Chuan Zhou

Ge Zhang, Jia Wu, Jian Yang et al. · allen-ai

Graph-structured data consisting of objects (i.e., nodes) and relationships among objects (i.e., edges) are ubiquitous. Graph-level learning is a matter of studying a collection of graphs instead of a single graph. Traditional graph-level learning methods used to be the mainstream. However, with the increasing scale and complexity of graphs, Graph-level Neural Networks (GLNNs, deep learning-based graph-level learning methods) have been attractive due to their superiority in modeling high-dimensional data. Thus, a survey on GLNNs is necessary. To frame this survey, we propose a systematic taxonomy covering GLNNs upon deep neural networks, graph neural networks, and graph pooling. The representative and state-of-the-art models in each category are focused on this survey. We also investigate the reproducibility, benchmarks, and new graph datasets of GLNNs. Finally, we conclude future directions to further push forward GLNNs. The repository of this survey is available at https://github.com/GeZhangMQ/Awesome-Graph-level-Neural-Networks.

Fanzhen Liu, Xiaoxiao Ma, Jia Wu et al.

Graph anomaly detection in this paper aims to distinguish abnormal nodes that behave differently from the benign ones accounting for the majority of graph-structured instances. Receiving increasing attention from both academia and industry, yet existing research on this task still suffers from two critical issues when learning informative anomalous behavior from graph data. For one thing, anomalies are usually hard to capture because of their subtle abnormal behavior and the shortage of background knowledge about them, which causes severe anomalous sample scarcity. Meanwhile, the overwhelming majority of objects in real-world graphs are normal, bringing the class imbalance problem as well. To bridge the gaps, this paper devises a novel Data Augmentation-based Graph Anomaly Detection (DAGAD) framework for attributed graphs, equipped with three specially designed modules: 1) an information fusion module employing graph neural network encoders to learn representations, 2) a graph data augmentation module that fertilizes the training set with generated samples, and 3) an imbalance-tailored learning module to discriminate the distributions of the minority (anomalous) and majority (normal) classes. A series of experiments on three datasets prove that DAGAD outperforms ten state-of-the-art baseline detectors concerning various mostly-used metrics, together with an extensive ablation study validating the strength of our proposed modules.

Bo Xiong, Shichao Zhu, Mojtaba Nayyeri et al.

Recent knowledge graph (KG) embeddings have been advanced by hyperbolic geometry due to its superior capability for representing hierarchies. The topological structures of real-world KGs, however, are rather heterogeneous, i.e., a KG is composed of multiple distinct hierarchies and non-hierarchical graph structures. Therefore, a homogeneous (either Euclidean or hyperbolic) geometry is not sufficient for fairly representing such heterogeneous structures. To capture the topological heterogeneity of KGs, we present an ultrahyperbolic KG embedding (UltraE) in an ultrahyperbolic (or pseudo-Riemannian) manifold that seamlessly interleaves hyperbolic and spherical manifolds. In particular, we model each relation as a pseudo-orthogonal transformation that preserves the pseudo-Riemannian bilinear form. The pseudo-orthogonal transformation is decomposed into various operators (i.e., circular rotations, reflections and hyperbolic rotations), allowing for simultaneously modeling heterogeneous structures as well as complex relational patterns. Experimental results on three standard KGs show that UltraE outperforms previous Euclidean- and hyperbolic-based approaches.

Zhenyu Yang, Ge Zhang, Jia Wu et al.

Graphs have a superior ability to represent relational data, like chemical compounds, proteins, and social networks. Hence, graph-level learning, which takes a set of graphs as input, has been applied to many tasks including comparison, regression, classification, and more. Traditional approaches to learning a set of graphs heavily rely on hand-crafted features, such as substructures. But while these methods benefit from good interpretability, they often suffer from computational bottlenecks as they cannot skirt the graph isomorphism problem. Conversely, deep learning has helped graph-level learning adapt to the growing scale of graphs by extracting features automatically and encoding graphs into low-dimensional representations. As a result, these deep graph learning methods have been responsible for many successes. Yet, there is no comprehensive survey that reviews graph-level learning starting with traditional learning and moving through to the deep learning approaches. This article fills this gap and frames the representative algorithms into a systematic taxonomy covering traditional learning, graph-level deep neural networks, graph-level graph neural networks, and graph pooling. To ensure a thoroughly comprehensive survey, the evolutions, interactions, and communications between methods from four different branches of development are also examined. This is followed by a brief review of the benchmark data sets, evaluation metrics, and common downstream applications. The survey concludes with a broad overview of 12 current and future directions in this booming field.

Xin Zheng, Miao Zhang, Chunyang Chen et al.

