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Chuan Shi

Chuan Shi contributes to research discovery and scholarly infrastructure.

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Published work

19 published item(s)

preprint2026arXiv

Data-centric Prompt Tuning for Dynamic Graphs

Dynamic graphs have attracted increasing attention due to their ability to model complex and evolving relationships in real-world scenarios. Traditional approaches typically pre-train models using dynamic link prediction and directly apply the resulting node temporal embeddings to specific downstream tasks. However, the significant differences among downstream tasks often lead to performance degradation, especially under few-shot settings. Prompt tuning has emerged as an effective solution to this problem. Existing prompting methods are often strongly coupled with specific model architectures or pretraining tasks, which makes it difficult to adapt to recent or future model designs. Moreover, their exclusive focus on modifying node or temporal features while neglecting spatial structural information leads to limited expressiveness and degraded performance. To address these limitations, we propose DDGPrompt, a data-centric prompting framework designed to effectively refine pre-trained node embeddings at the input data level, enabling better adaptability to diverse downstream tasks. We first define a unified node expression feature matrix that aggregates all relevant temporal and structural information of each node, ensuring compatibility with a wide range of dynamic graph models. Then, we introduce three prompt matrices (temporal bias, edge weight, and feature mask) to adjust the feature matrix completely, achieving task-specific adaptation of node embeddings. We evaluate DDGPrompt under a strict few-shot setting on four public dynamic graph datasets. Experimental results demonstrate that our method significantly outperforms traditional methods and prompting approaches in scenarios with limited labels and cold-start conditions.

preprint2026arXiv

Position: How can Graphs Help Large Language Models?

With the rapid advancement of large language models (LLMs), classic graph learning tasks have greatly benefited from LLMs, including improved encoding of textual features, more efficient construction of graphs from text, and enhanced reasoning over knowledge graphs. In this paper, we ask a complementary question: How can graphs help LLMs? We address this question from three perspectives: 1) graphs provide an up-to-date knowledge source that helps reduce LLM hallucinations, 2) graph-based prompting techniques-such as Chain-of-Thought (CoT), Tree-of-Thought (ToT), and Graph-of-Thought (GoT)-enhance LLM reasoning capabilities, and 3) integrating graphs into LLMs improves their understanding of structured data, expanding their applicability to domains such as e-commerce, code, and relational databases (RDBs). We further outlook some future directions including designing sparse LLM architectures based on graphs and brain-inspired memory systems.

preprint2026arXiv

Revisiting Graph-Tokenizing Large Language Models: A Systematic Evaluation of Graph Token Understanding

The remarkable success of large language models (LLMs) has motivated researchers to adapt them as universal predictors for various graph tasks. As a widely recognized paradigm, Graph-Tokenizing LLMs (GTokenLLMs) compress complex graph data into graph tokens and treat them as prefix tokens for querying LLMs, leading many to believe that LLMs can understand graphs more effectively and efficiently. In this paper, we challenge this belief: \textit{Do GTokenLLMs fully understand graph tokens in the natural-language embedding space?} Motivated by this question, we formalize a unified framework for GTokenLLMs and propose an evaluation pipeline, \textbf{GTEval}, to assess graph-token understanding via instruction transformations at the format and content levels. We conduct extensive experiments on 6 representative GTokenLLMs with GTEval. The primary findings are as follows: (1) Existing GTokenLLMs do not fully understand graph tokens. They exhibit over-sensitivity or over-insensitivity to instruction changes, and rely heavily on text for reasoning; (2) Although graph tokens preserve task-relevant graph information and receive attention across LLM layers, their utilization varies across models and instruction variants; (3) Additional instruction tuning can improve performance on the original and seen instructions, but it does not fully address the challenge of graph-token understanding, calling for further improvement.

preprint2022arXiv

An Effective Graph Learning based Approach for Temporal Link Prediction: The First Place of WSDM Cup 2022

Temporal link prediction, as one of the most crucial work in temporal graphs, has attracted lots of attention from the research area. The WSDM Cup 2022 seeks for solutions that predict the existence probabilities of edges within time spans over temporal graph. This paper introduces the solution of AntGraph, which wins the 1st place in the competition. We first analysis the theoretical upper-bound of the performance by removing temporal information, which implies that only structure and attribute information on the graph could achieve great performance. Based on this hypothesis, then we introduce several well-designed features. Finally, experiments conducted on the competition datasets show the superiority of our proposal, which achieved AUC score of 0.666 on dataset A and 0.902 on dataset B, the ablation studies also prove the efficiency of each feature. Code is publicly available at https://github.com/im0qianqian/WSDM2022TGP-AntGraph.

