Multi-view learning is an emerging field of multi-modal fusion, which involves representing a single instance using multiple heterogeneous features to improve compatibility prediction. However, existing graph-based multi-view learning approaches are implemented on homogeneous assumptions and pairwise relationships, which may not adequately capture the complex interactions among real-world instances. In this paper, we design a compressed hypergraph neural network from the perspective of multi-view heterogeneous graph learning. This approach effectively captures rich multi-view heterogeneous semantic information, incorporating a hypergraph structure that simultaneously enables the exploration of higher-order correlations between samples in multi-view scenarios. Specifically, we introduce efficient hypergraph convolutional networks based on an explainable regularizer-centered optimization framework. Additionally, a low-rank approximation is adopted as hypergraphs to reformat the initial complex multi-view heterogeneous graph. Extensive experiments compared with several advanced node classification methods and multi-view classification methods have demonstrated the feasibility and effectiveness of the proposed method.

BACKGROUND: The asymmetrical distribution of expressed mRNAs tightly controls the precise synthesis of proteins within human cells. This non-uniform distribution, a cornerstone of developmental biology, plays a pivotal role in numerous cellular processes. To advance our comprehension of gene regulatory networks, it is essential to develop computational tools for accurately identifying the subcellular localizations of mRNAs. However, considering multi-localization phenomena remains limited in existing approaches, with none considering the influence of RNA\'s secondary structure.
RESULTS: In this study, we propose Allocator, a multi-view parallel deep learning framework that seamlessly integrates the RNA sequence-level and structure-level information, enhancing the prediction of mRNA multi-localization. The Allocator models equip four efficient feature extractors, each designed to handle different inputs. Two are tailored for sequence-based inputs, incorporating multilayer perceptron and multi-head self-attention mechanisms. The other two are specialized in processing structure-based inputs, employing graph neural networks. Benchmarking results underscore Allocator\'s superiority over state-of-the-art methods, showcasing its strength in revealing intricate localization associations.
METHODS: The webserver of Allocator is available at http://Allocator.unimelb-biotools.cloud.edu.au; the source code and datasets are available on GitHub (https://github.com/lifuyi774/Allocator) and Zenodo (https://doi.org/10.5281/zenodo.13235798).
BACKGROUND: Available at Bioinformatics online.

The complex systems in the real-world are commonly associated with multiple types of objects and relations, and heterogeneous graphs are ubiquitous data structures that can inherently represent multi-modal interactions between objects. Generating high-quality heterogeneous graphs allows us to understand the implicit distribution of heterogeneous graphs and provides benchmarks for downstream heterogeneous representation learning tasks. Existing works are limited to either merely generating the graph topology with neglecting local semantic information or only generating the graph without preserving the higher-order structural information and the global heterogeneous distribution in generated graphs. To this end, we formulate a general, end-to-end framework - HGEN for generating novel heterogeneous graphs with a newly proposed heterogeneous walk generator. On top of HGEN, we further develop a network motif generator to better characterize the higher-order structural distribution. A novel heterogeneous graph assembler is further developed to adaptively assemble novel heterogeneous graphs from the generated heterogeneous walks and motifs in a stratified manner. The extended model is proven to preserve the local semantic and heterogeneous global distribution of observed graphs with the theoretical guarantee. Lastly, comprehensive experiments on both synthetic and real-world practical datasets demonstrate the power and efficiency of the proposed method.

Electronic Health Records (EHRs) play a crucial role in shaping predictive are models, yet they encounter challenges such as significant data gaps and class imbalances. Traditional Graph Neural Network (GNN) approaches have limitations in fully leveraging neighbourhood data or demanding intensive computational requirements for regularisation. To address this challenge, we introduce CliqueFluxNet, a novel framework that innovatively constructs a patient similarity graph to maximise cliques, thereby highlighting strong inter-patient connections. At the heart of CliqueFluxNet lies its stochastic edge fluxing strategy - a dynamic process involving random edge addition and removal during training. This strategy aims to enhance the model\'s generalisability and mitigate overfitting. Our empirical analysis, conducted on MIMIC-III and eICU datasets, focuses on the tasks of mortality and readmission prediction. It demonstrates significant progress in representation learning, particularly in scenarios with limited data availability. Qualitative assessments further underscore CliqueFluxNet\'s effectiveness in extracting meaningful EHR representations, solidifying its potential for advancing GNN applications in healthcare analytics.

BACKGROUND: The intersection of artificial intelligence and medical image analysis has ushered in a new era of innovation and changed the landscape of brain tumor detection and diagnosis. Correct detection and classification of brain tumors based on medical images is crucial for early diagnosis and effective treatment. Convolutional Neural Network (CNN) models are widely used for disease detection. However, they are sometimes unable to sufficiently recognize the complex features of medical images.
METHODS: This paper proposes a fused Deep Learning (DL) model that combines Graph Neural Networks (GNN), which recognize relational dependencies of image regions, and CNN, which captures spatial features, is proposed to improve brain tumor detection. By integrating these two architectures, our model achieves a more comprehensive representation of brain tumor images and improves classification performance. The proposed model is evaluated on a public dataset of 10847 MRI images. The results show that the proposed model outperforms the existing pre-trained models and traditional CNN architectures.
RESULTS: The fused DL model achieves 93.68% accuracy in brain tumor classification. The results indicate that the proposed model outperforms the existing pre-trained models and traditional CNN architectures.
CONCLUSIONS: The numerical results suggest that the model should be further investigated for potential use in clinical trials to improve clinical decision-making.

