Managing evolving graph data presents substantial challenges in storage and privacy, and training graph neural networks (GNNs) on such data often leads to catastrophic forgetting, impairing performance on earlier tasks. Despite existing continual graph learning (CGL) methods mitigating this to some extent, they rely on centralized architectures and ignore the potential of distributed graph databases to leverage collective intelligence. To this end, we propose Federated Continual Graph Learning (FCGL) to adapt GNNs across multiple evolving graphs under storage and privacy constraints. Our empirical study highlights two core challenges: local graph forgetting (LGF), where clients lose prior knowledge when adapting to new tasks, and global expertise conflict (GEC), where the global GNN exhibits sub-optimal performance in both adapting to new tasks and retaining old ones, arising from inconsistent client expertise during server-side parameter aggregation. To address these, we introduce POWER, a framework that preserves experience nodes with maximum local-global coverage locally to mitigate LGF, and leverages pseudo-prototype reconstruction with trajectory-aware knowledge transfer to resolve GEC. Experiments on various graph datasets demonstrate POWER's superiority over federated adaptations of CGL baselines and vision-centric federated continual learning approaches.
This paper introduces a novel Laplacian matrix aiming to enable the construction of spectral convolutional networks and to extend the signal processing applications for directed graphs. Our proposal is inspired by a Haar-like transformation and produces a Hermitian matrix which is not only in one-to-one relation with the adjacency matrix, preserving both direction and weight information, but also enjoys desirable additional properties like scaling robustness, sensitivity, continuity, and directionality. We take a theoretical standpoint and support the conformity of our approach with the spectral graph theory. Then, we address two use-cases: graph learning (by introducing HaarNet, a spectral graph convolutional network built with our Haar-Laplacian) and graph signal processing. We show that our approach gives better results in applications like weight prediction and denoising on directed graphs.
Heterogeneous Graph Neural Networks (HGNNs) have achieved promising results in various heterogeneous graph learning tasks, owing to their superiority in capturing the intricate relationships and diverse relational semantics inherent in heterogeneous graph structures. However, the neighborhood-fetching latency incurred by structure dependency in HGNNs makes it challenging to deploy for latency-constrained applications that require fast inference. Inspired by recent GNN-to-MLP knowledge distillation frameworks, we introduce HG2M and HG2M+ to combine both HGNN's superior performance and MLP's efficient inference. HG2M directly trains student MLPs with node features as input and soft labels from teacher HGNNs as targets, and HG2M+ further distills reliable and heterogeneous semantic knowledge into student MLPs through reliable node distillation and reliable meta-path distillation. Experiments conducted on six heterogeneous graph datasets show that despite lacking structural dependencies, HG2Ms can still achieve competitive or even better performance than HGNNs and significantly outperform vanilla MLPs. Moreover, HG2Ms demonstrate a 379.24$\times$ speedup in inference over HGNNs on the large-scale IGB-3M-19 dataset, showcasing their ability for latency-sensitive deployments.
Pseudo labeling (PL) is a wide-applied strategy to enlarge the labeled dataset by self-annotating the potential samples during the training process. Several works have shown that it can improve the graph learning model performance in general. However, we notice that the incorrect labels can be fatal to the graph training process. Inappropriate PL may result in the performance degrading, especially on graph data where the noise can propagate. Surprisingly, the corresponding error is seldom theoretically analyzed in the literature. In this paper, we aim to give deep insights of PL on graph learning models. We first present the error analysis of PL strategy by showing that the error is bounded by the confidence of PL threshold and consistency of multi-view prediction. Then, we theoretically illustrate the effect of PL on convergence property. Based on the analysis, we propose a cautious pseudo labeling methodology in which we pseudo label the samples with highest confidence and multi-view consistency. Finally, extensive experiments demonstrate that the proposed strategy improves graph learning process and outperforms other PL strategies on link prediction and node classification tasks.
