Transformers have recently emerged as powerful neural networks for graph learning, showcasing state-of-the-art performance on several graph property prediction tasks. However, these results have been limited to small-scale graphs, where the computational feasibility of the global attention mechanism is possible. The next goal is to scale up these architectures to handle very large graphs on the scale of millions or even billions of nodes. With large-scale graphs, global attention learning is proven impractical due to its quadratic complexity w.r.t. the number of nodes. On the other hand, neighborhood sampling techniques become essential to manage large graph sizes, yet finding the optimal trade-off between speed and accuracy with sampling techniques remains challenging. This work advances representation learning on single large-scale graphs with a focus on identifying model characteristics and critical design constraints for developing scalable graph transformer (GT) architectures. We argue such GT requires layers that can adeptly learn both local and global graph representations while swiftly sampling the graph topology. As such, a key innovation of this work lies in the creation of a fast neighborhood sampling technique coupled with a local attention mechanism that encompasses a 4-hop reception field, but achieved through just 2-hop operations. This local node embedding is then integrated with a global node embedding, acquired via another self-attention layer with an approximate global codebook, before finally sent through a downstream layer for node predictions. The proposed GT framework, named LargeGT, overcomes previous computational bottlenecks and is validated on three large-scale node classification benchmarks. We report a 3x speedup and 16.8% performance gain on ogbn-products and snap-patents, while we also scale LargeGT on ogbn-papers100M with a 5.9% performance improvement.
Recent research demonstrates that GNNs are vulnerable to the model stealing attack, a nefarious endeavor geared towards duplicating the target model via query permissions. However, they mainly focus on node classification tasks, neglecting the potential threats entailed within the domain of graph classification tasks. Furthermore, their practicality is questionable due to unreasonable assumptions, specifically concerning the large data requirements and extensive model knowledge. To this end, we advocate following strict settings with limited real data and hard-label awareness to generate synthetic data, thereby facilitating the stealing of the target model. Specifically, following important data generation principles, we introduce three model stealing attacks to adapt to different actual scenarios: MSA-AU is inspired by active learning and emphasizes the uncertainty to enhance query value of generated samples; MSA-AD introduces diversity based on Mixup augmentation strategy to alleviate the query inefficiency issue caused by over-similar samples generated by MSA-AU; MSA-AUD combines the above two strategies to seamlessly integrate the authenticity, uncertainty, and diversity of the generated samples. Finally, extensive experiments consistently demonstrate the superiority of the proposed methods in terms of concealment, query efficiency, and stealing performance.
Hypergraphs are vital in modelling data with higher-order relations containing more than two entities, gaining prominence in machine learning and signal processing. Many hypergraph neural networks leverage message passing over hypergraph structures to enhance node representation learning, yielding impressive performances in tasks like hypergraph node classification. However, these message-passing-based models face several challenges, including oversmoothing as well as high latency and sensitivity to structural perturbations at inference time. To tackle those challenges, we propose an alternative approach where we integrate the information about hypergraph structures into training supervision without explicit message passing, thus also removing the reliance on it at inference. Specifically, we introduce Hypergraph-MLP, a novel learning framework for hypergraph-structured data, where the learning model is a straightforward multilayer perceptron (MLP) supervised by a loss function based on a notion of signal smoothness on hypergraphs. Experiments on hypergraph node classification tasks demonstrate that Hypergraph-MLP achieves competitive performance compared to existing baselines, and is considerably faster and more robust against structural perturbations at inference.
Graph neural networks (GNNs) have shown advantages in graph-based analysis tasks. However, most existing methods have the homogeneity assumption and show poor performance on heterophilic graphs, where the linked nodes have dissimilar features and different class labels, and the semantically related nodes might be multi-hop away. To address this limitation, this paper presents GraphRARE, a general framework built upon node relative entropy and deep reinforcement learning, to strengthen the expressive capability of GNNs. An innovative node relative entropy, which considers node features and structural similarity, is used to measure mutual information between node pairs. In addition, to avoid the sub-optimal solutions caused by mixing useful information and noises of remote nodes, a deep reinforcement learning-based algorithm is developed to optimize the graph topology. This algorithm selects informative nodes and discards noisy nodes based on the defined node relative entropy. Extensive experiments are conducted on seven real-world datasets. The experimental results demonstrate the superiority of GraphRARE in node classification and its capability to optimize the original graph topology.
