Graph Convolutional Network Combined with Semantic Feature Guidance for Deep Clustering

Geometric deep learning provides a principled and universal way for the integration of imaging and non-imaging modes in the medical field. Graph Convolutional Networks (GCNs) have been widely explored in a variety of problems, such as disease prediction, segmentation, and matrix completion. Using large, multi-modal data sets, graphs can capture the interaction of individual elements represented as nodes in the graphs. In particular, in medical applications, nodes can represent individuals (patients or healthy controls) in a potentially large population and are accompanied by a set of features, while the edges of the graph contain the associations between subjects in an intuitive way. This representation allows the inclusion of rich imaging and non-imaging information as well as individual subject characteristics in the task of disease classification. This article gives an overview of graph convolutional neural networks, focusing on the application of graph convolutional neural networks in disease prediction, and discusses the challenges and prospects of graph convolutional neural networks in disease prediction.

Single-cell RNA sequencing (scRNAseq) makes it possible to analyze gene expression profiles at the individual cell scale and to discover intrinsic and extrinsic cellular processes in biological research. Cell clustering is one of the most important steps in analyzing scRNAseq data. With rapid developments of single cell sequencing technologies, scRNAseq data grow in size and heterogeneity. However, traditional clustering methods like Kmeans with or without dimension reduction methods, cannot handle high sparse and massive scRNAseq data. Although some deep learning based methods have been proposed to denoise the data and cluster cells simultaneously, learning informative representations of cells for accurate cell clustering is still a challenging problem to be solved. In this work, we propose a deep learning model that combines a deep graph convolutional network (GCN) and a self-supervised mechanism. The GCN considers not only the gene expressions but also the relationship between cells to represent cells. The self-supervised mechanism is employed to provide the clustering assignments of cells. Moreover, we utilize the negative log-likelihood of the negative binomial (NB) function as loss in the data reconstruction due to the assumption that genes expression values can be represented by the NB model. We compared the performance of our proposed method with those of the existing clustering methods for scRNAseq data and conventional clustering methods. Results show that our method achieves better performance in terms of accuracy, adjusted random index (ARI), and normalized mutual information (NMI).

Video-based human action recognition is one of the most important and challenging areas of research in the field of computer vision. Human action recognition has found many pragmatic applications in video surveillance, human-computer interaction, entertainment, autonomous driving, etc. Owing to the recent development of deep learning methods for human action recognition, the performance of action recognition has significantly enhanced for challenging datasets. Deep learning techniques are mainly used for recognizing actions in images and videos comprising of Euclidean data. A recent development in deep learning methods is the extension of these techniques to non-Euclidean data or graph data with many nodes and edges. Human body skeleton resembles a graph, therefore, the graph convolutional network (GCN) is applicable to the non-Euclidean body skeleton. In the past few years, GCN has emerged as an important tool for skeleton-based action recognition. Therefore, we conduct a survey using GCN methods for action recognition. Herein, we present a comprehensive overview of recent GCN techniques for action recognition, propose a taxonomy for the categorization of GCN techniques for action recognition, carry out a detailed study of the benchmark datasets, enlist relevant resources and open-source codes, and finally provide an outline for future research directions and trends. To the best of authors' knowledge, this is the first survey for action recognition using GCN techniques.

miRNAs are important regulators for many crucial biological processes. Many recent studies have shown that miRNAs are closely related to various human diseases and can be potential biomarkers or therapeutic targets for some diseases, such as cancers. Therefore, accurately predicting miRNA-disease associations is of great importance for understanding and curing diseases. However, how to efficiently utilize the characteristics of miRNAs and diseases and the information on known miRNA-disease associations for prediction is still not fully explored. In this study, we propose a novel computational method for predicting miRNA-disease associations. The proposed method combines the graph convolutional network and the hypergraph convolutional network. The graph convolutional network is utilized to extract the information from miRNA-similarity data as well as disease-similarity data. Based on the representations of miRNAs and diseases learned by the graph convolutional network, we further use the hypergraph convolutional network to capture the complex high-order interactions in the known miRNA-disease associations. We conduct comprehensive experiments with different datasets and predictive tasks. The results show that the proposed method consistently outperforms several other state-of-the-art methods. We also discuss the influence of hyper-parameters and model structures on the performance of our method. Some case studies also demonstrate that the predictive results of the method can be verified by independent experiments.

Exploring the optimization of communication strategies for animation films in the context of cross-cultural communication, this research integrates the Internet of Things (IoT) and convolutional networks. The research constructs a collaborative filtering (CF) movie recommendation model based on a graph convolutional neural network (GCN) and investigates its application in cross-cultural communication. The fusion of IoT and convolutional networks in movie communication is also analyzed, and the effectiveness of the proposed GCN-CF model is validated through comparative experiments. The results indicate that, compared to other models, the GCN-CF model achieves the lowest Root Mean Square Error (RMSE) on the MovieLens 100 K and MovieLens 1 M datasets, with values of 0.8762 and 0.8275, respectively. Compared to traditional models, the GCN-CF model exhibits significantly superior performance in terms of RMSE, with reductions ranging from 0.6 to 5.2%, highlighting its heightened detection accuracy and overall performance. Moreover, the performance of the GCN-CF model is enhanced after introducing attention mechanisms and auxiliary information on both datasets, showing an improvement of 0.4% compared to the scenario without these additions. This data demonstrates the effectiveness of attention mechanisms and auxiliary information. Finally, the research presents an animation film communication strategy based on IoT and convolutional networks, offering novel insights for film production and communication, along with positive implications for cultural exchange and the advancement of the global media industry.