Graph Neural Networks (GNNs) have advanced relational data analysis but lack invariance learning techniques common in image classification. In node classification with GNNs, it is actually the ego-graph of the center node that is classified. This research extends the scale invariance concept to node classification by drawing an analogy to image processing: just as scale invariance being used in image classification to capture multi-scale features, we propose the concept of ``scaled ego-graphs''. Scaled ego-graphs generalize traditional ego-graphs by replacing undirected single-edges with ``scaled-edges'', which are ordered sequences of multiple directed edges. We empirically assess the performance of the proposed scale invariance in graphs on seven benchmark datasets, across both homophilic and heterophilic structures. Our scale-invariance-based graph learning outperforms inception models derived from random walks by being simpler, faster, and more accurate. The scale invariance explains inception models' success on homophilic graphs and limitations on heterophilic graphs. To ensure applicability of inception model to heterophilic graphs as well, we further present ScaleNet, an architecture that leverages multi-scaled features. ScaleNet achieves state-of-the-art results on five out of seven datasets (four homophilic and one heterophilic) and matches top performance on the remaining two, demonstrating its excellent applicability. This represents a significant advance in graph learning, offering a unified framework that enhances node classification across various graph types. Our code is available at https://github.com/Qin87/ScaleNet/tree/July25.
Inspired by the success of foundation models in applications such as ChatGPT, as graph data has been ubiquitous, one can envision the far-reaching impacts that can be brought by Graph Foundation Models (GFMs) with broader applications in the areas such as scientific research, social network analysis, drug discovery, and e-commerce. Despite the significant progress of pre-trained graph neural networks, there haven't been GFMs that can achieve desired performance on various graph-learning-related tasks. Building GFMs may rely on a vocabulary that encodes transferable patterns shared among different tasks and domains. Unlike image and text, defining such transferable patterns for graphs remains an open question. In this paper, we aim to bridge this gap by rethinking the transferable patterns on graphs as computation trees -- i.e., tree structures derived from the message-passing process. Based on this insight, we propose a cross-task, cross-domain graph foundation model named GFT, short for Graph Foundation model with transferable Tree vocabulary. By treating computation trees as tokens within the transferable vocabulary, GFT improves model generalization and reduces the risk of negative transfer. The theoretical analyses and extensive experimental studies have demonstrated the transferability of computation trees and shown the effectiveness of GFT across diverse tasks and domains in graph learning. The open source code and data are available at https://github.com/Zehong-Wang/GFT.
Incremental graph learning has gained significant attention for its ability to address the catastrophic forgetting problem in graph representation learning. However, traditional methods often rely on a large number of labels for node classification, which is impractical in real-world applications. This makes few-shot incremental learning on graphs a pressing need. Current methods typically require extensive training samples from meta-learning to build memory and perform intensive fine-tuning of GNN parameters, leading to high memory consumption and potential loss of previously learned knowledge. To tackle these challenges, we introduce Mecoin, an efficient method for building and maintaining memory. Mecoin employs Structured Memory Units to cache prototypes of learned categories, as well as Memory Construction Modules to update these prototypes for new categories through interactions between the nodes and the cached prototypes. Additionally, we have designed a Memory Representation Adaptation Module to store probabilities associated with each class prototype, reducing the need for parameter fine-tuning and lowering the forgetting rate. When a sample matches its corresponding class prototype, the relevant probabilities are retrieved from the MRaM. Knowledge is then distilled back into the GNN through a Graph Knowledge Distillation Module, preserving the model's memory. We analyze the effectiveness of Mecoin in terms of generalization error and explore the impact of different distillation strategies on model performance through experiments and VC-dimension analysis. Compared to other related works, Mecoin shows superior performance in accuracy and forgetting rate. Our code is publicly available on the https://github.com/Arvin0313/Mecoin-GFSCIL.git .