preprint2022arXiv

Be Confident! Towards Trustworthy Graph Neural Networks via Confidence Calibration

Despite Graph Neural Networks (GNNs) have achieved remarkable accuracy, whether the results are trustworthy is still unexplored. Previous studies suggest that many modern neural networks are over-confident on the predictions, however, surprisingly, we discover that GNNs are primarily in the opposite direction, i.e., GNNs are under-confident. Therefore, the confidence calibration for GNNs is highly desired. In this paper, we propose a novel trustworthy GNN model by designing a topology-aware post-hoc calibration function. Specifically, we first verify that the confidence distribution in a graph has homophily property, and this finding inspires us to design a calibration GNN model (CaGCN) to learn the calibration function. CaGCN is able to obtain a unique transformation from logits of GNNs to the calibrated confidence for each node, meanwhile, such transformation is able to preserve the order between classes, satisfying the accuracy-preserving property. Moreover, we apply the calibration GNN to self-training framework, showing that more trustworthy pseudo labels can be obtained with the calibrated confidence and further improve the performance. Extensive experiments demonstrate the effectiveness of our proposed model in terms of both calibration and accuracy.

preprint2022arXiv

Compact Graph Structure Learning via Mutual Information Compression

Graph Structure Learning (GSL) recently has attracted considerable attentions in its capacity of optimizing graph structure as well as learning suitable parameters of Graph Neural Networks (GNNs) simultaneously. Current GSL methods mainly learn an optimal graph structure (final view) from single or multiple information sources (basic views), however the theoretical guidance on what is the optimal graph structure is still unexplored. In essence, an optimal graph structure should only contain the information about tasks while compress redundant noise as much as possible, which is defined as "minimal sufficient structure", so as to maintain the accurancy and robustness. How to obtain such structure in a principled way? In this paper, we theoretically prove that if we optimize basic views and final view based on mutual information, and keep their performance on labels simultaneously, the final view will be a minimal sufficient structure. With this guidance, we propose a Compact GSL architecture by MI compression, named CoGSL. Specifically, two basic views are extracted from original graph as two inputs of the model, which are refinedly reestimated by a view estimator. Then, we propose an adaptive technique to fuse estimated views into the final view. Furthermore, we maintain the performance of estimated views and the final view and reduce the mutual information of every two views. To comprehensively evaluate the performance of CoGSL, we conduct extensive experiments on several datasets under clean and attacked conditions, which demonstrate the effectiveness and robustness of CoGSL.

preprint2022arXiv

Confidence May Cheat: Self-Training on Graph Neural Networks under Distribution Shift

Graph Convolutional Networks (GCNs) have recently attracted vast interest and achieved state-of-the-art performance on graphs, but its success could typically hinge on careful training with amounts of expensive and time-consuming labeled data. To alleviate labeled data scarcity, self-training methods have been widely adopted on graphs by labeling high-confidence unlabeled nodes and then adding them to the training step. In this line, we empirically make a thorough study for current self-training methods on graphs. Surprisingly, we find that high-confidence unlabeled nodes are not always useful, and even introduce the distribution shift issue between the original labeled dataset and the augmented dataset by self-training, severely hindering the capability of self-training on graphs. To this end, in this paper, we propose a novel Distribution Recovered Graph Self-Training framework (DR-GST), which could recover the distribution of the original labeled dataset. Specifically, we first prove the equality of loss function in self-training framework under the distribution shift case and the population distribution if each pseudo-labeled node is weighted by a proper coefficient. Considering the intractability of the coefficient, we then propose to replace the coefficient with the information gain after observing the same changing trend between them, where information gain is respectively estimated via both dropout variational inference and dropedge variational inference in DR-GST. However, such a weighted loss function will enlarge the impact of incorrect pseudo labels. As a result, we apply the loss correction method to improve the quality of pseudo labels. Both our theoretical analysis and extensive experiments on five benchmark datasets demonstrate the effectiveness of the proposed DR-GST, as well as each well-designed component in DR-GST.