Graph neural architecture search (NAS) has gained popularity in automatically designing powerful graph neural networks (GNNs) with relieving human efforts. However, existing graph NAS methods mainly work under the homophily assumption and overlook another important graph property, i.e., heterophily, which exists widely in various real-world applications. To date, automated heterophilic graph learning with NAS is still a research blank to be filled in. Due to the complexity and variety of heterophilic graphs, the critical challenge of heterophilic graph NAS mainly lies in developing the heterophily-specific search space and strategy. Therefore, in this paper, we propose a novel automated graph neural network on heterophilic graphs, namely Auto-HeG, to automatically build heterophilic GNN models with expressive learning abilities. Specifically, Auto-HeG incorporates heterophily into all stages of automatic heterophilic graph learning, including search space design, supernet training, and architecture selection. Through the diverse message-passing scheme with joint micro-level and macro-level designs, we first build a comprehensive heterophilic GNN search space, enabling Auto-HeG to integrate complex and various heterophily of graphs. With a progressive supernet training strategy, we dynamically shrink the initial search space according to layer-wise variation of heterophily, resulting in a compact and efficient supernet. Taking a heterophily-aware distance criterion as the guidance, we conduct heterophilic architecture selection in the leave-one-out pattern, so that specialized and expressive heterophilic GNN architectures can be derived. Extensive experiments illustrate the superiority of Auto-HeG in developing excellent heterophilic GNNs to human-designed models and graph NAS models.

Yang Liu, Chuan Zhou, Shuai Zhang et al.

Crystal Structure Prediction (CSP) remains a fundamental challenge with significant implications for materials discovery and the advancement of various scientific disciplines. Recent advances have demonstrated that generative models, particularly diffusion models, are especially promising for CSP. However, traditional graph-based representations, where atomic bonds are modeled as pairwise graph edges, fail to capture the intricate high-order interactions essential for accurately describing crystal structures. To address this limitation, we propose leveraging hypergraphs to represent crystal structures, enabling more expressive modeling of multi-way atomic interactions. Hypergraphs naturally encode complex high-order relationships and respect key symmetries -- such as permutation and periodic translation invariance -- that are crucial for characterizing crystalline materials. Building on this representation, we propose the \textbf{E}quivariant \textbf{H}ypergraph \textbf{Diff}usion Model (\textbf{EH-Diff}), a generative framework designed to exploit the symmetry-preserving properties of hypergraphs. EH-Diff provides an efficient and accurate method for predicting crystal structures, with rigorous theoretical guarantees on invariance preservation. Empirically, we conduct extensive experiments on four benchmark datasets, and the results demonstrate that EH-Diff outperforms state-of-the-art CSP methods even with a single diffusion sample.

Shichao Zhu, Chuan Zhou, Anfeng Cheng et al.

Self-supervised learning (especially contrastive learning) methods on heterogeneous graphs can effectively get rid of the dependence on supervisory data. Meanwhile, most existing representation learning methods embed the heterogeneous graphs into a single geometric space, either Euclidean or hyperbolic. This kind of single geometric view is usually not enough to observe the complete picture of heterogeneous graphs due to their rich semantics and complex structures. Under these observations, this paper proposes a novel self-supervised learning method, termed as Geometry Contrastive Learning (GCL), to better represent the heterogeneous graphs when supervisory data is unavailable. GCL views a heterogeneous graph from Euclidean and hyperbolic perspective simultaneously, aiming to make a strong merger of the ability of modeling rich semantics and complex structures, which is expected to bring in more benefits for downstream tasks. GCL maximizes the mutual information between two geometric views by contrasting representations at both local-local and local-global semantic levels. Extensive experiments on four benchmarks data sets show that the proposed approach outperforms the strong baselines, including both unsupervised methods and supervised methods, on three tasks, including node classification, node clustering and similarity search.

Xin Zheng, Miao Zhang, Chunyang Chen et al.

Evaluating the performance of graph neural networks (GNNs) is an essential task for practical GNN model deployment and serving, as deployed GNNs face significant performance uncertainty when inferring on unseen and unlabeled test graphs, due to mismatched training-test graph distributions. In this paper, we study a new problem, GNN model evaluation, that aims to assess the performance of a specific GNN model trained on labeled and observed graphs, by precisely estimating its performance (e.g., node classification accuracy) on unseen graphs without labels. Concretely, we propose a two-stage GNN model evaluation framework, including (1) DiscGraph set construction and (2) GNNEvaluator training and inference. The DiscGraph set captures wide-range and diverse graph data distribution discrepancies through a discrepancy measurement function, which exploits the outputs of GNNs related to latent node embeddings and node class predictions. Under the effective training supervision from the DiscGraph set, GNNEvaluator learns to precisely estimate node classification accuracy of the to-be-evaluated GNN model and makes an accurate inference for evaluating GNN model performance. Extensive experiments on real-world unseen and unlabeled test graphs demonstrate the effectiveness of our proposed method for GNN model evaluation.