Single-cell RNA sequencing (scRNA-seq) has revolutionized the field of cellular diversity research. Unsupervised clustering, a key technique in this exploration, allows for the identification of distinct cell types within a population. Graph-based deep clustering methods have shown promise in preserving the structural relationships between cells (nodes) within the data. However, these methods often neglect the inherent distribution of nodes in the graph, leading to incomplete representations of cell populations. Additionally, conventional graph convolutional networks (GCNs) can suffer from oversmoothing, a phenomenon where the network loses the ability to differentiate between samples with similar expression profiles. To address these limitations, we proposed scG-cluster, an innovative deep structural clustering method. This method incorporates two key innovations: (1) Dual-topology adjacency graph: scG-cluster integrates information about node distribution into the traditional adjacency graph used by GCNs. This enriches the graph representation by capturing the spatial relationships between cells in addition to their pairwise similarities. (2) Dual-topology adaptive graph convolutional network (TAGCN): The framework employs a TAGCN architecture with residual concatenation. This network utilizes an attention mechanism to dynamically weight features within the graph, focusing on the most informative aspects for clustering. Additionally, residual connections are implemented to combat oversmoothing, ensuring the network retains the ability to distinguish between subtle differences in cell expression profiles. Furthermore, scG-cluster iteratively refines the clustering centers, leading to enhanced stability and accuracy in the final cluster assignments. Extensive evaluations on six diverse scRNA-seq datasets demonstrate that scG-cluster consistently outperforms existing state-of-the-art methods in terms of both clustering accuracy and scalability. Ablation studies are also conducted to validate the significant contributions of both the residual connections and the attention mechanism to the overall performance of the model. The source code for scG-cluster is publicly available at https://github.com/xixi-wq/scG-cluster.

LightGCAN: A lightweight graph convolutional attention network for user preference modeling and personalized recommendation

Automatic building extraction from optical imagery remains a challenge due to, for example, the complexity of building shapes. Semantic segmentation is an efficient approach for this task. The latest development in deep convolutional neural networks (DCNNs) has made accurate pixel-level classification tasks possible. Yet one central issue remains: the precise delineation of boundaries. Deep architectures generally fail to produce fine-grained segmentation with accurate boundaries due to their progressive down-sampling. Hence, we introduce a generic framework to overcome the issue, integrating the graph convolutional network (GCN) and deep structured feature embedding (DSFE) into an end-to-end workflow. Furthermore, instead of using a classic graph convolutional neural network, we propose a gated graph convolutional network, which enables the refinement of weak and coarse semantic predictions to generate sharp borders and fine-grained pixel-level classification. Taking the semantic segmentation of building footprints as a practical example, we compared different feature embedding architectures and graph neural networks. Our proposed framework with the new GCN architecture outperforms state-of-the-art approaches. Although our main task in this work is building footprint extraction, the proposed method can be generally applied to other binary or multi-label segmentation tasks.

Cross-subject emotion recognition in brain-computer interface based on frequency band attention graph convolutional adversarial neural networks

Vehicle trajectory prediction is an important research basis for the decision making and path planning of the intelligent and connected vehicle. In the connected vehicle environment, vehicles share information and drive cooperatively, and the intelligent and connected vehicles are able to obtain more accurate and rich perception information, which provides a data basis for accurate prediction of vehicle trajectories. However, attaining accurate and effective vehicle trajectory predictions poses technical challenges due to insufficient extraction of vehicular spatial–temporal interaction features. In this paper, we propose a vehicle trajectory prediction model based on graph convolutional neural network (GCN) in a connected vehicle environment. Specifically, using the driving scene information obtained by the intelligent and connected vehicle, the spatial graph and temporal graph are constructed based on the spatial interaction coefficient (SIC) and self-attention mechanism, respectively. Then, the graph data are entered into the interaction extraction module, and the spatial interaction features and temporal interaction features are extracted separately using the graph convolutional networks, which are fused to obtain the spatial–temporal interaction information. Finally, the interaction features are learned based on the convolutional neural networks to output the future trajectory information of all vehicles in the scene by one forward operation rather than a step-by-step process. The ablation experiment results show that the method proposed in this study to model the spatiotemporal interaction among vehicles based on SIC and self-attention mechanism reduces the prediction error by 5% and 12%, respectively. The results from the model comparison experiment show that the proposed method engenders an 8% improvement in prediction accuracy over the state-of-the-art solution, providing technical and theoretical support for trajectory prediction research of intelligent and connected vehicles.