preprint2022arXiv

Data-Free Adversarial Knowledge Distillation for Graph Neural Networks

Graph neural networks (GNNs) have been widely used in modeling graph structured data, owing to its impressive performance in a wide range of practical applications. Recently, knowledge distillation (KD) for GNNs has enabled remarkable progress in graph model compression and knowledge transfer. However, most of the existing KD methods require a large volume of real data, which are not readily available in practice, and may preclude their applicability in scenarios where the teacher model is trained on rare or hard to acquire datasets. To address this problem, we propose the first end-to-end framework for data-free adversarial knowledge distillation on graph structured data (DFAD-GNN). To be specific, our DFAD-GNN employs a generative adversarial network, which mainly consists of three components: a pre-trained teacher model and a student model are regarded as two discriminators, and a generator is utilized for deriving training graphs to distill knowledge from the teacher model into the student model. Extensive experiments on various benchmark models and six representative datasets demonstrate that our DFAD-GNN significantly surpasses state-of-the-art data-free baselines in the graph classification task.

preprint2022arXiv

Debiased Graph Neural Networks with Agnostic Label Selection Bias

Most existing Graph Neural Networks (GNNs) are proposed without considering the selection bias in data, i.e., the inconsistent distribution between the training set with test set. In reality, the test data is not even available during the training process, making selection bias agnostic. Training GNNs with biased selected nodes leads to significant parameter estimation bias and greatly impacts the generalization ability on test nodes. In this paper, we first present an experimental investigation, which clearly shows that the selection bias drastically hinders the generalization ability of GNNs, and theoretically prove that the selection bias will cause the biased estimation on GNN parameters. Then to remove the bias in GNN estimation, we propose a novel Debiased Graph Neural Networks (DGNN) with a differentiated decorrelation regularizer. The differentiated decorrelation regularizer estimates a sample weight for each labeled node such that the spurious correlation of learned embeddings could be eliminated. We analyze the regularizer in causal view and it motivates us to differentiate the weights of the variables based on their contribution on the confounding bias. Then, these sample weights are used for reweighting GNNs to eliminate the estimation bias, thus help to improve the stability of prediction on unknown test nodes. Comprehensive experiments are conducted on several challenging graph datasets with two kinds of label selection biases. The results well verify that our proposed model outperforms the state-of-the-art methods and DGNN is a flexible framework to enhance existing GNNs.

preprint2022arXiv

KGNN: Distributed Framework for Graph Neural Knowledge Representation

Knowledge representation learning has been commonly adopted to incorporate knowledge graph (KG) into various online services. Although existing knowledge representation learning methods have achieved considerable performance improvement, they ignore high-order structure and abundant attribute information, resulting unsatisfactory performance on semantics-rich KGs. Moreover, they fail to make prediction in an inductive manner and cannot scale to large industrial graphs. To address these issues, we develop a novel framework called KGNN to take full advantage of knowledge data for representation learning in the distributed learning system. KGNN is equipped with GNN based encoder and knowledge aware decoder, which aim to jointly explore high-order structure and attribute information together in a fine-grained fashion and preserve the relation patterns in KGs, respectively. Extensive experiments on three datasets for link prediction and triplet classification task demonstrate the effectiveness and scalability of KGNN framework.

preprint2022arXiv

Space4HGNN: A Novel, Modularized and Reproducible Platform to Evaluate Heterogeneous Graph Neural Network

Heterogeneous Graph Neural Network (HGNN) has been successfully employed in various tasks, but we cannot accurately know the importance of different design dimensions of HGNNs due to diverse architectures and applied scenarios. Besides, in the research community of HGNNs, implementing and evaluating various tasks still need much human effort. To mitigate these issues, we first propose a unified framework covering most HGNNs, consisting of three components: heterogeneous linear transformation, heterogeneous graph transformation, and heterogeneous message passing layer. Then we build a platform Space4HGNN by defining a design space for HGNNs based on the unified framework, which offers modularized components, reproducible implementations, and standardized evaluation for HGNNs. Finally, we conduct experiments to analyze the effect of different designs. With the insights found, we distill a condensed design space and verify its effectiveness.

preprint2021arXiv

Beyond Low-frequency Information in Graph Convolutional Networks

Graph neural networks (GNNs) have been proven to be effective in various network-related tasks. Most existing GNNs usually exploit the low-frequency signals of node features, which gives rise to one fundamental question: is the low-frequency information all we need in the real world applications? In this paper, we first present an experimental investigation assessing the roles of low-frequency and high-frequency signals, where the results clearly show that exploring low-frequency signal only is distant from learning an effective node representation in different scenarios. How can we adaptively learn more information beyond low-frequency information in GNNs? A well-informed answer can help GNNs enhance the adaptability. We tackle this challenge and propose a novel Frequency Adaptation Graph Convolutional Networks (FAGCN) with a self-gating mechanism, which can adaptively integrate different signals in the process of message passing. For a deeper understanding, we theoretically analyze the roles of low-frequency signals and high-frequency signals on learning node representations, which further explains why FAGCN can perform well on different types of networks. Extensive experiments on six real-world networks validate that FAGCN not only alleviates the over-smoothing problem, but also has advantages over the state-of-the-arts.

