Rong-Hua Li

Longlong Lin, Rong-Hua Li, Tao Jia

Conductance-based graph clustering has been recognized as a fundamental operator in numerous graph analysis applications. Despite the significant success of conductance-based graph clustering, existing algorithms are either hard to obtain satisfactory clustering qualities, or have high time and space complexity to achieve provable clustering qualities. To overcome these limitations, we devise a powerful \textit{peeling}-based graph clustering framework \textit{PCon}. We show that many existing solutions can be reduced to our framework. Namely, they first define a score function for each vertex, then iteratively remove the vertex with the smallest score. Finally, they output the result with the smallest conductance during the peeling process. Based on our framework, we propose two novel algorithms \textit{PCon\_core} and \emph{PCon\_de} with linear time and space complexity, which can efficiently and effectively identify clusters from massive graphs with more than a few billion edges. Surprisingly, we prove that \emph{PCon\_de} can identify clusters with near-constant approximation ratio, resulting in an important theoretical improvement over the well-known quadratic Cheeger bound. Empirical results on real-life and synthetic datasets show that our algorithms can achieve 5$\sim$42 times speedup with a high clustering accuracy, while using 1.4$\sim$7.8 times less memory than the baseline algorithms.

Xunkai Li, Yinlin Zhu, Boyang Pang et al.

Federated graph learning (FGL) is a promising distributed training paradigm for graph neural networks across multiple local systems without direct data sharing. This approach inherently involves large-scale distributed graph processing, which closely aligns with the challenges and research focuses of graph-based data systems. Despite the proliferation of FGL, the diverse motivations from real-world applications, spanning various research backgrounds and settings, pose a significant challenge to fair evaluation. To fill this gap, we propose OpenFGL, a unified benchmark designed for the primary FGL scenarios: Graph-FL and Subgraph-FL. Specifically, OpenFGL includes 42 graph datasets from 18 application domains, 8 federated data simulation strategies that emphasize different graph properties, and 5 graph-based downstream tasks. Additionally, it offers 18 recently proposed SOTA FGL algorithms through a user-friendly API, enabling a thorough comparison and comprehensive evaluation of their effectiveness, robustness, and efficiency. Our empirical results demonstrate the capabilities of FGL while also highlighting its potential limitations, providing valuable insights for future research in this growing field, particularly in fostering greater interdisciplinary collaboration between FGL and data systems.

Zening Li, Rong-Hua Li, Meihao Liao et al.

Graph embedding has become a powerful tool for learning latent representations of nodes in a graph. Despite its superior performance in various graph-based machine learning tasks, serious privacy concerns arise when the graph data contains personal or sensitive information. To address this issue, we investigate and develop graph embedding algorithms that satisfy local differential privacy (LDP). We introduce a novel privacy-preserving graph embedding framework, named PrivGE, to protect node data privacy. Specifically, we propose an LDP mechanism to obfuscate node data and utilize personalized PageRank as the proximity measure to learn node representations. Furthermore, we provide a theoretical analysis of the privacy guarantees and utility offered by the PrivGE framework. Extensive experiments on several real-world graph datasets demonstrate that PrivGE achieves an optimal balance between privacy and utility, and significantly outperforms existing methods in node classification and link prediction tasks.

Xunkai Li, Zhengyu Wu, Jiayi Wu et al.

With the increasing prevalence of cross-domain Text-Attributed Graph (TAG) Data (e.g., citation networks, recommendation systems, social networks, and ai4science), the integration of Graph Neural Networks (GNNs) and Large Language Models (LLMs) into a unified Model architecture (e.g., LLM as enhancer, LLM as collaborators, LLM as predictor) has emerged as a promising technological paradigm. The core of this new graph learning paradigm lies in the synergistic combination of GNNs' ability to capture complex structural relationships and LLMs' proficiency in understanding informative contexts from the rich textual descriptions of graphs. Therefore, we can leverage graph description texts with rich semantic context to fundamentally enhance Data quality, thereby improving the representational capacity of model-centric approaches in line with data-centric machine learning principles. By leveraging the strengths of these distinct neural network architectures, this integrated approach addresses a wide range of TAG-based Task (e.g., graph learning, graph reasoning, and graph question answering), particularly in complex industrial scenarios (e.g., supervised, few-shot, and zero-shot settings). In other words, we can treat text as a medium to enable cross-domain generalization of graph learning Model, allowing a single graph model to effectively handle the diversity of downstream graph-based Task across different data domains. This work serves as a foundational reference for researchers and practitioners looking to advance graph learning methodologies in the rapidly evolving landscape of LLM. We consistently maintain the related open-source materials at \url{https://github.com/xkLi-Allen/Awesome-GNN-in-LLMs-Papers}.

Xunkai Li, Zhengyu Wu, Wentao Zhang et al.

