Yifang Qin

Si-Yu Yi, Wei Ju, Yifang Qin et al. · pku

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 in recent years. However, most existing methods overlook the inherent relational information among the non-independent and non-identically 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 paper, we propose a novel self-supervised deep graph clustering method named Relational Redundancy-Free Graph Clustering (R$^2$FGC) to tackle the problem. It extracts the attribute- and structure-level relational information from both global and local views based on an autoencoder and a graph autoencoder. To obtain effective representations of the semantic information, we preserve the consistent relation among augmented nodes, whereas the redundant relation is further reduced for learning discriminative embeddings. In addition, a simple yet valid strategy is utilized to alleviate the over-smoothing issue. Extensive experiments are performed on widely used benchmark datasets to validate the superiority of our R$^2$FGC over state-of-the-art baselines. Our codes are available at https://github.com/yisiyu95/R2FGC.

Wei Ju, Yifang Qin, Ziyue Qiao et al.

Point-of-Interest (POI) recommendation, which benefits from the proliferation of GPS-enabled devices and location-based social networks (LBSNs), plays an increasingly important role in recommender systems. It aims to provide users with the convenience to discover their interested places to visit based on previous visits and current status. Most existing methods usually merely leverage recurrent neural networks (RNNs) to explore sequential influences for recommendation. Despite the effectiveness, these methods not only neglect topological geographical influences among POIs, but also fail to model high-order sequential substructures. To tackle the above issues, we propose a Kernel-Based Graph Neural Network (KBGNN) for next POI recommendation, which combines the characteristics of both geographical and sequential influences in a collaborative way. KBGNN consists of a geographical module and a sequential module. On the one hand, we construct a geographical graph and leverage a message passing neural network to capture the topological geographical influences. On the other hand, we explore high-order sequential substructures in the user-aware sequential graph using a graph kernel neural network to capture user preferences. Finally, a consistency learning framework is introduced to jointly incorporate geographical and sequential information extracted from two separate graphs. In this way, the two modules effectively exchange knowledge to mutually enhance each other. Extensive experiments conducted on two real-world LBSN datasets demonstrate the superior performance of our proposed method over the state-of-the-arts. Our codes are available at https://github.com/Fang6ang/KBGNN.

Wei Ju, Zheng Fang, Yiyang Gu et al. · uw

Graph representation learning aims to effectively encode high-dimensional sparse graph-structured data into low-dimensional dense vectors, which is a fundamental task that has been widely studied in a range of fields, including machine learning and data mining. Classic graph embedding methods follow the basic idea that the embedding vectors of interconnected nodes in the graph can still maintain a relatively close distance, thereby preserving the structural information between the nodes in the graph. However, this is sub-optimal due to: (i) traditional methods have limited model capacity which limits the learning performance; (ii) existing techniques typically rely on unsupervised learning strategies and fail to couple with the latest learning paradigms; (iii) representation learning and downstream tasks are dependent on each other which should be jointly enhanced. With the remarkable success of deep learning, deep graph representation learning has shown great potential and advantages over shallow (traditional) methods, there exist a large number of deep graph representation learning techniques have been proposed in the past decade, especially graph neural networks. In this survey, we conduct a comprehensive survey on current deep graph representation learning algorithms by proposing a new taxonomy of existing state-of-the-art literature. Specifically, we systematically summarize the essential components of graph representation learning and categorize existing approaches by the ways of graph neural network architectures and the most recent advanced learning paradigms. Moreover, this survey also provides the practical and promising applications of deep graph representation learning. Last but not least, we state new perspectives and suggest challenging directions which deserve further investigations in the future.

Yifang Qin, Yifan Wang, Fang Sun et al.

Point-of-Interest (POI) recommendation plays a vital role in various location-aware services. It has been observed that POI recommendation is driven by both sequential and geographical influences. However, since there is no annotated label of the dominant influence during recommendation, existing methods tend to entangle these two influences, which may lead to sub-optimal recommendation performance and poor interpretability. In this paper, we address the above challenge by proposing DisenPOI, a novel Disentangled dual-graph framework for POI recommendation, which jointly utilizes sequential and geographical relationships on two separate graphs and disentangles the two influences with self-supervision. The key novelty of our model compared with existing approaches is to extract disentangled representations of both sequential and geographical influences with contrastive learning. To be specific, we construct a geographical graph and a sequential graph based on the check-in sequence of a user. We tailor their propagation schemes to become sequence-/geo-aware to better capture the corresponding influences. Preference proxies are extracted from check-in sequence as pseudo labels for the two influences, which supervise the disentanglement via a contrastive loss. Extensive experiments on three datasets demonstrate the superiority of the proposed model.