preprint2021arXiv

Extract the Knowledge of Graph Neural Networks and Go Beyond it: An Effective Knowledge Distillation Framework

Semi-supervised learning on graphs is an important problem in the machine learning area. In recent years, state-of-the-art classification methods based on graph neural networks (GNNs) have shown their superiority over traditional ones such as label propagation. However, the sophisticated architectures of these neural models will lead to a complex prediction mechanism, which could not make full use of valuable prior knowledge lying in the data, e.g., structurally correlated nodes tend to have the same class. In this paper, we propose a framework based on knowledge distillation to address the above issues. Our framework extracts the knowledge of an arbitrary learned GNN model (teacher model), and injects it into a well-designed student model. The student model is built with two simple prediction mechanisms, i.e., label propagation and feature transformation, which naturally preserves structure-based and feature-based prior knowledge, respectively. In specific, we design the student model as a trainable combination of parameterized label propagation and feature transformation modules. As a result, the learned student can benefit from both prior knowledge and the knowledge in GNN teachers for more effective predictions. Moreover, the learned student model has a more interpretable prediction process than GNNs. We conduct experiments on five public benchmark datasets and employ seven GNN models including GCN, GAT, APPNP, SAGE, SGC, GCNII and GLP as the teacher models. Experimental results show that the learned student model can consistently outperform its corresponding teacher model by 1.4% - 4.7% on average. Code and data are available at https://github.com/BUPT-GAMMA/CPF

preprint2021arXiv

Heterogeneous Graph Attention Network

Graph neural network, as a powerful graph representation technique based on deep learning, has shown superior performance and attracted considerable research interest. However, it has not been fully considered in graph neural network for heterogeneous graph which contains different types of nodes and links. The heterogeneity and rich semantic information bring great challenges for designing a graph neural network for heterogeneous graph. Recently, one of the most exciting advancements in deep learning is the attention mechanism, whose great potential has been well demonstrated in various areas. In this paper, we first propose a novel heterogeneous graph neural network based on the hierarchical attention, including node-level and semantic-level attentions. Specifically, the node-level attention aims to learn the importance between a node and its metapath based neighbors, while the semantic-level attention is able to learn the importance of different meta-paths. With the learned importance from both node-level and semantic-level attention, the importance of node and meta-path can be fully considered. Then the proposed model can generate node embedding by aggregating features from meta-path based neighbors in a hierarchical manner. Extensive experimental results on three real-world heterogeneous graphs not only show the superior performance of our proposed model over the state-of-the-arts, but also demonstrate its potentially good interpretability for graph analysis.

preprint2021arXiv

Interpreting and Unifying Graph Neural Networks with An Optimization Framework

Graph Neural Networks (GNNs) have received considerable attention on graph-structured data learning for a wide variety of tasks. The well-designed propagation mechanism which has been demonstrated effective is the most fundamental part of GNNs. Although most of GNNs basically follow a message passing manner, litter effort has been made to discover and analyze their essential relations. In this paper, we establish a surprising connection between different propagation mechanisms with a unified optimization problem, showing that despite the proliferation of various GNNs, in fact, their proposed propagation mechanisms are the optimal solution optimizing a feature fitting function over a wide class of graph kernels with a graph regularization term. Our proposed unified optimization framework, summarizing the commonalities between several of the most representative GNNs, not only provides a macroscopic view on surveying the relations between different GNNs, but also further opens up new opportunities for flexibly designing new GNNs. With the proposed framework, we discover that existing works usually utilize naive graph convolutional kernels for feature fitting function, and we further develop two novel objective functions considering adjustable graph kernels showing low-pass or high-pass filtering capabilities respectively. Moreover, we provide the convergence proofs and expressive power comparisons for the proposed models. Extensive experiments on benchmark datasets clearly show that the proposed GNNs not only outperform the state-of-the-art methods but also have good ability to alleviate over-smoothing, and further verify the feasibility for designing GNNs with our unified optimization framework.