We introduce the Distributed-order fRActional Graph Operating Network (DRAGON), a novel continuous Graph Neural Network (GNN) framework that incorporates distributed-order fractional calculus. Unlike traditional continuous GNNs that utilize integer-order or single fractional-order differential equations, DRAGON uses a learnable probability distribution over a range of real numbers for the derivative orders. By allowing a flexible and learnable superposition of multiple derivative orders, our framework captures complex graph feature updating dynamics beyond the reach of conventional models. We provide a comprehensive interpretation of our framework's capability to capture intricate dynamics through the lens of a non-Markovian graph random walk with node feature updating driven by an anomalous diffusion process over the graph. Furthermore, to highlight the versatility of the DRAGON framework, we conduct empirical evaluations across a range of graph learning tasks. The results consistently demonstrate superior performance when compared to traditional continuous GNN models. The implementation code is available at \url{https://github.com/zknus/NeurIPS-2024-DRAGON}.
Graph neural network (GNN) has captured wide attention due to its capability of graph representation learning for graph-structured data. However, the distributed data silos limit the performance of GNN. Vertical federated learning (VFL), an emerging technique to process distributed data, successfully makes GNN possible to handle the distributed graph-structured data. Despite the prosperous development of vertical federated graph learning (VFGL), the robustness of VFGL against the adversarial attack has not been explored yet. Although numerous adversarial attacks against centralized GNNs are proposed, their attack performance is challenged in the VFGL scenario. To the best of our knowledge, this is the first work to explore the adversarial attack against VFGL. A query-efficient hybrid adversarial attack framework is proposed to significantly improve the centralized adversarial attacks against VFGL, denoted as NA2, short for Neuron-based Adversarial Attack. Specifically, a malicious client manipulates its local training data to improve its contribution in a stealthy fashion. Then a shadow model is established based on the manipulated data to simulate the behavior of the server model in VFGL. As a result, the shadow model can improve the attack success rate of various centralized attacks with a few queries. Extensive experiments on five real-world benchmarks demonstrate that NA2 improves the performance of the centralized adversarial attacks against VFGL, achieving state-of-the-art performance even under potential adaptive defense where the defender knows the attack method. Additionally, we provide interpretable experiments of the effectiveness of NA2 via sensitive neurons identification and visualization of t-SNE.
The message-passing mechanism of graph convolutional networks (i.e., GCNs) enables label information to be propagated to a broader range of neighbors, thereby increasing the utilization of labels. However, the label information is not always effectively utilized in the traditional GCN framework. To address this issue, we propose a new two-step framework called ELU-GCN. In the first stage, ELU-GCN conducts graph learning to learn a new graph structure (i.e., ELU-graph), which enables the message passing can effectively utilize label information. In the second stage, we design a new graph contrastive learning on the GCN framework for representation learning by exploring the consistency and mutually exclusive information between the learned ELU graph and the original graph. Moreover, we theoretically demonstrate that the proposed method can ensure the generalization ability of GCNs. Extensive experiments validate the superiority of our method.
Link prediction is a critical problem in graph learning with broad applications such as recommender systems and knowledge graph completion. Numerous research efforts have been directed at solving this problem, including approaches based on similarity metrics and Graph Neural Networks (GNN). However, most existing solutions are still rooted in conventional supervised learning, which makes it challenging to adapt over time to changing customer interests and to address the inherent dilemma of exploitation versus exploration in link prediction. To tackle these challenges, this paper reformulates link prediction as a sequential decision-making process, where each link prediction interaction occurs sequentially. We propose a novel fusion algorithm, PRB (PageRank Bandits), which is the first to combine contextual bandits with PageRank for collaborative exploitation and exploration. We also introduce a new reward formulation and provide a theoretical performance guarantee for PRB. Finally, we extensively evaluate PRB in both online and offline settings, comparing it with bandit-based and graph-based methods. The empirical success of PRB demonstrates the value of the proposed fusion approach. Our code is released at https://github.com/jiaruzouu/PRB.