Wei Ju, Yiyang Gu, Binqi Chen et al.

This paper studies the problem of graph-level clustering, which is a novel yet challenging task. This problem is critical in a variety of real-world applications such as protein clustering and genome analysis in bioinformatics. Recent years have witnessed the success of deep clustering coupled with graph neural networks (GNNs). However, existing methods focus on clustering among nodes given a single graph, while exploring clustering on multiple graphs is still under-explored. In this paper, we propose a general graph-level clustering framework named Graph-Level Contrastive Clustering (GLCC) given multiple graphs. Specifically, GLCC first constructs an adaptive affinity graph to explore instance- and cluster-level contrastive learning (CL). Instance-level CL leverages graph Laplacian based contrastive loss to learn clustering-friendly representations while cluster-level CL captures discriminative cluster representations incorporating neighbor information of each sample. Moreover, we utilize neighbor-aware pseudo-labels to reward the optimization of representation learning. The two steps can be alternatively trained to collaborate and benefit each other. Experiments on a range of well-known datasets demonstrate the superiority of our proposed GLCC over competitive baselines.

Jingyang Yuan, Xiao Luo, Yifang Qin et al.

Node classification on graphs is a significant task with a wide range of applications, including social analysis and anomaly detection. Even though graph neural networks (GNNs) have produced promising results on this task, current techniques often presume that label information of nodes is accurate, which may not be the case in real-world applications. To tackle this issue, we investigate the problem of learning on graphs with label noise and develop a novel approach dubbed Consistent Graph Neural Network (CGNN) to solve it. Specifically, we employ graph contrastive learning as a regularization term, which promotes two views of augmented nodes to have consistent representations. Since this regularization term cannot utilize label information, it can enhance the robustness of node representations to label noise. Moreover, to detect noisy labels on the graph, we present a sample selection technique based on the homophily assumption, which identifies noisy nodes by measuring the consistency between the labels with their neighbors. Finally, we purify these confident noisy labels to permit efficient semantic graph learning. Extensive experiments on three well-known benchmark datasets demonstrate the superiority of our CGNN over competing approaches.

Zhengyang Mao, Wei Ju, Yifang Qin et al.

Graph classification is a crucial task in many real-world multimedia applications, where graphs can represent various multimedia data types such as images, videos, and social networks. Previous efforts have applied graph neural networks (GNNs) in balanced situations where the class distribution is balanced. However, real-world data typically exhibit long-tailed class distributions, resulting in a bias towards the head classes when using GNNs and limited generalization ability over the tail classes. Recent approaches mainly focus on re-balancing different classes during model training, which fails to explicitly introduce new knowledge and sacrifices the performance of the head classes. To address these drawbacks, we propose a novel framework called Retrieval Augmented Hybrid Network (RAHNet) to jointly learn a robust feature extractor and an unbiased classifier in a decoupled manner. In the feature extractor training stage, we develop a graph retrieval module to search for relevant graphs that directly enrich the intra-class diversity for the tail classes. Moreover, we innovatively optimize a category-centered supervised contrastive loss to obtain discriminative representations, which is more suitable for long-tailed scenarios. In the classifier fine-tuning stage, we balance the classifier weights with two weight regularization techniques, i.e., Max-norm and weight decay. Experiments on various popular benchmarks verify the superiority of the proposed method against state-of-the-art approaches.

Jingyang Yuan, Xiao Luo, Yifang Qin et al.

Graph Neural Networks (GNNs) have garnered considerable interest due to their exceptional performance in a wide range of graph machine learning tasks. Nevertheless, the majority of GNN-based approaches have been examined using well-annotated benchmark datasets, leading to suboptimal performance in real-world graph learning scenarios. To bridge this gap, the present paper investigates the problem of graph transfer learning in the presence of label noise, which transfers knowledge from a noisy source graph to an unlabeled target graph. We introduce a novel technique termed Balance Alignment and Information-aware Examination (ALEX) to address this challenge. ALEX first employs singular value decomposition to generate different views with crucial structural semantics, which help provide robust node representations using graph contrastive learning. To mitigate both label shift and domain shift, we estimate a prior distribution to build subgraphs with balanced label distributions. Building on this foundation, an adversarial domain discriminator is incorporated for the implicit domain alignment of complex multi-modal distributions. Furthermore, we project node representations into a different space, optimizing the mutual information between the projected features and labels. Subsequently, the inconsistency of similarity structures is evaluated to identify noisy samples with potential overfitting. Comprehensive experiments on various benchmark datasets substantiate the outstanding superiority of the proposed ALEX in different settings.