Deep learning has achieved remarkable success in graph-related tasks, yet this accomplishment heavily relies on large-scale high-quality annotated datasets. However, acquiring such datasets can be cost-prohibitive, leading to the practical use of labels obtained from economically efficient sources such as web searches and user tags. Unfortunately, these labels often come with noise, compromising the generalization performance of deep networks. To tackle this challenge and enhance the robustness of deep learning models against label noise in graph-based tasks, we propose a method called ERASE (Error-Resilient representation learning on graphs for lAbel noiSe tolerancE). The core idea of ERASE is to learn representations with error tolerance by maximizing coding rate reduction. Particularly, we introduce a decoupled label propagation method for learning representations. Before training, noisy labels are pre-corrected through structural denoising. During training, ERASE combines prototype pseudo-labels with propagated denoised labels and updates representations with error resilience, which significantly improves the generalization performance in node classification. The proposed method allows us to more effectively withstand errors caused by mislabeled nodes, thereby strengthening the robustness of deep networks in handling noisy graph data. Extensive experimental results show that our method can outperform multiple baselines with clear margins in broad noise levels and enjoy great scalability. Codes are released at https://github.com/eraseai/erase.
Spectral Graph Neural Networks (GNNs) have achieved tremendous success in graph machine learning, with polynomial filters applied for graph convolutions, where all nodes share the identical filter weights to mine their local contexts. Despite the success, existing spectral GNNs usually fail to deal with complex networks (e.g., WWW) due to such homogeneous spectral filtering setting that ignores the regional heterogeneity as typically seen in real-world networks. To tackle this issue, we propose a novel diverse spectral filtering (DSF) framework, which automatically learns node-specific filter weights to exploit the varying local structure properly. Particularly, the diverse filter weights consist of two components -- A global one shared among all nodes, and a local one that varies along network edges to reflect node difference arising from distinct graph parts -- to balance between local and global information. As such, not only can the global graph characteristics be captured, but also the diverse local patterns can be mined with awareness of different node positions. Interestingly, we formulate a novel optimization problem to assist in learning diverse filters, which also enables us to enhance any spectral GNNs with our DSF framework. We showcase the proposed framework on three state-of-the-arts including GPR-GNN, BernNet, and JacobiConv. Extensive experiments over 10 benchmark datasets demonstrate that our framework can consistently boost model performance by up to 4.92% in node classification tasks, producing diverse filters with enhanced interpretability. Code is available at \url{https://github.com/jingweio/DSF}.
Local Attention-guided Message Passing Mechanism (LAMP) adopted in Graph Attention Networks (GATs) is designed to adaptively learn the importance of neighboring nodes for better local aggregation on the graph, which can bring the representations of similar neighbors closer effectively, thus showing stronger discrimination ability. However, existing GATs suffer from a significant discrimination ability decline in heterophilic graphs because the high proportion of dissimilar neighbors can weaken the self-attention of the central node, jointly resulting in the deviation of the central node from similar nodes in the representation space. This kind of effect generated by neighboring nodes is called the Distraction Effect (DE) in this paper. To estimate and weaken the DE of neighboring nodes, we propose a Causally graph Attention network for Trimming heterophilic graph (CAT). To estimate the DE, since the DE are generated through two paths (grab the attention assigned to neighbors and reduce the self-attention of the central node), we use Total Effect to model DE, which is a kind of causal estimand and can be estimated from intervened data; To weaken the DE, we identify the neighbors with the highest DE (we call them Distraction Neighbors) and remove them. We adopt three representative GATs as the base model within the proposed CAT framework and conduct experiments on seven heterophilic datasets in three different sizes. Comparative experiments show that CAT can improve the node classification accuracy of all base GAT models. Ablation experiments and visualization further validate the enhancement of discrimination ability brought by CAT. The source code is available at https://github.com/GeoX-Lab/CAT.
