The widespread adoption of graph neural networks (GNNs) has brought increased attention to fairness issues related to sensitive attributes, such as gender and race, in practical scenarios. However, this concern remains largely unexplored in the context of graph clustering. Conventional fair graph clustering methods primarily depend on spectral clustering approaches. Meanwhile, we argue that existing graph learning works mainly focus on a single type of fairness, whereas graph clustering should achieve group equality-informed individual fairness. In this paper, we introduce for the first time a fairness-aware framework termed FairGC for deep graph clustering, which integrates the dual objectives of individual and group fairness while maintaining accurate clustering results. Specifically, we construct two views with distinct semantics using Siamese encoders. Then, we apply multi-step random walks on view-specific affinity graphs to capture high-order affinities of node pairs, thereby reformulating the contrastive learning with a focus on individual similarity. Besides, we utilize adversarial learning by making node representations independent of the estimated sensitive attributes to further eliminate group biases of clustering results. Extensive experiments on four benchmarks demonstrate the effectiveness and superiority of our proposed framework FairGC.

Spatial transcriptomics (ST) enables joint profiling of gene expression and spatial positions, thereby revealing spatially resolved biological functions. However, many existing ST analysis methods often fail to explicitly quantify the belief and uncertainty in decisions caused by noisy ST data, making it difficult to handle spots of varying quality in a fine-grained manner. In addition, domain identification is a fundamental and critical task in ST, but commonly used models that separate expression learning and clustering often struggle to learn cluster-friendly latent representations effectively. To address these issues, we propose PREST, a prototype-based evidence-aware integration framework for ST data. PREST performs multi-scale representation learning with fine-grained attention fusion and introduces learnable class prototypes to quantify belief and uncertainty in model decisions. We aim to align overall belief scores with latent semantic information to enhance uncertainty quantification and prototype learning, thereby promoting the learning of clustering-friendly representations. PREST further integrates an uncertainty-aware reconstruction module and spatial regularization to reduce overfitting to unreliable spots and promote denoised, discriminative representations. Extensive experiments on several benchmark datasets validate the effectiveness and superiority of our proposed PREST across various downstream tasks.

Graph-level classification involves analyzing the property of the whole graph, which is typically solved by using graph neural networks (GNNs). Existing efforts generally assume a balanced class distribution. However, real-world data often exhibit long-tailed distributions, i.e., tail classes have significantly fewer samples than head classes, and thus directly applying GNNs is eventually biased toward the head classes, resulting in limited generalization over the tail classes. Moreover, the predictions of existing algorithms are usually not trustworthy, and the trained classifiers remain ignorant to their predictive confidence. Towards this end, in this paper we develop a principled framework called GraphEVER for long-tailed graph-level classification. Technically, GraphEVER incorporates the beliefs of multiple experts and leverages the idea of subjective logic within the Dempster-Shafer Evidence Theory (DST). It can provide the evidence and uncertainty estimation for each expert, where the evidence is parameterized by a Dirichlet distribution to model class probability distribution, and the uncertainty is quantified via a well-defined theoretical framework. In this way, diverse experts can be integrated under DST to endow the classifier with both reliability and robustness. Moreover, we propose an evidence-based routing mechanism to dynamically assign experts, such that the tail classes can receive more attention, while the head classes can reduce redundant engaged experts, further cutting down the computational cost and improving the efficiency. Extensive experiments on seven datasets verify the superiority of our proposed framework.

Out-of-Distribution (OOD) detection, which seeks to identify samples deviating from the In-Distribution (ID) training distribution at test time, is crucial for building robust machine learning systems. While extensive efforts have been made for Euclidean data, OOD detection on graph-structured data remains relatively underexplored. On the one hand, the specific properties of a graph may be attributed to its substructures. On the other hand, acquiring labeled data for graph learning is typically time-consuming and labor-intensive. Toward this end, in this paper, we propose a novel kernel-enhanced graph substructure learning framework termed KEGOD for unsupervised graph OOD detection. Specifically, we introduce a learnable graph generator to construct the augmented graph view that preserves distinguishable structure information. Then, for both the input graph and augmented view, a graph neural network (GNN) branch and a graph kernel (GK) branch are incorporated to explore graph latent patterns. By performing multi-branch concordance learning on the extracted graph patterns, our KEGOD captures complementary ID structural semantics in both implicit and explicit manners, enabling reliable detection of OOD graphs through semantic inconsistency. Finally, we build a self-adaptive training mechanism to automatically control diverse sensitivities of the graph patterns. Experimental results on several public graph datasets reveal the superiority of our KEGOD. Our code is available at~ https://github.com/jamesyifan/KEGOD.