Graph convolutional neural networks have difficulties in model training takes a lot of time and lack of universality in meta-path design when processing knowledge graphs. To solve these issues, this paper proposes an efficient recommendation algorithm integrating knowledge graphs with graph convolutional networks(EKG-GCN). The algorithm is mainly based on the graph convolution algorithm. Firstly, the relationship between users and entities is standardized and scored, then a new neighborhood aggregation method is proposed. Some nodes in the knowledge graph are set as central nodes. A distance-influence function is set up according to the distance from other nodes to the central node, and the feature extraction of information in the knowledge graph is completed according to the distance-influence function. Finally, the knowledge graph features are used as an auxiliary to complete the recommendation task. In the experiment, three data sets were selected to compare with other advanced models, and it was found that the model is in an advantageous position in terms of training time and recommendation effect, and has a certain degree of universality.

Detecting anomalous traffic behaviors with seasonal deep Kalman filter graph convolutional neural networks

The objective of extracting relations between document components lies in identifying the Within a single document, the focus often lies on understanding the connections between different entities. This type of analysis goes beyond individual sentences, as it demands an understanding of how information from multiple sentences interacts to form these connections. Over recent years, the importance of exploring relationships involving several entities simultaneously has grown significantly. To advance the field of studying such connections across entire documents, a novel collection of data points, known as DocRED, has been introduced. Currently, the standard approach for this task involves using BiLSTM networks to process the entire document as a whole. However, this method struggles to effectively capture the intricate relationships that exist among various entities. To overcome this limitation, a new model designed for document-level relationship identification has been developed, which leverages Graph Convolutional Networks (GCN). GCNs are particularly useful here because they can gather information from surrounding entities, allowing for a more detailed modeling of their interactions. The proposed approach starts by identifying coreferential links to gather features that represent the relationships between pairs of entities. These features are then analyzed using GCN to construct a graph structure that represents the entire document, ultimately revealing the complex interactions between different entities. Testing this model on the large-scale DocRED dataset from Tsinghua University has demonstrated its strong performance in this challenging task.

BACKGROUND Glioblastoma (GBM) is a molecularly and phenotypically heterogeneous tumor, with regional invasion patterns driving treatment resistance and universal recurrence. In infiltrative regions, GBM cells adopt at least two predominant invasive phenotypes: Neuronal-enriched (NEU), with synaptic and neurodevelopment programs, and Glycolytic/Plurimetabolic (GPM), with heightened immune and metabolic activity. These subtypes differ in therapeutic vulnerability and microenvironmental interactions; features not captured by conventional contrast-enhanced (T1+C) MRI due to minimal blood-brain barrier (BBB) disruption. Our group sought to develop predictive models to distinguish variability of NEU/GPM subtypes within infiltrative GBM, utilizing graph convolutional networks (GCN), advanced multiparametric MRI (mpMRI), and spatially-matched image-localized biopsies with transcriptomic profiling. METHODS We analyzed 18 mpMRI features —including conventional, diffusion-weighted, and Dynamic Susceptibility Contrast (DSC) perfusion MRI— of 101 image-localized biopsies from MRI non-enhancing infiltrative margins of 64 GBM patient tumors. Features were hierarchically clustered per modality; each cluster was represented as a node in a Neo4j graph. Edges connected nodes sharing overlapping samples. Nodes were annotated with NEU or GPM subtype proportion. GCNs were trained to classify subtype-enriched nodes using graph topology and node features. RESULTS GCNs achieved high predictive performance on held-out test data (AUC = 0.95 for NEU, 0.88 for GPM; 70:30 train-test split) with similar 5-fold cross-validation performance and generalized well to an independent cohort (AUC > 0.85, n = 45). Importantly, performance was robust without relying on T1+C imaging, enabling prediction beyond BBB-disrupted regions. GCNs outperformed traditional classifiers (logistic regression, random forest). CONCLUSION Our results demonstrate that GCN-modeling of mpMRI features enables non-invasive prediction of invasive GBM subtypes at the tumor margin. Unlike convolutional neural networks (CNN), which rely on spatial continuity, GCNs leverage relational structure between heterogeneous imaging features, making them ideal for modeling sparse, non-grid data. This may support non-invasive regional vulnerability detection, surgical targeting, and improved response assessment.

A graph convolutional network (GCN) employs a graph filtering kernel tailored for data with irregular structures. However, simply stacking more GCN layers does not improve performance; instead, the output converges to an uninformative low-dimensional subspace, where the convergence rate is characterized by the graph spectrum— this is the known over-smoothing problem in GCN. In this paper, we propose a sparse graph learning algorithm incorporating a new spectrum prior to compute a graph topology that circumvents over-smoothing while preserving pairwise correlations inherent in data. Specifically, based on a spectral analysis of multilayer GCN output, we derive a spectrum prior for the graph Laplacian matrix L to robustify the model expressiveness against over-smoothing. Then, we formulate a sparse graph learning problem with the spectrum prior, solved efficiently via block coordinate descent (BCD). Moreover, we optimize the weight parameter trading off the fidelity term with the spectrum prior, based on data smoothness on the original graph learned without spectrum manipulation. The output L is then normalized for supervised GCN training. Experiments show that our proposal produced deeper GCNs and higher prediction accuracy for regression and classification tasks compared to competing schemes.