Despite Graph neural networks' significant performance gain over many classic techniques in various graph-related downstream tasks, their successes are restricted in shallow models due to over-smoothness and the difficulties of optimizations among many other issues. In this paper, to alleviate the over-smoothing issue, we propose a soft graph normalization method to preserve the diversities of node embeddings and prevent indiscrimination due to possible over-closeness. Combined with residual connections, we analyze the reason why the method can effectively capture the knowledge in both input graph structures and node features even with deep networks. Additionally, inspired by Curriculum Learning that learns easy examples before the hard ones, we propose a novel label-smoothing-based learning framework to enhance the optimization of deep GNNs, which iteratively smooths labels in an auxiliary graph and constructs many gradual non-smooth tasks for extracting increasingly complex knowledge and gradually discriminating nodes from coarse to fine. The method arguably reduces the risk of overfitting and generalizes better results. Finally, extensive experiments are carried out to demonstrate the effectiveness and potential of the proposed model and learning framework through comparison with twelve existing baselines including the state-of-the-art methods on twelve real-world node classification benchmarks.
Graph Contrastive Learning (GCL) is unsupervised graph representation learning that can obtain useful representation of unknown nodes. The node representation can be utilized as features of downstream tasks. However, GCL is vulnerable to poisoning attacks as with existing learning models. A state-of-the-art defense cannot sufficiently negate adverse effects by poisoned graphs although such a defense introduces adversarial training in the GCL. To achieve further improvement, pruning adversarial edges is important. To the best of our knowledge, the feasibility remains unexplored in the GCL domain. In this paper, we propose a simple defense for GCL, EdgePruner. We focus on the fact that the state-of-the-art poisoning attack on GCL tends to mainly add adversarial edges to create poisoned graphs, which means that pruning edges is important to sanitize the graphs. Thus, EdgePruner prunes edges that contribute to minimizing the contrastive loss based on the node representation obtained after training on poisoned graphs by GCL. Furthermore, we focus on the fact that nodes with distinct features are connected by adversarial edges in poisoned graphs. Thus, we introduce feature similarity between neighboring nodes to help more appropriately determine adversarial edges. This similarity is helpful in further eliminating adverse effects from poisoned graphs on various datasets. Finally, EdgePruner outputs a graph that yields the minimum contrastive loss as the sanitized graph. Our results demonstrate that pruning adversarial edges is feasible on six datasets. EdgePruner can improve the accuracy of node classification under the attack by up to 5.55% compared with that of the state-of-the-art defense. Moreover, we show that EdgePruner is immune to an adaptive attack.
Graph Comparative Learning (GCL) is a self-supervised method that combines the advantages of Graph Convolutional Networks (GCNs) and comparative learning, making it promising for learning node representations. However, the GCN encoders used in these methods rely on the Fourier transform to learn fixed graph representations, which is inherently limited by the uncertainty principle involving spatial and spectral localization trade-offs. To overcome the inflexibility of existing methods and the computationally expensive eigen-decomposition and dense matrix multiplication, this paper proposes an Adaptive Spectral Wavelet Transform-based Self-Supervised Graph Neural Network (ASWT-SGNN). The proposed method employs spectral adaptive polynomials to approximate the filter function and optimize the wavelet using contrast loss. This design enables the creation of local filters in both spectral and spatial domains, allowing flexible aggregation of neighborhood information at various scales and facilitating controlled transformation between local and global information. Compared to existing methods, the proposed approach reduces computational complexity and addresses the limitation of graph convolutional neural networks, which are constrained by graph size and lack flexible control over the neighborhood aspect. Extensive experiments on eight benchmark datasets demonstrate that ASWT-SGNN accurately approximates the filter function in high-density spectral regions, avoiding costly eigen-decomposition. Furthermore, ASWT-SGNN achieves comparable performance to state-of-the-art models in node classification tasks.
