Graph learning has shown significant advantages in organizing and leveraging complex data, making it promising for numerous real-world applications with heterogeneous information, particularly multi-omics data analysis. Despite its potential in such scenarios, existing methods are still in their infancy, lacking architectural potential and struggling to handle such complex data. In this paper, we propose the Multiplex Mixture of Graph Learners (MMoG) framework. MMoG first conducts fine-grained processing of consensus and unique information, constructing consistent features and multiplex graph structures. Then, a macroscopically shared group of sub-GNNs with diverse orders and architectures synergistically learn representations, providing a foundation for strong interaction between different views. Inspired by the mixture of experts (MoE), each sample in different omics adaptively determines the neighborhood ranges and architectures for information aggregation, while blocking unsuitable sub-GNNs. MMoG treats the complex multi-omics analysis as a multi-view learning problem, and essentially decomposes it into multiple sub-problems, allowing each omics/view to solve intersecting yet unique sub-problem groups. Additionally, we introduce mutual information-driven orthogonal loss and balancing loss to avoid view collapse. Extensive experiments on multi-omics data across multiple cancer types highlight MMoG's superiority.

Graph Neural Networks (GNNs) have expressed remarkable capability in processing graph-structured data. Recent studies have found that most GNNs rely on the homophily assumption of graphs, leading to unsatisfactory performance on heterophilous graphs. While certain methods have been developed to address heterophilous links, they lack more precise estimation of high-order relationships between nodes. This could result in the aggregation of excessive interference information during message propagation, thus degrading the representation ability of learned features. In this work, we propose a Disparity-induced Structural Refinement (DSR) method that enables adaptive and selective message propagation in GNN, to enhance representation learning in heterophilous graphs. We theoretically analyze the necessity of structural refinement during message passing grounded in the derivation of error bound for node classification. To this end, we design a disparity score that combines both features and structural information at the node level, reflecting the connectivity degree of hopping neighbor nodes. Based on the disparity score, we can adjust the aggregation of neighbor nodes, thereby mitigating the impact of irrelevant information during message passing. Experimental results demonstrate that our method achieves competitive performance, mostly outperforming advanced methods on both homophilous and heterophilous datasets.

In practical applications, the difficulty of multi-view data annotation poses a challenge for multi-view semi-supervised learning. Although some graph-based approaches have been proposed for this task, they often struggle with capturing long-range information and memory bottlenecks, and usually encounter over-smoothing. To address these issues, this paper proposes an implicit model, named multi-channel Equilibrium Graph Neural Network (MEGNN). Through an equilibrium point iterative process, the proposed MEGNN naturally captures long-range information and effectively reduces the consumption of memory compared with explicit models. Furthermore, the proposed method deals with the issue of over-smoothing in deep graph convolutional networks by residual connection and shrinkage factor. We analyze the effect of the shrinkage factor on the information capturing capability of the model, and demonstrate that the proposed method does not encounter over-smoothing. Comprehensive experimental results demonstrate that the proposed method outperforms the state-of-the-art methods.

Active learning, as a technique, aims to effectively label specific data points while operating within a designated query budget. Nevertheless, the majority of unsupervised active learning algorithms are based on shallow linear representation and lack sufficient interpretability. Furthermore, certain diversity-based methods face challenges in selecting samples that adequately represent the entire data distribution. Inspired by these reasons, in this paper, we propose an unsupervised active learning method on orthogonal projections to construct a deep neural network model. By optimizing the orthogonal projection process, we establish the connection between projection and active learning, consequently enhancing the interpretability of the proposed method. The proposed method can efficiently project the feature space onto a spanned subspace, deriving an indicator matrix while calculating the projection loss. Moreover, we consider the redundancy among samples to ensure both data point diversity and enhancement of clustering-based algorithms. Through extensive comparative experiments on six public datasets, the results demonstrate that the proposed method can effectively select more informative and representative samples and improve performance by up to 11%.