Wei Ju, Siyu Yi, Yifan Wang et al.

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.

Yifang Qin, Zhaobin Li, Arisa Watanabe et al.

Generative methods have gained widespread attention in Collaborative Filtering (CF) tasks for their ability to produce high-quality personalized samples aligned with users' interests. Among them, diffusion generative models have raised increasing attention in recommendation field. Despite that the pioneering efforts have applied the conventional diffusion process to model diffusive user interests, the incongruity between the Gaussian noise and the subtle nature of user's personalized interaction behavior has led to sub-optimal results. To this end, we introduce a specifically-tailored diffusion scheme for interaction systems, namely the interests burn-down process. The interests burn-down process delineates the decay of user interests towards candidate items, complemented by its reverse burn-up process that yields personalized recommendation for users. The inherent burn-down nature of this process adeptly models the diffusive user interests, aligning seamlessly with the requirements of CF tasks. We present a novel recommendation method StageCF to illustrate the superiority of this newly proposed diffusion process. Experimental results have demonstrated the effectiveness of StageCF against existing generative and diffusion-based baseline methods. Furthermore, comprehensive studies validate the functionality of interests burn-down process, shedding light on its capacity to generate personalized interactions.

Wei Ju, Yifan Wang, Yifang Qin et al. · pku

In recent years, deep learning on graphs has achieved remarkable success in various domains. However, the reliance on annotated graph data remains a significant bottleneck due to its prohibitive cost and time-intensive nature. To address this challenge, self-supervised learning (SSL) on graphs has gained increasing attention and has made significant progress. SSL enables machine learning models to produce informative representations from unlabeled graph data, reducing the reliance on expensive labeled data. While SSL on graphs has witnessed widespread adoption, one critical component, Graph Contrastive Learning (GCL), has not been thoroughly investigated in the existing literature. Thus, this survey aims to fill this gap by offering a dedicated survey on GCL. We provide a comprehensive overview of the fundamental principles of GCL, including data augmentation strategies, contrastive modes, and contrastive optimization objectives. Furthermore, we explore the extensions of GCL to other aspects of data-efficient graph learning, such as weakly supervised learning, transfer learning, and related scenarios. We also discuss practical applications spanning domains such as drug discovery, genomics analysis, recommender systems, and finally outline the challenges and potential future directions in this field.

Wei Ju, Yusheng Zhao, Yifang Qin et al.

This paper investigates traffic forecasting, which attempts to forecast the future state of traffic based on historical situations. This problem has received ever-increasing attention in various scenarios and facilitated the development of numerous downstream applications such as urban planning and transportation management. However, the efficacy of existing methods remains sub-optimal due to their tendency to model temporal and spatial relationships independently, thereby inadequately accounting for complex high-order interactions of both worlds. Moreover, the diversity of transitional patterns in traffic forecasting makes them challenging to capture for existing approaches, warranting a deeper exploration of their diversity. Toward this end, this paper proposes Conjoint Spatio-Temporal graph neural network (abbreviated as COOL), which models heterogeneous graphs from prior and posterior information to conjointly capture high-order spatio-temporal relationships. On the one hand, heterogeneous graphs connecting sequential observation are constructed to extract composite spatio-temporal relationships via prior message passing. On the other hand, we model dynamic relationships using constructed affinity and penalty graphs, which guide posterior message passing to incorporate complementary semantic information into node representations. Moreover, to capture diverse transitional properties to enhance traffic forecasting, we propose a conjoint self-attention decoder that models diverse temporal patterns from both multi-rank and multi-scale views. Experimental results on four popular benchmark datasets demonstrate that our proposed COOL provides state-of-the-art performance compared with the competitive baselines.

Wei Ju, Zhengyang Mao, Siyu Yi et al.

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.

Wei Ju, Yiyang Gu, Zhengyang Mao et al.