Federated Graph Learning (FGL) is a distributed machine learning paradigm that enables collaborative training on large-scale subgraphs across multiple local systems. Existing FGL studies fall into two categories: (i) FGL Optimization, which improves multi-client training in existing machine learning models; (ii) FGL Model, which enhances performance with complex local models and multi-client interactions. However, most FGL optimization strategies are designed specifically for the computer vision domain and ignore graph structure, presenting dissatisfied performance and slow convergence. Meanwhile, complex local model architectures in FGL Models studies lack scalability for handling large-scale subgraphs and have deployment limitations. To address these issues, we propose Federated Graph Topology-aware Aggregation (FedGTA), a personalized optimization strategy that optimizes through topology-aware local smoothing confidence and mixed neighbor features. During experiments, we deploy FedGTA in 12 multi-scale real-world datasets with the Louvain and Metis split. This allows us to evaluate the performance and robustness of FedGTA across a range of scenarios. Extensive experiments demonstrate that FedGTA achieves state-of-the-art performance while exhibiting high scalability and efficiency. The experiment includes ogbn-papers100M, the most representative large-scale graph database so that we can verify the applicability of our method to large-scale graph learning. To the best of our knowledge, our study is the first to bridge large-scale graph learning with FGL using this optimization strategy, contributing to the development of efficient and scalable FGL methods.

Xunkai Li, Yulin Zhao, Zhengyu Wu et al.

With the rapid advancement of AI applications, the growing needs for data privacy and model robustness have highlighted the importance of machine unlearning, especially in thriving graph-based scenarios. However, most existing graph unlearning strategies primarily rely on well-designed architectures or manual process, rendering them less user-friendly and posing challenges in terms of deployment efficiency. Furthermore, striking a balance between unlearning performance and framework generalization is also a pivotal concern. To address the above issues, we propose \underline{\textbf{M}}utual \underline{\textbf{E}}volution \underline{\textbf{G}}raph \underline{\textbf{U}}nlearning (MEGU), a new mutual evolution paradigm that simultaneously evolves the predictive and unlearning capacities of graph unlearning. By incorporating aforementioned two components, MEGU ensures complementary optimization in a unified training framework that aligns with the prediction and unlearning requirements. Extensive experiments on 9 graph benchmark datasets demonstrate the superior performance of MEGU in addressing unlearning requirements at the feature, node, and edge levels. Specifically, MEGU achieves average performance improvements of 2.7\%, 2.5\%, and 3.2\% across these three levels of unlearning tasks when compared to state-of-the-art baselines. Furthermore, MEGU exhibits satisfactory training efficiency, reducing time and space overhead by an average of 159.8x and 9.6x, respectively, in comparison to retraining GNN from scratch.

Xunkai Li, Zhengyu Wu, Wentao Zhang et al.

Recently, Federated Graph Learning (FGL) has attracted significant attention as a distributed framework based on graph neural networks, primarily due to its capability to break data silos. Existing FGL studies employ community split on the homophilous global graph by default to simulate federated semi-supervised node classification settings. Such a strategy assumes the consistency of topology between the multi-client subgraphs and the global graph, where connected nodes are highly likely to possess similar feature distributions and the same label. However, in real-world implementations, the varying perspectives of local data engineering result in various subgraph topologies, posing unique heterogeneity challenges in FGL. Unlike the well-known label Non-independent identical distribution (Non-iid) problems in federated learning, FGL heterogeneity essentially reveals the topological divergence among multiple clients, namely homophily or heterophily. To simulate and handle this unique challenge, we introduce the concept of structure Non-iid split and then present a new paradigm called \underline{Ada}ptive \underline{F}ederated \underline{G}raph \underline{L}earning (AdaFGL), a decoupled two-step personalized approach. To begin with, AdaFGL employs standard multi-client federated collaborative training to acquire the federated knowledge extractor by aggregating uploaded models in the final round at the server. Then, each client conducts personalized training based on the local subgraph and the federated knowledge extractor. Extensive experiments on the 12 graph benchmark datasets validate the superior performance of AdaFGL over state-of-the-art baselines. Specifically, in terms of test accuracy, our proposed AdaFGL outperforms baselines by significant margins of 3.24\% and 5.57\% on community split and structure Non-iid split, respectively.

Henan Sun, Xunkai Li, Zhengyu Wu et al.