The challenges posed by heterogeneous data in practical applications have made multiview semi-supervised classification a focus of attention for researchers. While several graph-based approaches have been suggested for this task, they tend to use homogeneous feature propagation, leading to even diffusion of node information to their neighbors. However, this diffusion strategy results in nodes acquiring information of equal proportion from dissimilar samples. In this article, we propose a solution to address these issues by introducing a graph diffusion-induced network for multiview semi-supervised classification. By formulating a discretized partial differential equation on a manifold, we derive a nonlinear and inhomogeneous diffusion equation to govern information propagation on the graph. Then, we investigate the impact of various nonlinear activation functions on random switching edge directions and their suppressive effects on information diffusion between different nodes. In addition, the cross-view consistency under the semi-supervised scenarios is defined and guaranteed for better information fusion. The comprehensive experimental results demonstrate the superiority of the proposed method compared with state-of-the-art approaches. The effectiveness of the proposed approach in handling diverse and heterogeneous data showcases its potential for advancing multiview semi-supervised classification techniques.

Federated Graph Learning (FGL) has garnered widespread attention by enabling collaborative training on multiple clients for semi-supervised classification tasks. However, most existing FGL studies do not well consider the missing inter-client topology information in real-world scenarios, causing insufficient feature aggregation of multi-hop neighbor clients during model training. Moreover, the classic FGL commonly adopts the FedAvg but neglects the high training costs when the number of clients expands, resulting in the overload of a single edge server. To address these important challenges, we propose a novel FGL framework, named SpreadFGL, to promote the information flow in edge-client collaboration and extract more generalized potential relationships between clients. In SpreadFGL, an adaptive graph imputation generator incorporated with a versatile assessor is first designed to exploit the potential links between subgraphs, without sharing raw data. Next, a new negative sampling mechanism is developed to make SpreadFGL concentrate on more refined information in downstream tasks. To facilitate load balancing at the edge layer, SpreadFGL follows a distributed training manner that enables fast model convergence. Using real-world testbed and benchmark graph datasets, extensive experiments demonstrate the effectiveness of the proposed SpreadFGL. The results show that SpreadFGL achieves higher accuracy and faster convergence against state-of-the-art algorithms.

In recent years, reconstructing features and learning node representations by graph autoencoders (GAE) have attracted much attention in deep graph node clustering. However, existing works often overemphasize structural information and overlook the impact of real-world prevalent noise on feature learning and clustering with graph data, which may be detrimental to robust training. To address these issues, the utilization of a masking strategy that specifically focuses on feature reconstruction may mitigate these limitations. In this article, we propose a graph node clustering generative method named deep masked graph node clustering (DMGNC), which leverages a masked autoencoder to effectively reconstruct node features, enabling the discovery of latent information crucial for accurate node clustering. Additionally, a clustering self-optimization module is designed to guide the iterative update of our end-to-end clustering framework. Further, we extend the masked graph autoencoder (MGA) and develop a contrastive method called deep masked graph node contrastive clustering (DMGNCC), which applies the MGA to graph node contrastive learning at both the node level and the class level in a united model. Extensive experimental results on real-world graph benchmark datasets demonstrate the effectiveness and superiority of the proposed method.

Existing multi-view graph learning methods often rely on consistent information for similar nodes within and across views, however they may lack adaptability when facing diversity challenges from noise, varied views, and complex data distributions. These challenges can be mainly categorized into: 1) View-specific diversity within intra-view from noise and incomplete information; 2) Cross-view diversity within inter-view caused by various latent semantics; 3) Cross-group diversity within inter-group due to data distribution differences. To this end, we propose a universal multi-view consensus graph learning framework that considers both original and generative graphs to balance consistency and diversity. Specifically, the proposed framework can be divided into the following four modules: i) Multi-channel graph module to extract principal node information, ensuring view-specific and cross-view consistency while mitigating view-specific and cross-view diversity within original graphs; ii) Generative module to produce cleaner and more realistic graphs, enriching graph structure while maintaining view-specific consistency and suppressing view-specific diversity; iii) Contrastive module to collaborate on generative semantics to facilitate cross-view consistency and reducing cross-view diversity within generative graphs; iv) Consensus graph module to consolidate learning a consensual graph, pursuing cross-group consistency and cross-group diversity. Extensive experimental results on real-world datasets demonstrate its effectiveness and superiority.