Self-supervised graph representation learning has recently shown considerable promise in a range of fields, including bioinformatics and social networks. A large number of graph contrastive learning approaches have shown promising performance for representation learning on graphs, which train models by maximizing agreement between original graphs and their augmented views (i.e., positive views). Unfortunately, these methods usually involve pre-defined augmentation strategies based on the knowledge of human experts. Moreover, these strategies may fail to generate challenging positive views to provide sufficient supervision signals. In this paper, we present a novel approach named Graph Pooling ContraSt (GPS) to address these issues. Motivated by the fact that graph pooling can adaptively coarsen the graph with the removal of redundancy, we rethink graph pooling and leverage it to automatically generate multi-scale positive views with varying emphasis on providing challenging positives and preserving semantics, i.e., strongly-augmented view and weakly-augmented view. Then, we incorporate both views into a joint contrastive learning framework with similarity learning and consistency learning, where our pooling module is adversarially trained with respect to the encoder for adversarial robustness. Experiments on twelve datasets on both graph classification and transfer learning tasks verify the superiority of the proposed method over its counterparts.

Yifang Qin, Yu Shi, Junfu Tan et al.

Predicting stable and metastable structures is central to molecular and materials discovery, but remains limited by the cost of searching high-dimensional energy landscapes. Deep generative models offer efficient structure sampling, yet their outputs remain shaped by training data and can underexplore minima that are rare but physically relevant. We introduce generative structure search (GSS), a unified framework that formulates diffusion-based generation and random structure search (RSS) as limiting regimes of a common sampling process driven by learned score fields and physical forces. Coupling these drivers lets GSS use data priors to accelerate sampling while retaining energy-guided exploration of local minima. Across molecular and crystalline systems, GSS recovers diverse metastable structures with more than tenfold lower sampling cost than RSS for broad coverage and remains effective for compositions outside the training distribution. The results establish a physically grounded generative search strategy for discovering structures beyond the reach of data-driven sampling alone.

Wei Ju, Zhengyang Mao, Siyu Yi et al.

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 C$^3$GNN that integrates the idea of clustering into contrastive learning to enhance class-imbalanced graph classification. Technically, C$^3$GNN 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.

Hourun Li, Yusheng Zhao, Zhengyang Mao et al.

Intelligent Transportation System (ITS) is crucial for improving traffic congestion, reducing accidents, optimizing urban planning, and more. However, the complexity of traffic networks has rendered traditional machine learning and statistical methods less effective. With the advent of artificial intelligence, deep learning frameworks have achieved remarkable progress across various fields and are now considered highly effective in many areas. Since 2019, Graph Neural Networks (GNNs) have emerged as a particularly promising deep learning approach within the ITS domain, owing to their robust ability to model graph-structured data and address complex problems. Consequently, there has been increasing scholarly attention to the applications of GNNs in transportation, which have demonstrated excellent performance. Nevertheless, current research predominantly focuses on traffic forecasting, with other ITS domains, such as autonomous vehicles and demand prediction, receiving less attention. This paper aims to review the applications of GNNs across six representative and emerging ITS research areas: traffic forecasting, vehicle control system, traffic signal control, transportation safety, demand prediction, and parking management. We have examined a wide range of graph-related studies from 2018 to 2023, summarizing their methodologies, features, and contributions in detailed tables and lists. Additionally, we identify the challenges of applying GNNs in ITS and propose potential future research directions.

Xiao Luo, Yusheng Zhao, Yifang Qin et al.

Graph neural networks have pushed state-of-the-arts in graph classifications recently. Typically, these methods are studied within the context of supervised end-to-end training, which necessities copious task-specific labels. However, in real-world circumstances, labeled data could be limited, and there could be a massive corpus of unlabeled data, even from unknown classes as a complementary. Towards this end, we study the problem of semi-supervised universal graph classification, which not only identifies graph samples which do not belong to known classes, but also classifies the remaining samples into their respective classes. This problem is challenging due to a severe lack of labels and potential class shifts. In this paper, we propose a novel graph neural network framework named UGNN, which makes the best of unlabeled data from the subgraph perspective. To tackle class shifts, we estimate the certainty of unlabeled graphs using multiple subgraphs, which facilities the discovery of unlabeled data from unknown categories. Moreover, we construct semantic prototypes in the embedding space for both known and unknown categories and utilize posterior prototype assignments inferred from the Sinkhorn-Knopp algorithm to learn from abundant unlabeled graphs across different subgraph views. Extensive experiments on six datasets verify the effectiveness of UGNN in different settings.