Recently, graph neural networks (GNNs) have shown prominent performance in semi-supervised node classification by leveraging knowledge from the graph database. However, most existing GNNs follow the homophily assumption, where connected nodes are more likely to exhibit similar feature distributions and the same labels, and such an assumption has proven to be vulnerable in a growing number of practical applications. As a supplement, heterophily reflects dissimilarity in connected nodes, which has gained significant attention in graph learning. To this end, data engineers aim to develop a powerful GNN model that can ensure performance under both homophily and heterophily. Despite numerous attempts, most existing GNNs struggle to achieve optimal node representations due to the constraints of undirected graphs. The neglect of directed edges results in sub-optimal graph representations, thereby hindering the capacity of GNNs. To address this issue, we introduce AMUD, which quantifies the relationship between node profiles and topology from a statistical perspective, offering valuable insights for Adaptively Modeling the natural directed graphs as the Undirected or Directed graph to maximize the benefits from subsequent graph learning. Furthermore, we propose Adaptive Directed Pattern Aggregation (ADPA) as a new directed graph learning paradigm for AMUD. Empirical studies have demonstrated that AMUD guides efficient graph learning. Meanwhile, extensive experiments on 16 benchmark datasets substantiate the impressive performance of ADPA, outperforming baselines by significant margins of 3.96.

Xunkai Li, Jingyuan Ma, Zhengyu Wu et al.

Scalable graph neural networks (GNNs) have emerged as a promising technique, which exhibits superior predictive performance and high running efficiency across numerous large-scale graph-based web applications. However, (i) Most scalable GNNs tend to treat all nodes in graphs with the same propagation rules, neglecting their topological uniqueness; (ii) Existing node-wise propagation optimization strategies are insufficient on web-scale graphs with intricate topology, where a full portrayal of nodes' local properties is required. Intuitively, different nodes in web-scale graphs possess distinct topological roles, and therefore propagating them indiscriminately or neglect local contexts may compromise the quality of node representations. This intricate topology in web-scale graphs cannot be matched by small-scale scenarios. To address the above issues, we propose \textbf{A}daptive \textbf{T}opology-aware \textbf{P}ropagation (ATP), which reduces potential high-bias propagation and extracts structural patterns of each node in a scalable manner to improve running efficiency and predictive performance. Remarkably, ATP is crafted to be a plug-and-play node-wise propagation optimization strategy, allowing for offline execution independent of the graph learning process in a new perspective. Therefore, this approach can be seamlessly integrated into most scalable GNNs while remain orthogonal to existing node-wise propagation optimization strategies. Extensive experiments on 12 datasets, including the most representative large-scale ogbn-papers100M, have demonstrated the effectiveness of ATP. Specifically, ATP has proven to be efficient in improving the performance of prevalent scalable GNNs for semi-supervised node classification while addressing redundant computational costs.

Yinlin Zhu, Xunkai Li, Zhengyu Wu et al.

Subgraph federated learning (subgraph-FL) is a new distributed paradigm that facilitates the collaborative training of graph neural networks (GNNs) by multi-client subgraphs. Unfortunately, a significant challenge of subgraph-FL arises from subgraph heterogeneity, which stems from node and topology variation, causing the impaired performance of the global GNN. Despite various studies, they have not yet thoroughly investigated the impact mechanism of subgraph heterogeneity. To this end, we decouple node and topology variation, revealing that they correspond to differences in label distribution and structure homophily. Remarkably, these variations lead to significant differences in the class-wise knowledge reliability of multiple local GNNs, misguiding the model aggregation with varying degrees. Building on this insight, we propose topology-aware data-free knowledge distillation technology (FedTAD), enhancing reliable knowledge transfer from the local model to the global model. Extensive experiments on six public datasets consistently demonstrate the superiority of FedTAD over state-of-the-art baselines.

Enjun Du, Xunkai Li, Tian Jin et al.

The era of foundation models has revolutionized AI research, yet Graph Foundation Models (GFMs) remain constrained by the scarcity of large-scale graph corpora. Traditional graph data synthesis techniques primarily focus on simplistic structural operations, lacking the capacity to generate semantically rich nodes with meaningful textual attributes: a critical limitation for real-world applications. While large language models (LLMs) demonstrate exceptional text generation capabilities, their direct application to graph synthesis is impeded by context window limitations, hallucination phenomena, and structural consistency challenges. To address these issues, we introduce GraphMaster, the first multi-agent framework specifically designed for graph data synthesis in data-limited environments. GraphMaster orchestrates four specialized LLM agents (Manager, Perception, Enhancement, and Evaluation) that collaboratively optimize the synthesis process through iterative refinement, ensuring both semantic coherence and structural integrity. To rigorously evaluate our approach, we create new data-limited "Sub" variants of six standard graph benchmarks, specifically designed to test synthesis capabilities under realistic constraints. Additionally, we develop a novel interpretability assessment framework that combines human evaluation with a principled Grassmannian manifold-based analysis, providing both qualitative and quantitative measures of semantic coherence. Experimental results demonstrate that GraphMaster significantly outperforms traditional synthesis methods across multiple datasets, establishing a strong foundation for advancing GFMs in data-scarce environments.

Xunkai Li, Meihao Liao, Zhengyu Wu et al.