Gehang Zhang, Bowen Yu, Jiangxia Cao et al.

Graph contrastive learning (GCL) has recently achieved substantial advancements. Existing GCL approaches compare two different ``views'' of the same graph in order to learn node/graph representations. The underlying assumption of these studies is that the graph augmentation strategy is capable of generating several different graph views such that the graph views are structurally different but semantically similar to the original graphs, and thus the ground-truth labels of the original and augmented graph/nodes can be regarded identical in contrastive learning. However, we observe that this assumption does not always hold. For instance, the deletion of a super-node within a social network can exert a substantial influence on the partitioning of communities for other nodes. Similarly, any perturbation to nodes or edges in a molecular graph will change the labels of the graph. Therefore, we believe that augmenting the graph, accompanied by an adaptation of the labels used for the contrastive loss, will facilitate the encoder to learn a better representation. Based on this idea, we propose ID-MixGCL, which allows the simultaneous interpolation of input nodes and corresponding identity labels to obtain soft-confidence samples, with a controllable degree of change, leading to the capture of fine-grained representations from self-supervised training on unlabeled graphs. Experimental results demonstrate that ID-MixGCL improves performance on graph classification and node classification tasks, as demonstrated by significant improvements on the Cora, IMDB-B, IMDB-M, and PROTEINS datasets compared to state-of-the-art techniques, by 3-29% absolute points.

Ming Jin, Yizhen Zheng, Yuan-Fang Li et al.

Graph representation learning plays a vital role in processing graph-structured data. However, prior arts on graph representation learning heavily rely on labeling information. To overcome this problem, inspired by the recent success of graph contrastive learning and Siamese networks in visual representation learning, we propose a novel self-supervised approach in this paper to learn node representations by enhancing Siamese self-distillation with multi-scale contrastive learning. Specifically, we first generate two augmented views from the input graph based on local and global perspectives. Then, we employ two objectives called cross-view and cross-network contrastiveness to maximize the agreement between node representations across different views and networks. To demonstrate the effectiveness of our approach, we perform empirical experiments on five real-world datasets. Our method not only achieves new state-of-the-art results but also surpasses some semi-supervised counterparts by large margins. Code is made available at https://github.com/GRAND-Lab/MERIT

Yixin Liu, Ming Jin, Shirui Pan et al.

Deep learning on graphs has attracted significant interests recently. However, most of the works have focused on (semi-) supervised learning, resulting in shortcomings including heavy label reliance, poor generalization, and weak robustness. To address these issues, self-supervised learning (SSL), which extracts informative knowledge through well-designed pretext tasks without relying on manual labels, has become a promising and trending learning paradigm for graph data. Different from SSL on other domains like computer vision and natural language processing, SSL on graphs has an exclusive background, design ideas, and taxonomies. Under the umbrella of graph self-supervised learning, we present a timely and comprehensive review of the existing approaches which employ SSL techniques for graph data. We construct a unified framework that mathematically formalizes the paradigm of graph SSL. According to the objectives of pretext tasks, we divide these approaches into four categories: generation-based, auxiliary property-based, contrast-based, and hybrid approaches. We further describe the applications of graph SSL across various research fields and summarize the commonly used datasets, evaluation benchmark, performance comparison and open-source codes of graph SSL. Finally, we discuss the remaining challenges and potential future directions in this research field.

Xixun Lin, Yucheng Ning, Jingwen Zhang et al.

Driven by the rapid advancements of Large Language Models (LLMs), LLM-based agents have emerged as powerful intelligent systems capable of human-like cognition, reasoning, and interaction. These agents are increasingly being deployed across diverse real-world applications, including student education, scientific research, and financial analysis. However, despite their remarkable potential, LLM-based agents remain vulnerable to hallucination issues, which can result in erroneous task execution and undermine the reliability of the overall system design. Addressing this critical challenge requires a deep understanding and a systematic consolidation of recent advances on LLM-based agents. To this end, we present the first comprehensive survey of hallucinations in LLM-based agents. By carefully analyzing the complete workflow of agents, we propose a new taxonomy that identifies different types of agent hallucinations occurring at different stages. Furthermore, we conduct an in-depth examination of eighteen triggering causes underlying the emergence of agent hallucinations. Through a detailed review of a large number of existing studies, we summarize approaches for hallucination mitigation and detection, and highlight promising directions for future research. We hope this survey will inspire further efforts toward addressing hallucinations in LLM-based agents, ultimately contributing to the development of more robust and reliable agent systems.