Graph Neural Networks (GNNs) have become essential in interpreting relational data across various domains, yet, they often struggle to generalize to unseen graph data that differs markedly from training instances. In this paper, we introduce a novel framework called General Retrieval-Augmented Graph Learning (RAGraph), which brings external graph data into the general graph foundation model to improve model generalization on unseen scenarios. On the top of our framework is a toy graph vector library that we established, which captures key attributes, such as features and task-specific label information. During inference, the RAGraph adeptly retrieves similar toy graphs based on key similarities in downstream tasks, integrating the retrieved data to enrich the learning context via the message-passing prompting mechanism. Our extensive experimental evaluations demonstrate that RAGraph significantly outperforms state-of-the-art graph learning methods in multiple tasks such as node classification, link prediction, and graph classification across both dynamic and static datasets. Furthermore, extensive testing confirms that RAGraph consistently maintains high performance without the need for task-specific fine-tuning, highlighting its adaptability, robustness, and broad applicability.
Graph learning is naturally well suited for use in symbolic, object-centric planning due to its ability to exploit relational structures exhibited in planning domains and to take as input planning instances with arbitrary numbers of objects. Numeric planning is an extension of symbolic planning in which states may now also exhibit numeric variables. In this work, we propose data-efficient and interpretable machine learning models for learning to solve numeric planning tasks. This involves constructing a new graph kernel for graphs with both continuous and categorical attributes, as well as new optimisation methods for learning heuristic functions for numeric planning. Experiments show that our graph kernels are vastly more efficient and generalise better than graph neural networks for numeric planning, and also yield competitive coverage performance compared to domain-independent numeric planners. Code is available at https://github.com/DillonZChen/goose
Personalized Federated Graph Learning (pFGL) facilitates the decentralized training of Graph Neural Networks (GNNs) without compromising privacy while accommodating personalized requirements for non-IID participants. In cross-domain scenarios, structural heterogeneity poses significant challenges for pFGL. Nevertheless, previous pFGL methods incorrectly share non-generic knowledge globally and fail to tailor personalized solutions locally under domain structural shift. We innovatively reveal that the spectral nature of graphs can well reflect inherent domain structural shifts. Correspondingly, our method overcomes it by sharing generic spectral knowledge. Moreover, we indicate the biased message-passing schemes for graph structures and propose the personalized preference module. Combining both strategies, we propose our pFGL framework FedSSP which Shares generic Spectral knowledge while satisfying graph Preferences. Furthermore, We perform extensive experiments on cross-dataset and cross-domain settings to demonstrate the superiority of our framework. The code is available at https://github.com/OakleyTan/FedSSP.
Distribution shifts on graphs -- the discrepancies in data distribution between training and employing a graph machine learning model -- are ubiquitous and often unavoidable in real-world scenarios. These shifts may severely deteriorate model performance, posing significant challenges for reliable graph machine learning. Consequently, there has been a surge in research on graph machine learning under distribution shifts, aiming to train models to achieve satisfactory performance on out-of-distribution (OOD) test data. In our survey, we provide an up-to-date and forward-looking review of deep graph learning under distribution shifts. Specifically, we cover three primary scenarios: graph OOD generalization, training-time graph OOD adaptation, and test-time graph OOD adaptation. We begin by formally formulating the problems and discussing various types of distribution shifts that can affect graph learning, such as covariate shifts and concept shifts. To provide a better understanding of the literature, we introduce a systematic taxonomy that classifies existing methods into model-centric and data-centric approaches, investigating the techniques used in each category. We also summarize commonly used datasets in this research area to facilitate further investigation. Finally, we point out promising research directions and the corresponding challenges to encourage further study in this vital domain. We also provide a continuously updated reading list at https://github.com/kaize0409/Awesome-Graph-OOD.
Causal discovery in real-world systems, such as biological networks, is often complicated by feedback loops and incomplete data. Standard algorithms, which assume acyclic structures or fully observed data, struggle with these challenges. To address this gap, we propose MissNODAG, a differentiable framework for learning both the underlying cyclic causal graph and the missingness mechanism from partially observed data, including data missing not at random. Our framework integrates an additive noise model with an expectation-maximization procedure, alternating between imputing missing values and optimizing the observed data likelihood, to uncover both the cyclic structures and the missingness mechanism. We demonstrate the effectiveness of MissNODAG through synthetic experiments and an application to real-world gene perturbation data.