Most existing graph neural networks (GNNs) are limited to undirected graphs, whose restricted scope of the captured relational information hinders their expressive capabilities and deployments in real-world scenarios. Compared with undirected graphs, directed graphs (digraphs) fit the demand for modeling more complex topological systems by capturing more intricate relationships between nodes, such as formulating transportation and financial networks. While some directed GNNs have been introduced, their inspiration mainly comes from deep learning architectures, which lead to redundant complexity and computation, making them inapplicable to large-scale databases. To address these issues, we propose LightDiC, a scalable variant of the digraph convolution based on the magnetic Laplacian. Since topology-related computations are conducted solely during offline pre-processing, LightDiC achieves exceptional scalability, enabling downstream predictions to be trained separately without incurring recursive computational costs. Theoretical analysis shows that LightDiC utilizes directed information to achieve message passing based on the complex field, which corresponds to the proximal gradient descent process of the Dirichlet energy optimization function from the perspective of digraph signal denoising, ensuring its expressiveness. Experimental results demonstrate that LightDiC performs comparably well or even outperforms other SOTA methods in various downstream tasks, with fewer learnable parameters and higher training efficiency. Notably, LightDiC is the first DiGNN to provide satisfactory results in the most representative large-scale database (ogbn-papers100M).

Bowen Fan, Yuming Ai, Xunkai Li et al.

Graph Machine Learning is essential for understanding and analyzing relational data. However, privacy-sensitive applications demand the ability to efficiently remove sensitive information from trained graph neural networks (GNNs), avoiding the unnecessary time and space overhead caused by retraining models from scratch. To address this issue, Graph Unlearning (GU) has emerged as a critical solution, with the potential to support dynamic graph updates in data management systems and enable scalable unlearning in distributed data systems while ensuring privacy compliance. Unlike machine unlearning in computer vision or other fields, GU faces unique difficulties due to the non-Euclidean nature of graph data and the recursive message-passing mechanism of GNNs. Additionally, the diversity of downstream tasks and the complexity of unlearning requests further amplify these challenges. Despite the proliferation of diverse GU strategies, the absence of a benchmark providing fair comparisons for GU, and the limited flexibility in combining downstream tasks and unlearning requests, have yielded inconsistencies in evaluations, hindering the development of this domain. To fill this gap, we present OpenGU, the first GU benchmark, where 16 SOTA GU algorithms and 37 multi-domain datasets are integrated, enabling various downstream tasks with 13 GNN backbones when responding to flexible unlearning requests. Based on this unified benchmark framework, we are able to provide a comprehensive and fair evaluation for GU. Through extensive experimentation, we have drawn $8$ crucial conclusions about existing GU methods, while also gaining valuable insights into their limitations, shedding light on potential avenues for future research.

Henan Sun, Xunkai Li, Daohan Su et al.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

Xunkai Li, Bowen Fan, Zhengyu Wu et al.

Machine unlearning, as a pivotal technology for enhancing model robustness and data privacy, has garnered significant attention in prevalent web mining applications, especially in thriving graph-based scenarios. However, most existing graph unlearning (GU) approaches face significant challenges due to the intricate interactions among web-scale graph elements during the model training: (1) The gradient-driven node entanglement hinders the complete knowledge removal in response to unlearning requests; (2) The billion-level graph elements in the web scenarios present inevitable scalability issues. To break the above limitations, we open up a new perspective by drawing a connection between GU and conventional social influence maximization. To this end, we propose Node Influence Maximization (NIM) through the decoupled influence propagation model and fine-grained influence function in a scalable manner, which is crafted to be a plug-and-play strategy to identify potential nodes affected by unlearning entities. This approach enables offline execution independent of GU, allowing it to be seamlessly integrated into most GU methods to improve their unlearning performance. Based on this, we introduce Scalable Graph Unlearning (SGU) as a new fine-tuned framework, which balances the forgetting and reasoning capability of the unlearned model by entity-specific optimizations. Extensive experiments on 14 datasets, including large-scale ogbn-papers100M, have demonstrated the effectiveness of our approach. Specifically, NIM enhances the forgetting capability of most GU methods, while SGU achieves comprehensive SOTA performance and maintains scalability.

Zihao Zhang, Xunkai Li, Rong-Hua Li et al.