Yang Liu, Chuan Zhou, Peng Zhang et al.

In recent years, there has been notable interest in investigating combinatorial optimization (CO) problems by neural-based framework. An emerging strategy to tackle these challenging problems involves the adoption of graph neural networks (GNNs) as an alternative to traditional algorithms, a subject that has attracted considerable attention. Despite the growing popularity of GNNs and traditional algorithm solvers in the realm of CO, there is limited research on their integrated use and the correlation between them within an end-to-end framework. The primary focus of our work is to formulate a more efficient and precise framework for CO by employing decision-focused learning on graphs. Additionally, we introduce a decision-focused framework that utilizes GNNs to address CO problems with auxiliary support. To realize an end-to-end approach, we have designed two cascaded modules: (a) an unsupervised trained graph predictive model, and (b) a solver for quadratic binary unconstrained optimization. Empirical evaluations are conducted on various classical tasks, including maximum cut, maximum independent set, and minimum vertex cover. The experimental results on classical CO problems (i.e. MaxCut, MIS, and MVC) demonstrate the superiority of our method over both the standalone GNN approach and classical methods.

Yang Liu, Peng Zhang, Yang Gao et al.

In recent years, graph neural networks (GNNs) have become increasingly popular for solving NP-hard combinatorial optimization (CO) problems, such as maximum cut and maximum independent set. The core idea behind these methods is to represent a CO problem as a graph and then use GNNs to learn the node/graph embedding with combinatorial information. Although these methods have achieved promising results, given a specific CO problem, the design of GNN architectures still requires heavy manual work with domain knowledge. Existing automated GNNs are mostly focused on traditional graph learning problems, which is inapplicable to solving NP-hard CO problems. To this end, we present a new class of \textbf{AUTO}mated \textbf{G}NNs for solving \textbf{NP}-hard problems, namely \textbf{AutoGNP}. We represent CO problems by GNNs and focus on two specific problems, i.e., mixed integer linear programming and quadratic unconstrained binary optimization. The idea of AutoGNP is to use graph neural architecture search algorithms to automatically find the best GNNs for a given NP-hard combinatorial optimization problem. Compared with existing graph neural architecture search algorithms, AutoGNP utilizes two-hop operators in the architecture search space. Moreover, AutoGNP utilizes simulated annealing and a strict early stopping policy to avoid local optimal solutions. Empirical results on benchmark combinatorial problems demonstrate the superiority of our proposed model.

He Zhang, Xingliang Yuan, Chuan Zhou et al.

Graph neural networks (GNNs) offer promising learning methods for graph-related tasks. However, GNNs are at risk of adversarial attacks. Two primary limitations of the current evasion attack methods are highlighted: (1) The current GradArgmax ignores the "long-term" benefit of the perturbation. It is faced with zero-gradient and invalid benefit estimates in certain situations. (2) In the reinforcement learning-based attack methods, the learned attack strategies might not be transferable when the attack budget changes. To this end, we first formulate the perturbation space and propose an evaluation framework and the projective ranking method. We aim to learn a powerful attack strategy then adapt it as little as possible to generate adversarial samples under dynamic budget settings. In our method, based on mutual information, we rank and assess the attack benefits of each perturbation for an effective attack strategy. By projecting the strategy, our method dramatically minimizes the cost of learning a new attack strategy when the attack budget changes. In the comparative assessment with GradArgmax and RL-S2V, the results show our method owns high attack performance and effective transferability. The visualization of our method also reveals various attack patterns in the generation of adversarial samples.

Bo Xiong, Shichao Zhu, Nico Potyka et al.

Graph convolutional networks (GCNs) are powerful frameworks for learning embeddings of graph-structured data. GCNs are traditionally studied through the lens of Euclidean geometry. Recent works find that non-Euclidean Riemannian manifolds provide specific inductive biases for embedding hierarchical or spherical data. However, they cannot align well with data of mixed graph topologies. We consider a larger class of pseudo-Riemannian manifolds that generalize hyperboloid and sphere. We develop new geodesic tools that allow for extending neural network operations into geodesically disconnected pseudo-Riemannian manifolds. As a consequence, we derive a pseudo-Riemannian GCN that models data in pseudo-Riemannian manifolds of constant nonzero curvature in the context of graph neural networks. Our method provides a geometric inductive bias that is sufficiently flexible to model mixed heterogeneous topologies like hierarchical graphs with cycles. We demonstrate the representational capabilities of this method by applying it to the tasks of graph reconstruction, node classification and link prediction on a series of standard graphs with mixed topologies. Empirical results demonstrate that our method outperforms Riemannian counterparts when embedding graphs of complex topologies.