Graph-structured data exhibits universality and widespread applicability across diverse domains, such as social network analysis, biochemistry, financial fraud detection, and network security. Significant strides have been made in leveraging Graph Neural Networks (GNNs) to achieve remarkable success in these areas. However, in real-world scenarios, the training environment for models is often far from ideal, leading to substantial performance degradation of GNN models due to various unfavorable factors, including imbalance in data distribution, the presence of noise in erroneous data, privacy protection of sensitive information, and generalization capability for out-of-distribution (OOD) scenarios. To tackle these issues, substantial efforts have been devoted to improving the performance of GNN models in practical real-world scenarios, as well as enhancing their reliability and robustness. In this paper, we present a comprehensive survey that systematically reviews existing GNN models, focusing on solutions to the four mentioned real-world challenges including imbalance, noise, privacy, and OOD in practical scenarios that many existing reviews have not considered. Specifically, we first highlight the four key challenges faced by existing GNNs, paving the way for our exploration of real-world GNN models. Subsequently, we provide detailed discussions on these four aspects, dissecting how these solutions contribute to enhancing the reliability and robustness of GNN models. Last but not least, we outline promising directions and offer future perspectives in the field.

This paper studies the problem of class-imbalanced graph classification, which aims at effectively classifying the graph categories in scenarios with imbalanced class distributions. While graph neural networks (GNNs) have achieved remarkable success, their modeling ability on imbalanced graph-structured data remains suboptimal, which typically leads to predictions biased towards the majority classes. On the other hand, existing class-imbalanced learning methods in vision may overlook the rich graph semantic substructures of the majority classes and excessively emphasize learning from the minority classes. To address these challenges, we propose a simple yet powerful approach called C3GNN that integrates the idea of clustering into contrastive learning to enhance class-imbalanced graph classification. Technically, C3GNN clusters graphs from each majority class into multiple subclasses, with sizes comparable to the minority class, mitigating class imbalance. It also employs the Mixup technique to generate synthetic samples, enriching the semantic diversity of each subclass. Furthermore, supervised contrastive learning is used to hierarchically learn effective graph representations, enabling the model to thoroughly explore semantic substructures in majority classes while avoiding excessive focus on minority classes. Extensive experiments on real-world graph benchmark datasets verify the superior performance of our proposed method against competitive baselines.

Graph domain adaptation is a key subfield of graph transfer learning that aims to bridge domain gaps by transferring knowledge from a label-rich source graph to an unlabeled target graph. However, most existing methods assume balanced labels in the source graph, which often fails in practice and leads to biased knowledge transfer. To address this, in this paper, we propose a prototype-anchored learning and alignment framework for class-imbalanced graph domain adaptation. Specifically, we incorporate pointwise node mutual information into the graph encoder to capture high-order topological proximity and learn generalized node representations. Leveraging this, we then introduce categorical prototypes with adversarial proto-instances for prototype-anchored learning and recalibration to represent the source graph under an imbalanced class distribution. Finally, we introduce a weighted prototype contrastive adaptation strategy that aligns target pseudo-labels with source prototypes to handle class imbalance during adaptation. Extensive experiments show that our PALA outperforms the state-of-the-art methods. Our code is available at https://github.com/maxin88scu/PALA.

Graph transfer learning, especially in unsupervised domain adaptation, aims to transfer knowledge from a label-abundant source graph to an unlabeled target graph. However, most existing approaches overlook the common issue of label imbalance in the source domain, typically assuming a balanced label distribution that rarely holds in practice. Moreover, they face challenges arising from biased knowledge in the source graph and substantial domain distribution shifts. To remedy the above challenges, we propose a dual-branch prototype-enhanced contrastive framework for class-imbalanced graph domain adaptation in this paper. Specifically, we introduce a dual-branch graph encoder to capture both local and global information, generating class-specific prototypes from a distilled anchor set. Then, a prototype-enhanced contrastive learning framework is introduced. On the one hand, we encourage class alignment between the two branches based on constructed prototypes to alleviate the bias introduced by class imbalance. On the other hand, we infer the pseudo-labels for the target domain and align sample pairs across domains that share similar semantics to reduce domain discrepancies. Experimental results show that our ImGDA outperforms the state-of-the-art methods across multiple datasets and settings. The code is available at: https://github.com/maxin88scu/ImGDA.