Recent advancements in Large Language Models (LLMs) and the proliferation of Text-Attributed Graphs (TAGs) across various domains have positioned LLM-enhanced TAG learning as a critical research area. By utilizing rich graph descriptions, this paradigm leverages LLMs to generate high-quality embeddings, thereby enhancing the representational capacity of Graph Neural Networks (GNNs). However, the field faces significant challenges: (1) the absence of a unified framework to systematize the diverse optimization perspectives arising from the complex interactions between LLMs and GNNs, and (2) the lack of a robust method capable of handling real-world TAGs, which often suffer from texts and edge sparsity, leading to suboptimal performance. To address these challenges, we propose UltraTAG, a unified pipeline for LLM-enhanced TAG learning. UltraTAG provides a unified comprehensive and domain-adaptive framework that not only organizes existing methodologies but also paves the way for future advancements in the field. Building on this framework, we propose UltraTAG-S, a robust instantiation of UltraTAG designed to tackle the inherent sparsity issues in real-world TAGs. UltraTAG-S employs LLM-based text propagation and text augmentation to mitigate text sparsity, while leveraging LLM-augmented node selection techniques based on PageRank and edge reconfiguration strategies to address edge sparsity. Our extensive experiments demonstrate that UltraTAG-S significantly outperforms existing baselines, achieving improvements of 2.12\% and 17.47\% in ideal and sparse settings, respectively. Moreover, as the data sparsity ratio increases, the performance improvement of UltraTAG-S also rises, which underscores the effectiveness and robustness of UltraTAG-S.

Henan Sun, Xunkai Li, Lei Zhu et al.

Out-Of-Distribution (OOD) generalization has gained increasing attentions for machine learning on graphs, as graph neural networks (GNNs) often exhibit performance degradation under distribution shifts. Existing graph OOD methods tend to follow the basic ideas of invariant risk minimization and structural causal models, interpreting the invariant knowledge across datasets under various distribution shifts as graph topology or graph spectrum. However, these interpretations may be inconsistent with real-world scenarios, as neither invariant topology nor spectrum is assured. In this paper, we advocate the learnable random walk (LRW) perspective as the instantiation of invariant knowledge, and propose LRW-OOD to realize graph OOD generalization learning. Instead of employing fixed probability transition matrix (i.e., degree-normalized adjacency matrix), we parameterize the transition matrix with an LRW-sampler and a path encoder. Furthermore, we propose the kernel density estimation (KDE)-based mutual information (MI) loss to generate random walk sequences that adhere to OOD principles. Extensive experiment demonstrates that our model can effectively enhance graph OOD generalization under various types of distribution shifts and yield a significant accuracy improvement of 3.87% over state-of-the-art graph OOD generalization baselines.

Zhengyu Wu, Xunkai Li, Yinlin Zhu et al.

In recent years, Federated Graph Learning (FGL) has gained significant attention for its distributed training capabilities in graph-based machine intelligence applications, mitigating data silos while offering a new perspective for privacy-preserve large-scale graph learning. However, multi-level FGL heterogeneity presents various client-server collaboration challenges: (1) Model-level: The variation in clients for expected performance and scalability necessitates the deployment of heterogeneous models. Unfortunately, most FGL methods rigidly demand identical client models due to the direct model weight aggregation on the server. (2) Data-level: The intricate nature of graphs, marked by the entanglement of node profiles and topology, poses an optimization dilemma. This implies that models obtained by federated training struggle to achieve superior performance. (3) Communication-level: Some FGL methods attempt to increase message sharing among clients or between clients and the server to improve training, which inevitably leads to high communication costs. In this paper, we propose FedPG as a general prototype-guided optimization method for the above multi-level FGL heterogeneity. Specifically, on the client side, we integrate multi-level topology-aware prototypes to capture local graph semantics. Subsequently, on the server side, leveraging the uploaded prototypes, we employ topology-guided contrastive learning and personalized technology to tailor global prototypes for each client, broadcasting them to improve local training. Experiments demonstrate that FedPG outperforms SOTA baselines by an average of 3.57\% in accuracy while reducing communication costs by 168x.

Xunkai Li, Daohan Su, Zhengyu Wu et al.

The $q$-parameterized magnetic Laplacian serves as the foundation of directed graph (digraph) convolution, enabling this kind of digraph neural network (MagDG) to encode node features and structural insights by complex-domain message passing. As a generalization of undirected methods, MagDG shows superior capability in modeling intricate web-scale topology. Despite the great success achieved by existing MagDGs, limitations still exist: (1) Hand-crafted $q$: The performance of MagDGs depends on selecting an appropriate $q$-parameter to construct suitable graph propagation equations in the complex domain. This parameter tuning, driven by downstream tasks, limits model flexibility and significantly increases manual effort. (2) Coarse Message Passing: Most approaches treat all nodes with the same complex-domain propagation and aggregation rules, neglecting their unique digraph contexts. This oversight results in sub-optimal performance. To address the above issues, we propose two key techniques: (1) MAP is crafted to be a plug-and-play complex-domain propagation optimization strategy in the context of digraph learning, enabling seamless integration into any MagDG to improve predictions while enjoying high running efficiency. (2) MAP++ is a new digraph learning framework, further incorporating a learnable mechanism to achieve adaptively edge-wise propagation and node-wise aggregation in the complex domain for better performance. Extensive experiments on 12 datasets demonstrate that MAP enjoys flexibility for it can be incorporated with any MagDG, and scalability as it can deal with web-scale digraphs. MAP++ achieves SOTA predictive performance on 4 different downstream tasks.