Yixin Liu, Zhao Li, Shirui Pan et al.

Anomaly detection on attributed networks attracts considerable research interests due to wide applications of attributed networks in modeling a wide range of complex systems. Recently, the deep learning-based anomaly detection methods have shown promising results over shallow approaches, especially on networks with high-dimensional attributes and complex structures. However, existing approaches, which employ graph autoencoder as their backbone, do not fully exploit the rich information of the network, resulting in suboptimal performance. Furthermore, these methods do not directly target anomaly detection in their learning objective and fail to scale to large networks due to the full graph training mechanism. To overcome these limitations, in this paper, we present a novel contrastive self-supervised learning framework for anomaly detection on attributed networks. Our framework fully exploits the local information from network data by sampling a novel type of contrastive instance pair, which can capture the relationship between each node and its neighboring substructure in an unsupervised way. Meanwhile, a well-designed graph neural network-based contrastive learning model is proposed to learn informative embedding from high-dimensional attributes and local structure and measure the agreement of each instance pairs with its outputted scores. The multi-round predicted scores by the contrastive learning model are further used to evaluate the abnormality of each node with statistical estimation. In this way, the learning model is trained by a specific anomaly detection-aware target. Furthermore, since the input of the graph neural network module is batches of instance pairs instead of the full network, our framework can adapt to large networks flexibly. Experimental results show that our proposed framework outperforms the state-of-the-art baseline methods on all seven benchmark datasets.

Xixun Lin, Jia Wu, Chuan Zhou et al.

User cold-start recommendation is a long-standing challenge for recommender systems due to the fact that only a few interactions of cold-start users can be exploited. Recent studies seek to address this challenge from the perspective of meta learning, and most of them follow a manner of parameter initialization, where the model parameters can be learned by a few steps of gradient updates. While these gradient-based meta-learning models achieve promising performances to some extent, a fundamental problem of them is how to adapt the global knowledge learned from previous tasks for the recommendations of cold-start users more effectively. In this paper, we develop a novel meta-learning recommender called task-adaptive neural process (TaNP). TaNP is a new member of the neural process family, where making recommendations for each user is associated with a corresponding stochastic process. TaNP directly maps the observed interactions of each user to a predictive distribution, sidestepping some training issues in gradient-based meta-learning models. More importantly, to balance the trade-off between model capacity and adaptation reliability, we introduce a novel task-adaptive mechanism. It enables our model to learn the relevance of different tasks and customize the global knowledge to the task-related decoder parameters for estimating user preferences. We validate TaNP on multiple benchmark datasets in different experimental settings. Empirical results demonstrate that TaNP yields consistent improvements over several state-of-the-art meta-learning recommenders.

Shichao Zhu, Shirui Pan, Chuan Zhou et al.

While numerous approaches have been developed to embed graphs into either Euclidean or hyperbolic spaces, they do not fully utilize the information available in graphs, or lack the flexibility to model intrinsic complex graph geometry. To utilize the strength of both Euclidean and hyperbolic geometries, we develop a novel Geometry Interaction Learning (GIL) method for graphs, a well-suited and efficient alternative for learning abundant geometric properties in graph. GIL captures a more informative internal structural features with low dimensions while maintaining conformal invariance of each space. Furthermore, our method endows each node the freedom to determine the importance of each geometry space via a flexible dual feature interaction learning and probability assembling mechanism. Promising experimental results are presented for five benchmark datasets on node classification and link prediction tasks.

Yang Gao, Hong Yang, Peng Zhang et al.

Graph Neural Networks (GNNs) have been popularly used for analyzing non-Euclidean data such as social network data and biological data. Despite their success, the design of graph neural networks requires a lot of manual work and domain knowledge. In this paper, we propose a Graph Neural Architecture Search method (GraphNAS for short) that enables automatic search of the best graph neural architecture based on reinforcement learning. Specifically, GraphNAS first uses a recurrent network to generate variable-length strings that describe the architectures of graph neural networks, and then trains the recurrent network with reinforcement learning to maximize the expected accuracy of the generated architectures on a validation data set. Extensive experimental results on node classification tasks in both transductive and inductive learning settings demonstrate that GraphNAS can achieve consistently better performance on the Cora, Citeseer, Pubmed citation network, and protein-protein interaction network. On node classification tasks, GraphNAS can design a novel network architecture that rivals the best human-invented architecture in terms of test set accuracy.