Graph neural networks (GNNs) have shown remarkable success in graph-level classification tasks. However, most of the existing GNN-based studies are based on balanced datasets, while many real-world datasets exhibit long-tailed distributions. In such datasets, the tail classes receive limited attention during training, leading to prediction bias and degraded performance. To address this issue, a range of long-tailed learning strategies have been proposed, such as data re-balancing and transfer learning. However, these approaches encounter several challenges, including insufficient representation capacity for tail classes and their evaluation solely on uniform test data, limiting their capacity to handle unknown class distributions. To tackle these challenges, we introduce a novel framework, namely Knowledge-diverse Experts (KDEX) for long-tailed graph classification. Our KDEX leverages a dynamic memory module to enable the transfer of knowledge from head to tail, which improves the representation ability of the tail. To deal with unknown test distributions, KDEX introduces a knowledge-diverse expert training approach to train experts with different capacities in managing various test distributions. Moreover, we train the hierarchical router in a self-supervised manner to dynamically aggregate each knowledge-diverse expert during testing. Experimental results on multiple benchmarks reveal that our KDEX outperforms current baselines in both standard and test-agnostic long-tailed graph classification.

This paper studies the problem of semi-supervised learning on graphs, which has recently aroused widespread interest in relational data mininThe focal point of exploration in this area has been the utilization of graph neural networks (GNNs), which stand out for excellent performance. Previous methods, however, typically rely on the limited labeled data while ignoring the abundant structural information in unlabeled nodes inherently on graphs, easily resulting in overfitting, especially in scenarios where only a few label nodes are available. Even worse, GNNs, despite their success, are constrained by their ability to solely capture local neighborhood information through message-passing mechanisms, thereby falling short in modeling higher-order dependencies among nodes. To circumvent the above drawbacks, we propose a simple yet effective framework calledHypergraph COnsistencyLeArning (HOLA). Specifically, we employ a collaborative distillation framework consisting of a teacher network and a student network. To achieve effective interaction, we propose momentum distillation, a self-training method that enables the student network to learn from pseudo-targets generated by a momentum teacher network. Further, a novel hypergraph structure learning network is developed to model complex high-order relations among nodes with relational consistency learning, thereby transferring the knowledge to the student network. Extensive experiments conducted on a variety of benchmark datasets demonstrate the superior performance of the HOLA over various state-of-the-art methods.

This paper studies the problem of graph zero-shot learning, which aims at recognizing novel classes of nodes on the graph that are never seen during training. The key to graph zero-shot learning is establishing the mathematical relationship to transfer the prior knowledge of nodes from seen classes to unseen classes. However, the problem is largely under-explored and existing methods typically focus on acquiring supervision signals from seen classes or simply establishing connections between classes based solely on a semantic description matrix, such that the learned representations lack generalizable properties to unseen classes. To address this issue, this paper proposes GraphGCR that learns generalizable contrastive representations from the perspective of uniformity and alignment. Technically, GraphGCR leverages graph diffusion to extend supervised contrastive learning, encouraging the representations of semantics from different classes to be distributed uniformly and meanwhile achieve the alignment of node features and class semantics with the assistance of graph structural information. Moreover, to effectively enhance model generalizability, we further develop a class generator to synthesize features of unseen classes by embedding propagation and interpolation, thereby enriching the diversity of classes. Theoretical analysis also shows that our proposed framework exhibits strong discriminative property, which significantly enhances graph zero-shot learning. Experimental findings reveal that our GraphGCR achieves significant performance improvements over state-of-the-art methods across various benchmark datasets.