BACKGROUND: Immune checkpoint inhibitors (ICIs) are potent and precise therapies for various cancer types, significantly improving survival rates in patients who respond positively to them. However, only a minority of patients benefit from ICI treatments.
OBJECTIVE: Identifying ICI responders before treatment could greatly conserve medical resources, minimize potential drug side effects, and expedite the search for alternative therapies. Our goal is to introduce a novel deep-learning method to predict ICI treatment responses in cancer patients.
METHODS: The proposed deep-learning framework leverages graph neural network and biological pathway knowledge. We trained and tested our method using ICI-treated patients\' data from several clinical trials covering melanoma, gastric cancer, and bladder cancer.
RESULTS: Our results demonstrate that this predictive model outperforms current state-of-the-art methods and tumor microenvironment-based predictors. Additionally, the model quantifies the importance of pathways, pathway interactions, and genes in its predictions. A web server for IRnet has been developed and deployed, providing broad accessibility to users at https://irnet.missouri.edu.
CONCLUSIONS: IRnet is a competitive tool for predicting patient responses to immunotherapy, specifically ICIs. Its interpretability also offers valuable insights into the mechanisms underlying ICI treatments.

Graph neural networks (GNN) are widely used in recommendation systems, but traditional centralized methods raise privacy concerns. To address this, we introduce a federated framework for privacy-preserving GNN-based recommendations. This framework allows distributed training of GNN models using local user data. Each client trains a GNN using its own user-item graph and uploads gradients to a central server for aggregation. To overcome limited data, we propose expanding local graphs using Software Guard Extension (SGX) and Local Differential Privacy (LDP). SGX computes node intersections for subgraph exchange and expansion, while local differential privacy ensures privacy. Additionally, we introduce a personalized approach with Prototype Networks (PN) and Model-Agnostic Meta-Learning (MAML) to handle data heterogeneity. This enhances the encoding abilities of the federated meta-learner, enabling precise fine-tuning and quick adaptation to diverse client graph data. We leverage SGX and local differential privacy for secure parameter sharing and defense against malicious servers. Comprehensive experiments across six datasets demonstrate our method\'s superiority over centralized GNN-based recommendations, while preserving user privacy.

Alzheimer\'s disease (AD) is a chronic neurodegenerative disease. Early diagnosis are very important to timely treatment and delay the progression of the disease. In the past decade, many computer-aided diagnostic (CAD) algorithms have been proposed for classification of AD. In this paper, we propose a novel graph neural network method, termed Brain Graph Attention Network (BGAN) for classification of AD. First, brain graph data are used to model classification of AD as a graph classification task. Second, a local attention layer is designed to capture and aggregate messages of interactions between node neighbors. And, a global attention layer is introduced to obtain the contribution of each node for graph representation. Finally, using the BGAN to implement AD classification. We train and test on two open public databases for AD classification task. Compared to classic models, the experimental results show that our model is superior to six classic models. We demonstrate that BGAN is a powerful classification model for AD. In addition, our model can provide an analysis of brain regions in order to judge which regions are related to AD disease and which regions are related to AD progression.

Physics-based models are computationally time-consuming and infeasible for real-time scenarios of urban drainage networks, and a surrogate model is needed to accelerate the online predictive modelling. Fully-connected neural networks (NNs) are potential surrogate models, but may suffer from low interpretability and efficiency in fitting complex targets. Owing to the state-of-the-art modelling power of graph neural networks (GNNs) and their match with urban drainage networks in the graph structure, this work proposes a GNN-based surrogate of the flow routing model for the hydraulic prediction problem of drainage networks, which regards recent hydraulic states as initial conditions, and future runoff and control policy as boundary conditions. To incorporate hydraulic constraints and physical relationships into drainage modelling, physics-guided mechanisms are designed on top of the surrogate model to restrict the prediction variables with flow balance and flooding occurrence constraints. According to case results in a stormwater network, the GNN-based model is more cost-effective with better hydraulic prediction accuracy than the NN-based model after equal training epochs, and the designed mechanisms further limit prediction errors with interpretable domain knowledge. As the model structure adheres to the flow routing mechanisms and hydraulic constraints in urban drainage networks, it provides an interpretable and effective solution for data-driven surrogate modelling. Simultaneously, the surrogate model accelerates the predictive modelling of urban drainage networks for real-time use compared with the physics-based model.

Traffic flow prediction is crucial for efficient traffic management. It involves predicting vehicle movement patterns to reduce congestion and enhance traffic flow. However, the highly non-linear and complex patterns commonly observed in traffic flow pose significant challenges for this task. Current Graph Neural Network (GNN) models often construct shallow networks, which limits their ability to extract deeper spatio-temporal representations. Neural ordinary differential equations for traffic prediction address over-smoothing but require significant computational resources, leading to inefficiencies, and sometimes deeper networks may lead to poorer predictions for complex traffic information. In this study, we propose an Adaptive Decision spatio-temporal Neural Ordinary Differential Network, which can adaptively determine the number of layers of ODE according to the complexity of traffic information. It can solve the over-smoothing problem better, improving overall efficiency and prediction accuracy. In addition, traditional temporal convolution methods make it difficult to deal with complex and variable traffic time information with a large time span. Therefore, we introduce a multi-kernel temporal dynamic expansive convolution to handle the traffic time information. Multi-kernel temporal dynamic expansive convolution employs a dynamic dilation strategy, dynamically adjusting the network\'s receptive field across levels, effectively capturing temporal dependencies, and can better adapt to the changing time data of traffic information. Additionally, multi-kernel temporal dynamic expansive convolution integrates multi-scale convolution kernels, enabling the model to learn features across diverse temporal scales. We evaluated our proposed method on several real-world traffic datasets. Experimental results show that our method outperformed state-of-the-art benchmarks.