preprint2020arXiv

AM-GCN: Adaptive Multi-channel Graph Convolutional Networks

Graph Convolutional Networks (GCNs) have gained great popularity in tackling various analytics tasks on graph and network data. However, some recent studies raise concerns about whether GCNs can optimally integrate node features and topological structures in a complex graph with rich information. In this paper, we first present an experimental investigation. Surprisingly, our experimental results clearly show that the capability of the state-of-the-art GCNs in fusing node features and topological structures is distant from optimal or even satisfactory. The weakness may severely hinder the capability of GCNs in some classification tasks, since GCNs may not be able to adaptively learn some deep correlation information between topological structures and node features. Can we remedy the weakness and design a new type of GCNs that can retain the advantages of the state-of-the-art GCNs and, at the same time, enhance the capability of fusing topological structures and node features substantially? We tackle the challenge and propose an adaptive multi-channel graph convolutional networks for semi-supervised classification (AM-GCN). The central idea is that we extract the specific and common embeddings from node features, topological structures, and their combinations simultaneously, and use the attention mechanism to learn adaptive importance weights of the embeddings. Our extensive experiments on benchmark data sets clearly show that AM-GCN extracts the most correlated information from both node features and topological structures substantially, and improves the classification accuracy with a clear margin.

preprint2020arXiv

Decorrelated Clustering with Data Selection Bias

Most of existing clustering algorithms are proposed without considering the selection bias in data. In many real applications, however, one cannot guarantee the data is unbiased. Selection bias might bring the unexpected correlation between features and ignoring those unexpected correlations will hurt the performance of clustering algorithms. Therefore, how to remove those unexpected correlations induced by selection bias is extremely important yet largely unexplored for clustering. In this paper, we propose a novel Decorrelation regularized K-Means algorithm (DCKM) for clustering with data selection bias. Specifically, the decorrelation regularizer aims to learn the global sample weights which are capable of balancing the sample distribution, so as to remove unexpected correlations among features. Meanwhile, the learned weights are combined with k-means, which makes the reweighted k-means cluster on the inherent data distribution without unexpected correlation influence. Moreover, we derive the updating rules to effectively infer the parameters in DCKM. Extensive experiments results on real world datasets well demonstrate that our DCKM algorithm achieves significant performance gains, indicating the necessity of removing unexpected feature correlations induced by selection bias when clustering.

preprint2020arXiv

Heterogeneous Graph Neural Network for Recommendation

The prosperous development of e-commerce has spawned diverse recommendation systems. As a matter of fact, there exist rich and complex interactions among various types of nodes in real-world recommendation systems, which can be constructed as heterogeneous graphs. How learn representative node embedding is the basis and core of the personalized recommendation system. Meta-path is a widely used structure to capture the semantics beneath such interactions and show potential ability in improving node embedding. In this paper, we propose Heterogeneous Graph neural network for Recommendation (HGRec) which injects high-order semantic into node embedding via aggregating multi-hops meta-path based neighbors and fuses rich semantics via multiple meta-paths based on attention mechanism to get comprehensive node embedding. Experimental results demonstrate the importance of rich high-order semantics and also show the potentially good interpretability of HGRec.

preprint2020arXiv

Structural Deep Clustering Network

Clustering is a fundamental task in data analysis. Recently, deep clustering, which derives inspiration primarily from deep learning approaches, achieves state-of-the-art performance and has attracted considerable attention. Current deep clustering methods usually boost the clustering results by means of the powerful representation ability of deep learning, e.g., autoencoder, suggesting that learning an effective representation for clustering is a crucial requirement. The strength of deep clustering methods is to extract the useful representations from the data itself, rather than the structure of data, which receives scarce attention in representation learning. Motivated by the great success of Graph Convolutional Network (GCN) in encoding the graph structure, we propose a Structural Deep Clustering Network (SDCN) to integrate the structural information into deep clustering. Specifically, we design a delivery operator to transfer the representations learned by autoencoder to the corresponding GCN layer, and a dual self-supervised mechanism to unify these two different deep neural architectures and guide the update of the whole model. In this way, the multiple structures of data, from low-order to high-order, are naturally combined with the multiple representations learned by autoencoder. Furthermore, we theoretically analyze the delivery operator, i.e., with the delivery operator, GCN improves the autoencoder-specific representation as a high-order graph regularization constraint and autoencoder helps alleviate the over-smoothing problem in GCN. Through comprehensive experiments, we demonstrate that our propose model can consistently perform better over the state-of-the-art techniques.