Graph Transformers are popular neural networks that extend the well-known Transformer architecture to the graph domain. These architectures operate by applying self-attention on graph nodes and incorporating graph structure through the use of positional encodings (e.g., Laplacian positional encoding) or structural encodings (e.g., random-walk structural encoding). The quality of such encodings is critical, since they provide the necessary $\textit{graph inductive biases}$ to condition the model on graph structure. In this work, we propose $\textit{motif structural encoding}$ (MoSE) as a flexible and powerful structural encoding framework based on counting graph homomorphisms. Theoretically, we compare the expressive power of MoSE to random-walk structural encoding and relate both encodings to the expressive power of standard message passing neural networks. Empirically, we observe that MoSE outperforms other well-known positional and structural encodings across a range of architectures, and it achieves state-of-the-art performance on a widely studied molecular property prediction dataset.
Existing graph learning-based cognitive diagnosis (CD) methods have made relatively good results, but their student, exercise, and concept representations are learned and exchanged in an implicit unified graph, which makes the interaction-agnostic exercise and concept representations be learned poorly, failing to provide high robustness against noise in students' interactions. Besides, lower-order exercise latent representations obtained in shallow layers are not well explored when learning the student representation. To tackle the issues, this paper suggests a meta multigraph-assisted disentangled graph learning framework for CD (DisenGCD), which learns three types of representations on three disentangled graphs: student-exercise-concept interaction, exercise-concept relation, and concept dependency graphs, respectively. Specifically, the latter two graphs are first disentangled from the interaction graph. Then, the student representation is learned from the interaction graph by a devised meta multigraph learning module; multiple learnable propagation paths in this module enable current student latent representation to access lower-order exercise latent representations, which can lead to more effective nad robust student representations learned; the exercise and concept representations are learned on the relation and dependency graphs by graph attention modules. Finally, a novel diagnostic function is devised to handle three disentangled representations for prediction. Experiments show better performance and robustness of DisenGCD than state-of-the-art CD methods and demonstrate the effectiveness of the disentangled learning framework and meta multigraph module. The source code is available at \textcolor{red}{\url{https://github.com/BIMK/Intelligent-Education/tree/main/DisenGCD}}.
Line graph transformation has been widely studied in graph theory, where each node in a line graph corresponds to an edge in the original graph. This has inspired a series of graph neural networks (GNNs) applied to transformed line graphs, which have proven effective in various graph representation learning tasks. However, there is limited theoretical study on how line graph transformation affects the expressivity of GNN models. In this study, we focus on two types of graphs known to be challenging to the Weisfeiler-Leman (WL) tests: Cai-F\"urer-Immerman (CFI) graphs and strongly regular graphs, and show that applying line graph transformation helps exclude these challenging graph properties, thus potentially assist WL tests in distinguishing these graphs. We empirically validate our findings by conducting a series of experiments that compare the accuracy and efficiency of graph isomorphism tests and GNNs on both line-transformed and original graphs across these graph structure types.
Transformers serve as the backbone architectures of Foundational Models, where domain-specific tokenizers allow them to adapt to various domains. Graph Transformers (GTs) have recently emerged as leading models in geometric deep learning, outperforming Graph Neural Networks (GNNs) in various graph learning tasks. However, the development of tokenizers for graphs has lagged behind other modalities. To address this, we introduce GQT (\textbf{G}raph \textbf{Q}uantized \textbf{T}okenizer), which decouples tokenizer training from Transformer training by leveraging multi-task graph self-supervised learning, yielding robust and generalizable graph tokens. Furthermore, the GQT utilizes Residual Vector Quantization (RVQ) to learn hierarchical discrete tokens, resulting in significantly reduced memory requirements and improved generalization capabilities. By combining the GQT with token modulation, a Transformer encoder achieves state-of-the-art performance on 20 out of 22 benchmarks, including large-scale homophilic and heterophilic datasets.