasets are presented. We demonstrate that the hypergraph structure captures significantly richer correlations than the graph structure, encompassing all pairwise correlations as well as higher-order interactions through hyperedges. For WSIs with a vast number of pixels and complex correlations, hypergraph-based methods effectively capture topological and semantic information while mitigating the exponential growth of pairwise edges, offering practical advantages for large-scale medical image analysis.

The goal of the hypergraph foundation model (HGFM) is to learn an encoder based on the hypergraph computational paradigm through self-supervised pretraining on high-order correlation structures, enabling the encoder to rapidly adapt to various downstream tasks in scenarios, where no labeled data or only a small amount of labeled data are available. The initial exploratory work has been applied to brain disease diagnosis tasks. However, existing methods primarily rely on graph-based approaches to learn low-order correlation patterns between brain regions in brain networks, neglecting the modeling and learning of complex correlations between different brain diseases and patients. This article proposes an HGFM for brain disease diagnosis, which conducts multidimensional pretraining tasks to explore latent cross-dimensional high-order correlation patterns on various brain disease datasets. HGFM is a high-order correlation-driven foundation model for brain disease diagnosis and effectively improves prediction performance. Specifically, HGFM first performs brain functional network link prediction tasks on individual brain networks and group interaction network link prediction tasks on group brain networks, constructing an HGFM for brain disease diagnosis. In downstream tasks, it achieves predictions for different brain disease diagnosis tasks through few-shot learning fine-tuning methods. The proposed method is evaluated on functional magnetic resonance imaging (fMRI) data from 4409 patients across four brain diseases. Results show that it outperforms existing state-of-the-art methods in all brain disease diagnosis tasks, demonstrating its potential value in clinical applications.

Computer-aided diagnosis (CAD) can help pathologists improve diagnostic accuracy together with consistency and repeatability for cancers. However, the CAD models trained with the histopathological images only from a single center (hospital) generally suffer from the generalization problem due to the straining inconsistencies among different centers. In this work, we propose a pseudo-data based self-supervised federated learning (FL) framework, named SSL-FT-BT, to improve both the diagnostic accuracy and generalization of CAD models. Specifically, the pseudo histopathological images are generated from each center, which contain both inherent and specific properties corresponding to the real images in this center, but do not include the privacy information. These pseudo images are then shared in the central server for self-supervised learning (SSL) to pre-train the backbone of global mode. A multi-task SSL is then designed to effectively learn both the center-specific information and common inherent representation according to the data characteristics. Moreover, a novel Barlow Twins based FL (FL-BT) algorithm is proposed to improve the local training for the CAD models in each center by conducting model contrastive learning, which benefits the optimization of the global model in the FL procedure. The experimental results on four public histopathological image datasets indicate the effectiveness of the proposed SSL-FL-BT on both diagnostic accuracy and generalization.

Self-supervised learning (SSL) can alleviate the issue of small sample size, which has shown its effectiveness for the computer-aided diagnosis (CAD) models. However, since the conventional SSL methods share the identical backbone in both the pretext and downstream tasks, the pretext network generally cannot be well trained in the pre-training stage, if the pretext task is totally different from the downstream one. In this work, we propose a novel task-driven SSL method, namely Self-Supervised Bi-channel Transformer Networks (SSBTN), to improve the diagnostic accuracy of a CAD model by enhancing SSL flexibility. In SSBTN, we innovatively integrate two different networks for the pretext and downstream tasks, respectively, into a unified framework. Consequently, the pretext task can be flexibly designed based on the data characteristics, and the corresponding designed pretext network thus learns more effective feature representation to be transferred to the downstream network. Furthermore, a transformer-based transfer module is developed to efficiently enhance knowledge transfer by conducting feature alignment between two different networks. The proposed SSBTN is evaluated on two publicly available datasets, namely the full-field digital mammography INbreast dataset and the wireless video capsule CrohnIPI dataset. The experimental results indicate that the proposed SSBTN outperforms all the compared algorithms.

The B-mode ultrasound (BUS) based computer-aided diagnosis (CAD) has shown its effectiveness for developmental dysplasia of the hip (DDH) in infants. In this work, a two-stage meta-learning based deep exclusivity regularized machine (TML-DERM) is proposed for the BUS-based CAD of DDH. TML-DERM integrates deep neural network (DNN) and exclusivity regularized machine into a unified framework to simultaneously improve the feature representation and classification performance. Moreover, the first-stage meta-learning is mainly conducted on the DNN module to alleviate the overfitting issue caused by the significantly increased parameters in DNN, and a random sampling strategy is adopted to self-generate the meta-tasks; while the second-stage meta-learning mainly learns the combination of multiple weak classifiers by a weight vector to improve the classification performance, and also optimizes the unified framework again. The experimental results on a DDH ultrasound dataset show the proposed TML-DERM algorithm achieves the superior classification performance with the mean accuracy of 85.89%, sensitivity of 86.54%, and specificity of 85.23%.

Transfer learning (TL) can effectively improve diagnosis accuracy of single-modal-imaging-based computer-aided diagnosis (CAD) by transferring knowledge from other related imaging modalities, which offers a way to alleviate the small-sample-size problem. However, medical imaging data generally have the following characteristics for the TL-based CAD: 1) The source domain generally has limited data, which increases the difficulty to explore transferable information for the target domain; 2) Samples in both domains often have been labeled for training the CAD model, but the existing TL methods cannot make full use of label information to improve knowledge transfer. In this work, we propose a novel doubly supervised transfer classifier (DSTC) algorithm. In particular, DSTC integrates the support vector machine plus (SVM+) classifier and the low-rank representation (LRR) into a unified framework. The former makes full use of the shared labels to guide the knowledge transfer between the paired data, while the latter adopts the block-diagonal low-rank (BLR) to perform supervised TL between the unpaired data. Furthermore, we introduce the Schatten-p norm for BLR to obtain a tighter approximation to the rank function. The proposed DSTC algorithm is evaluated on the Alzheimer's disease neuroimaging initiative (ADNI) dataset and the bimodal breast ultrasound image (BBUI) dataset. The experimental results verify the effectiveness of the proposed DSTC algorithm.