Zekai Chen, Xunkai Li, Sirui Zhang et al.

De novo ligand design is a fundamental task that seeks to generate protein or molecule candidates that can effectively dock with protein receptors and achieve strong binding affinity entirely from scratch. It holds paramount significance for a wide spectrum of biomedical applications. However, most existing studies are constrained by the \textbf{Pseudo De Novo}, \textbf{Limited Docking Modeling}, and \textbf{Inflexible Ligand Type}. To address these issues, we propose MagicDock, a forward-looking framework grounded in the progressive pipeline and differentiable surface modeling. (1) We adopt a well-designed gradient inversion framework. To begin with, general docking knowledge of receptors and ligands is incorporated into the backbone model. Subsequently, the docking knowledge is instantiated as reverse gradient flows by binding prediction, which iteratively guide the de novo generation of ligands. (2) We emphasize differentiable surface modeling in the docking process, leveraging learnable 3D point-cloud representations to precisely capture binding details, thereby ensuring that the generated ligands preserve docking validity through direct and interpretable spatial fingerprints. (3) We introduce customized designs for different ligand types and integrate them into a unified gradient inversion framework with flexible triggers, thereby ensuring broad applicability. Moreover, we provide rigorous theoretical guarantees for each component of MagicDock. Extensive experiments across 9 scenarios demonstrate that MagicDock achieves average improvements of 27.1\% and 11.7\% over SOTA baselines specialized for protein or molecule ligand design, respectively.

Zhihan Zhang, Xunkai Li, Yilong Zuo et al.

Text-attributed graphs (TAGs) have become a key form of graph-structured data in modern data management and analytics, combining structural relationships with rich textual semantics for diverse applications. However, the effectiveness of analytical models, particularly graph neural networks (GNNs), is highly sensitive to data quality. Our empirical analysis shows that both conventional and LLM-enhanced GNNs degrade notably under textual, structural, and label imperfections, underscoring TAG quality as a key bottleneck for reliable analytics. Existing studies have explored data-level optimization for TAGs, but most focus on specific degradation types and target a single aspect like structure or label, lacking a systematic and comprehensive perspective on data quality improvement. To address this gap, we propose LAGA (Large Language and Graph Agent), a unified multi-agent framework for comprehensive TAG quality optimization. LAGA formulates graph quality control as a data-centric process, integrating detection, planning, action, and evaluation agents into an automated loop. It holistically enhances textual, structural, and label aspects through coordinated multi-modal optimization. Extensive experiments on 5 datasets and 16 baselines across 9 scenarios demonstrate the effectiveness, robustness and scalability of LAGA, confirming the importance of data-centric quality optimization for reliable TAG analytics.

Junzhi She, Xunkai Li, Rong-Hua Li et al.

Directed graphs are ubiquitous across numerous domains, where the directionality of edges encodes critical causal dependencies. However, existing GNNs and graph Transformers tailored for directed graphs face two major challenges: (1) effectively capturing long-range causal dependencies derived from directed edges; (2) balancing accuracy and training efficiency when processing large-scale graph datasets. In recent years, state space models (SSMs) have achieved substantial progress in causal sequence tasks, and their variants designed for graphs have demonstrated state-of-the-art accuracy while maintaining high efficiency across various graph learning benchmarks. However, existing graph state space models are exclusively designed for undirected graphs, which limits their performance in directed graph learning. To this end, we propose an innovative approach DirEgo2Token which sequentializes directed graphs via k-hop ego graphs. This marks the first systematic extension of state space models to the field of directed graph learning. Building upon this, we develop DirGraphSSM, a novel directed graph neural network architecture that implements state space models on directed graphs via the message-passing mechanism. Experimental results demonstrate that DirGraphSSM achieves state-of-the-art performance on three representative directed graph learning tasks while attaining competitive performance on two additional tasks with 1.5$\times $ to 2$\times $ training speed improvements compared to existing state-of-the-art models.

Xunkai Li, Daohan Su, Sicheng Liu et al.

Inspired by the success of LLMs, GFMs are designed to learn the optimal embedding functions from multi-domain text-attributed graphs for the downstream cross-task generalization capability. Among the diverse architectures, graph VQ-MAE stands out among the increasingly diverse landscape of GFM. This is attributed to its ability to jointly encode topology and textual attributes from multiple domains into discrete embedding spaces with clear semantic boundaries. Despite its potential, domain generalization conflicts cause imperceptible pitfalls. In this paper, we instantiate two of them, and they are just like two sides of the same GFM optimization coin - Side 1 Model Degradation: The encoder and codebook fail to capture the diversity of inputs; Side 2 Representation Collapse: The hidden embedding and codebook vector fail to preserve semantic separability due to constraints from narrow representation subspaces. These two pitfalls (sides) collectively impair the decoder and generate the low-quality reconstructed supervision, causing the GFM optimization dilemma during pre-training (coin). Through empirical investigation, we attribute the above challenges to Information Bottleneck and Regularization Deficit. To address them, we propose MoT - (1) Information Tinker for Two Pitfalls, which utilizes an edge-wise semantic fusion strategy and a mixture-of-codebooks with domain-aware routing to improve information capacity. (2) Regularization Tinker for Optimization Coin, which utilizes two additional regularizations to further improve gradient supervision in our proposed Information Tinker. Notably, as a flexible architecture, MoT adheres to the scaling laws of GFM, offering a controllable model scale. Compared to SOTA baselines, experiments on 22 datasets across 6 domains demonstrate that MoT achieves significant improvements in supervised, few-shot, and zero-shot scenarios.