Graph representation learning is a fundamental research theme and can be generalized to benefit multiple downstream tasks from the node and link levels to the higher graph level. In practice, it is desirable to develop task-agnostic general graph representation learning methods that are typically trained in an unsupervised manner. Related research reveals that the power of graph representation learning methods depends on whether they can differentiate distinct graph structures as different embeddings and map isomorphic graphs to consistent embeddings (i.e., the isomorphic consistency of graph models). However, for task-agnostic general graph representation learning, existing unsupervised graph models, represented by the variational graph auto-encoders (VGAEs), can only keep the isomorphic consistency within the subgraphs of 1-hop neighborhoods and thus usually manifest inferior performance on the more difficult higher-level tasks. To overcome the limitations of existing unsupervised methods, in this paper, we propose the Isomorphic-Consistent VGAE (IsoC-VGAE) for multi-level task-agnostic graph representation learning. We first devise a decoding scheme to provide a theoretical guarantee of keeping the isomorphic consistency under the settings of unsupervised learning. We then propose the Inverse Graph Neural Network (Inv-GNN) decoder as its intuitive realization, which trains the model via reconstructing the GNN node embeddings with multi-hop neighborhood information, so as to maintain the high-order isomorphic consistency within the VGAE framework. We conduct extensive experiments on the representative graph learning tasks at different levels, including node classification, link prediction and graph classification, and the results verify that our proposed model generally outperforms both the state-of-the-art unsupervised methods and representative supervised methods.
Recent studies have shown that attackers can catastrophically reduce the performance of GNNs by maliciously modifying the graph structure or node features on the graph. Adversarial training, which has been shown to be one of the most effective defense mechanisms against adversarial attacks in computer vision, holds great promise for enhancing the robustness of GNNs. There is limited research on defending against attacks by performing adversarial training on graphs, and it is crucial to delve deeper into this approach to optimize its effectiveness. Therefore, based on robust adversarial training on graphs, we propose a hierarchical constraint refinement framework (HC-Ref) that enhances the anti-perturbation capabilities of GNNs and downstream classifiers separately, ultimately leading to improved robustness. We propose corresponding adversarial regularization terms that are conducive to adaptively narrowing the domain gap between the normal part and the perturbation part according to the characteristics of different layers, promoting the smoothness of the predicted distribution of both parts. Moreover, existing research on graph robust adversarial training primarily concentrates on training from the standpoint of node feature perturbations and seldom takes into account alterations in the graph structure. This limitation makes it challenging to prevent attacks based on topological changes in the graph. This paper generates adversarial examples by utilizing graph structure perturbations, offering an effective approach to defend against attack methods that are based on topological changes. Extensive experiments on two real-world graph benchmarks show that HC-Ref successfully resists various attacks and has better node classification performance compared to several baseline methods.
Deep Graph Learning (DGL) has emerged as a crucial technique across various domains. However, recent studies have exposed vulnerabilities in DGL models, such as susceptibility to evasion and poisoning attacks. While empirical and provable robustness techniques have been developed to defend against graph modification attacks (GMAs), the problem of certified robustness against graph injection attacks (GIAs) remains largely unexplored. To bridge this gap, we introduce the node-aware bi-smoothing framework, which is the first certifiably robust approach for general node classification tasks against GIAs. Notably, the proposed node-aware bi-smoothing scheme is model-agnostic and is applicable for both evasion and poisoning attacks. Through rigorous theoretical analysis, we establish the certifiable conditions of our smoothing scheme. We also explore the practical implications of our node-aware bi-smoothing schemes in two contexts: as an empirical defense approach against real-world GIAs and in the context of recommendation systems. Furthermore, we extend two state-of-the-art certified robustness frameworks to address node injection attacks and compare our approach against them. Extensive evaluations demonstrate the effectiveness of our proposed certificates.
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.
A machine learning model is traditionally considered robust if its prediction remains (almost) constant under input perturbations with small norm. However, real-world tasks like molecular property prediction or point cloud segmentation have inherent equivariances, such as rotation or permutation equivariance. In such tasks, even perturbations with large norm do not necessarily change an input's semantic content. Furthermore, there are perturbations for which a model's prediction explicitly needs to change. For the first time, we propose a sound notion of adversarial robustness that accounts for task equivariance. We then demonstrate that provable robustness can be achieved by (1) choosing a model that matches the task's equivariances (2) certifying traditional adversarial robustness. Certification methods are, however, unavailable for many models, such as those with continuous equivariances. We close this gap by developing the framework of equivariance-preserving randomized smoothing, which enables architecture-agnostic certification. We additionally derive the first architecture-specific graph edit distance certificates, i.e. sound robustness guarantees for isomorphism equivariant tasks like node classification. Overall, a sound notion of robustness is an important prerequisite for future work at the intersection of robust and geometric machine learning.