In this paper, we study semi-supervised graph classification, which aims at accurately predicting the categories of graphs in scenarios with limited labeled graphs and abundant unlabeled graphs. Despite the promising capability of graph neural networks (GNNs), they typically require a large number of costly labeled graphs, while a wealth of unlabeled graphs fail to be effectively utilized. Moreover, GNNs are inherently limited to encoding local neighborhood information using message-passing mechanisms, thus lacking the ability to model higher-order dependencies among nodes. To tackle these challenges, we propose a Hypergraph-Enhanced DuAL framework named HEAL for semi-supervised graph classification, which captures graph semantics from the perspective of the hypergraph and the line graph, respectively. Specifically, to better explore the higher-order relationships among nodes, we design a hypergraph structure learning to adaptively learn complex node dependencies beyond pairwise relations. Meanwhile, based on the learned hypergraph, we introduce a line graph to capture the interaction between hyperedges, thereby better mining the underlying semantic structures. Finally, we develop a relational consistency learning to facilitate knowledge transfer between the two branches and provide better mutual guidance. Extensive experiments on real-world graph datasets verify the effectiveness of the proposed method against existing state-of-the-art methods.

Graph clustering, which learns the node representations for effective cluster assignments, is a fundamental yet challenging task in data analysis and has received considerable attention accompanied by graph neural networks (GNNs) in recent years. However, most existing methods overlook the inherent relational information among the nonindependent and nonidentically distributed nodes in a graph. Due to the lack of exploration of relational attributes, the semantic information of the graph-structured data fails to be fully exploited which leads to poor clustering performance. In this article, we propose a novel self-supervised deep graph clustering method named relational redundancy-free graph clustering (R2FGC) to tackle the problem. It extracts the attribute- and structure-level relational information from both global and local views based on an autoencoder (AE) and a graph AE (GAE). To obtain effective representations of the semantic information, we preserve the consistent relationship among augmented nodes, whereas the redundant relationship is further reduced for learning discriminative embeddings. In addition, a simple yet valid strategy is used to alleviate the oversmoothing issue. Extensive experiments are performed on widely used benchmark datasets to validate the superiority of our R2FGC over state-of-the-art baselines. Our codes are available at https://github.com/yisiyu95/R2FGC.

Semi-supervised node classification is a crucial challenge in relational data mining and has attracted increasing interest in research on graph neural networks (GNNs). However, previous approaches merely utilize labeled nodes to supervise the overall optimization, but fail to sufficiently explore the information of their underlying label distribution. Even worse, they often overlook the robustness of models, which may cause instability of network outputs to random perturbations. To address the aforementioned shortcomings, we develop a novel framework termed Hybrid Curriculum Pseudo-Labeling (HCPL) for efficient semi-supervised node classification. Technically, HCPL iteratively annotates unlabeled nodes by training a GNN model on the labeled samples and any previously pseudo-labeled samples, and repeatedly conducts this process. To improve the model robustness, we introduce a hybrid pseudo-labeling strategy that incorporates both prediction confidence and uncertainty under random perturbations, therefore mitigating the influence of erroneous pseudo-labels. Finally, we leverage the idea of curriculum learning to start from annotating easy samples, and gradually explore hard samples as the iteration grows. Extensive experiments on a number of benchmarks demonstrate that our HCPL beats various state-of-the-art baselines in diverse settings.

Graph classification, aiming at learning the graph-level representations for effective class assignments, has received outstanding achievements, which heavily relies on high-quality datasets that have balanced class distribution. In fact, most real-world graph data naturally presents a long-tailed form, where the head classes occupy much more samples than the tail classes, it thus is essential to study the graph-level classification over long-tailed data while still remaining largely unexplored. However, most existing long-tailed learning methods in visions fail to jointly optimize the representation learning and classifier training, as well as neglect the mining of the hard-to-classify classes. Directly applying existing methods to graphs may lead to sub-optimal performance, since the model trained on graphs would be more sensitive to the long-tailed distribution due to the complex topological characteristics. Hence, in this paper, we propose a novel long-tailed graph-level classification framework viaCollaborativeMulti-expert Learning (CoMe) to tackle the problem. To equilibrate the contributions of head and tail classes, we first develop balanced contrastive learning from the view of representation learning, and then design an individual-expert classifier training based on hard class mining. In addition, we execute gated fusion and disentangled knowledge distillation among the multiple experts to promote the collaboration in a multi-expert framework. Comprehensive experiments are performed on seven widely-used benchmark datasets to demonstrate the superiority of our method CoMe over state-of-the-art baselines.