Meihao Liao, Yueyang Pan, Rong-Hua Li et al.

Resistance distance computation is a fundamental problem in graph analysis, yet existing random walk-based methods are limited to approximate solutions and suffer from poor efficiency on small-treewidth graphs (e.g., road networks). In contrast, shortest-path distance computation achieves remarkable efficiency on such graphs by leveraging cut properties and tree decompositions. Motivated by this disparity, we first analyze the cut property of resistance distance. While a direct generalization proves impractical due to costly matrix operations, we overcome this limitation by integrating tree decompositions, revealing that the resistance distance $r(s,t)$ depends only on labels along the paths from $s$ and $t$ to the root of the decomposition. This insight enables compact labelling structures. Based on this, we propose \treeindex, a novel index method that constructs a resistance distance labelling of size $O(n \cdot h_{\mathcal{G}})$ in $O(n \cdot h_{\mathcal{G}}^2 \cdot d_{\max})$ time, where $h_{\mathcal{G}}$ (tree height) and $d_{\max}$ (maximum degree) behave as small constants in many real-world small-treewidth graphs (e.g., road networks). Our labelling supports exact single-pair queries in $O(h_{\mathcal{G}})$ time and single-source queries in $O(n \cdot h_{\mathcal{G}})$ time. Extensive experiments show that TreeIndex substantially outperforms state-of-the-art approaches. For instance, on the full USA road network, it constructs a $405$ GB labelling in $7$ hours (single-threaded) and answers exact single-pair queries in $10^{-3}$ seconds and single-source queries in $190$ seconds--the first exact method scalable to such large graphs.

Yuming Ai, Xunkai Li, Jiaqi Chao et al.

The demand for data privacy has led to the development of frameworks like Federated Graph Learning (FGL), which facilitate decentralized model training. However, a significant operational challenge in such systems is adhering to the right to be forgotten. This principle necessitates robust mechanisms for two distinct types of data removal: the selective erasure of specific entities and their associated knowledge from local subgraphs and the wholesale removal of a user's entire dataset and influence. Existing methods often struggle to fully address both unlearning requirements, frequently resulting in incomplete data removal or the persistence of residual knowledge within the system. This work introduces a unified framework, conceived to provide a comprehensive solution to these challenges. The proposed framework employs a bifurcated strategy tailored to the specific unlearning request. For fine-grained Meta Unlearning, it uses prototype gradients to direct the initial local forgetting process, which is then refined by generating adversarial graphs to eliminate any remaining data traces among affected clients. In the case of complete client unlearning, the framework utilizes adversarial graph generation exclusively to purge the departed client's contributions from the remaining network. Extensive experiments on multiple benchmark datasets validate the proposed approach. The framework achieves substantial improvements in model prediction accuracy across both client and meta-unlearning scenarios when compared to existing methods. Furthermore, additional studies confirm its utility as a plug-in module, where it materially enhances the predictive capabilities and unlearning effectiveness of other established methods.

Zhengyu Wu, Xunkai Li, Yinlin Zhu et al.

In the era of big data applications, Federated Graph Learning (FGL) has emerged as a prominent solution that reconcile the tradeoff between optimizing the collective intelligence between decentralized datasets holders and preserving sensitive information to maximum. Existing FGL surveys have contributed meaningfully but largely focus on integrating Federated Learning (FL) and Graph Machine Learning (GML), resulting in early stage taxonomies that emphasis on methodology and simulated scenarios. Notably, a data centric perspective, which systematically examines FGL methods through the lens of data properties and usage, remains unadapted to reorganize FGL research, yet it is critical to assess how FGL studies manage to tackle data centric constraints to enhance model performances. This survey propose a two-level data centric taxonomy: Data Characteristics, which categorizes studies based on the structural and distributional properties of datasets used in FGL, and Data Utilization, which analyzes the training procedures and techniques employed to overcome key data centric challenges. Each taxonomy level is defined by three orthogonal criteria, each representing a distinct data centric configuration. Beyond taxonomy, this survey examines FGL integration with Pretrained Large Models, showcases realistic applications, and highlights future direction aligned with emerging trends in GML.