Model Parsing defines the research task of predicting hyperparameters of the generative model (GM), given a generated image as input. Since a diverse set of hyperparameters is jointly employed by the generative model, and dependencies often exist among them, it is crucial to learn these hyperparameter dependencies for the improved model parsing performance. To explore such important dependencies, we propose a novel model parsing method called Learnable Graph Pooling Network (LGPN). Specifically, we transform model parsing into a graph node classification task, using graph nodes and edges to represent hyperparameters and their dependencies, respectively. Furthermore, LGPN incorporates a learnable pooling-unpooling mechanism tailored to model parsing, which adaptively learns hyperparameter dependencies of GMs used to generate the input image. We also extend our proposed method to CNN-generated image detection and coordinate attacks detection. Empirically, we achieve state-of-the-art results in model parsing and its extended applications, showing the effectiveness of our method. Our source code are available.
Graph Neural Networks (GNNs) have displayed considerable promise in graph representation learning across various applications. The core learning process requires the initialization of model weight matrices within each GNN layer, which is typically accomplished via classic initialization methods such as Xavier initialization. However, these methods were originally motivated to stabilize the variance of hidden embeddings and gradients across layers of Feedforward Neural Networks (FNNs) and Convolutional Neural Networks (CNNs) to avoid vanishing gradients and maintain steady information flow. In contrast, within the GNN context classical initializations disregard the impact of the input graph structure and message passing on variance. In this paper, we analyze the variance of forward and backward propagation across GNN layers and show that the variance instability of GNN initializations comes from the combined effect of the activation function, hidden dimension, graph structure and message passing. To better account for these influence factors, we propose a new initialization method for Variance Instability Reduction within GNN Optimization (Virgo), which naturally tends to equate forward and backward variances across successive layers. We conduct comprehensive experiments on 15 datasets to show that Virgo can lead to superior model performance and more stable variance at initialization on node classification, link prediction and graph classification tasks. Codes are in https://github.com/LspongebobJH/virgo_icml2023.
Many Graph Neural Networks (GNNs) add self-loops to a graph to include feature information about a node itself at each layer. However, if the GNN consists of more than one layer, this information can return to its origin via cycles in the graph topology. Intuition suggests that this "backflow" of information should be larger in graphs with self-loops compared to graphs without. In this work, we counter this intuition and show that for certain GNN architectures, the information a node gains from itself can be smaller in graphs with self-loops compared to the same graphs without. We adopt an analytical approach for the study of statistical graph ensembles with a given degree sequence and show that this phenomenon, which we call the self-loop paradox, can depend both on the number of GNN layers $k$ and whether $k$ is even or odd. We experimentally validate our theoretical findings in a synthetic node classification task and investigate its practical relevance in 23 real-world graphs.
Graph contrastive learning has shown great promise when labeled data is scarce, but large unlabeled datasets are available. However, it often does not take uncertainty estimation into account. We show that a variational Bayesian neural network approach can be used to improve not only the uncertainty estimates but also the downstream performance on semi-supervised node-classification tasks. Moreover, we propose a new measure of uncertainty for contrastive learning, that is based on the disagreement in likelihood due to different positive samples.
Contrastive learning (CL) has emerged as a powerful framework for learning representations of images and text in a self-supervised manner while enhancing model robustness against adversarial attacks. More recently, researchers have extended the principles of contrastive learning to graph-structured data, giving birth to the field of graph contrastive learning (GCL). However, whether GCL methods can deliver the same advantages in adversarial robustness as their counterparts in the image and text domains remains an open question. In this paper, we introduce a comprehensive robustness evaluation protocol tailored to assess the robustness of GCL models. We subject these models to adaptive adversarial attacks targeting the graph structure, specifically in the evasion scenario. We evaluate node and graph classification tasks using diverse real-world datasets and attack strategies. With our work, we aim to offer insights into the robustness of GCL methods and hope to open avenues for potential future research directions.