Yanzhe Wen, Xunkai Li, Qi Zhang et al.

Recently, large language models (LLMs) have significantly advanced text-attributed graph (TAG) learning. However, existing methods inadequately handle data uncertainty in open-world scenarios, especially concerning limited labeling and unknown-class nodes. Prior solutions typically rely on isolated semantic or structural approaches for unknown-class rejection, lacking effective annotation pipelines. To address these limitations, we propose Open-world Graph Assistant (OGA), an LLM-based framework that combines adaptive label traceability, which integrates semantics and topology for unknown-class rejection, and a graph label annotator to enable model updates using newly annotated nodes. Comprehensive experiments demonstrate OGA's effectiveness and practicality.

Zhengyu Wu, Boyang Pang, Xunkai Li et al.

Federated Graph Learning (FGL) enables privacy-preserving, distributed training of graph neural networks without sharing raw data. Among its approaches, subgraph-FL has become the dominant paradigm, with most work focused on improving overall node classification accuracy. However, these methods often overlook fairness due to the complexity of node features, labels, and graph structures. In particular, they perform poorly on nodes with disadvantaged properties, such as being in the minority class within subgraphs or having heterophilous connections (neighbors with dissimilar labels or misleading features). This reveals a critical issue: high accuracy can mask degraded performance on structurally or semantically marginalized nodes. To address this, we advocate for two fairness goals: (1) improving representation of minority class nodes for class-wise fairness and (2) mitigating topological bias from heterophilous connections for topology-aware fairness. We propose FairFGL, a novel framework that enhances fairness through fine-grained graph mining and collaborative learning. On the client side, the History-Preserving Module prevents overfitting to dominant local classes, while the Majority Alignment Module refines representations of heterophilous majority-class nodes. The Gradient Modification Module transfers minority-class knowledge from structurally favorable clients to improve fairness. On the server side, FairFGL uploads only the most influenced subset of parameters to reduce communication costs and better reflect local distributions. A cluster-based aggregation strategy reconciles conflicting updates and curbs global majority dominance . Extensive evaluations on eight benchmarks show FairFGL significantly improves minority-group performance , achieving up to a 22.62 percent Macro-F1 gain while enhancing convergence over state-of-the-art baselines.

Xiang Wu, Xunkai Li, Rong-Hua Li et al.

Dynamic graphs (DGs), which capture time-evolving relationships between graph entities, have widespread real-world applications. To efficiently encode DGs for downstream tasks, most dynamic graph neural networks follow the traditional message-passing mechanism and extend it with time-based techniques. Despite their effectiveness, the growth of historical interactions introduces significant scalability issues, particularly in industry scenarios. To address this limitation, we propose ScaDyG, with the core idea of designing a time-aware scalable learning paradigm as follows: 1) Time-aware Topology Reformulation: ScaDyG first segments historical interactions into time steps (intra and inter) based on dynamic modeling, enabling weight-free and time-aware graph propagation within pre-processing. 2) Dynamic Temporal Encoding: To further achieve fine-grained graph propagation within time steps, ScaDyG integrates temporal encoding through a combination of exponential functions in a scalable manner. 3) Hypernetwork-driven Message Aggregation: After obtaining the propagated features (i.e., messages), ScaDyG utilizes hypernetwork to analyze historical dependencies, implementing node-wise representation by an adaptive temporal fusion. Extensive experiments on 12 datasets demonstrate that ScaDyG performs comparably well or even outperforms other SOTA methods in both node and link-level downstream tasks, with fewer learnable parameters and higher efficiency.

Yichun Yang, Rong-Hua Li, Meihao Liao et al.

Graph propagation (GP) computation plays a crucial role in graph data analysis, supporting various applications such as graph node similarity queries, graph node ranking, graph clustering, and graph neural networks. Existing methods, mainly relying on power iteration or push computation frameworks, often face challenges with slow convergence rates when applied to large-scale graphs. To address this issue, we propose a novel and powerful approach that accelerates power iteration and push methods using Chebyshev polynomials. Specifically, we first present a novel Chebyshev expansion formula for general GP functions, offering a new perspective on GP computation and achieving accelerated convergence. Building on these theoretical insights, we develop a novel Chebyshev power iteration method (\ltwocheb) and a novel Chebyshev push method (\chebpush). Our \ltwocheb method demonstrates an approximate acceleration of $O(\sqrt{N})$ compared to existing power iteration techniques for both personalized PageRank and heat kernel PageRank computations, which are well-studied GP problems. For \chebpush, we propose an innovative subset Chebyshev recurrence technique, enabling the design of a push-style local algorithm with provable error guarantee and reduced time complexity compared to existing push methods. We conduct extensive experiments using 5 large real-world datasets to evaluate our proposed algorithms, demonstrating their superior efficiency compared to state-of-the-art approaches.