Graph Neural Networks (GNNs) are a powerful tool for handling structured graph data and addressing tasks such as node classification, graph classification, and clustering. However, the sparse nature of GNN computation poses new challenges for performance optimization compared to traditional deep neural networks. We address these challenges by providing a unified view of GNN computation, I/O, and memory. By analyzing the computational graphs of the Graph Convolutional Network (GCN) and Graph Attention (GAT) layers -- two widely used GNN layers -- we propose alternative computation strategies. We present adaptive operator reordering with caching, which achieves a speedup of up to 2.43x for GCN compared to the current state-of-the-art. Furthermore, an exploration of different caching schemes for GAT yields a speedup of up to 1.94x. The proposed optimizations save memory, are easily implemented across various hardware platforms, and have the potential to alleviate performance bottlenecks in training large-scale GNN models.
Unsupervised GAD methods assume the lack of anomaly labels, i.e., whether a node is anomalous or not. One common observation we made from previous unsupervised methods is that they not only assume the absence of such anomaly labels, but also the absence of class labels (the class a node belongs to used in a general node classification task). In this work, we study the utility of class labels for unsupervised GAD; in particular, how they enhance the detection of structural anomalies. To this end, we propose a Class Label-aware Graph Anomaly Detection framework (CLAD) that utilizes a limited amount of labeled nodes to enhance the performance of unsupervised GAD. Extensive experiments on ten datasets demonstrate the superior performance of CLAD in comparison to existing unsupervised GAD methods, even in the absence of ground-truth class label information. The source code for CLAD is available at \url{https://github.com/jhkim611/CLAD}.
Graph transformers need strong inductive biases to derive meaningful attention scores. Yet, current methods often fall short in capturing longer ranges, hierarchical structures, or community structures, which are common in various graphs such as molecules, social networks, and citation networks. This paper presents a Hierarchical Distance Structural Encoding (HDSE) method to model node distances in a graph, focusing on its multi-level, hierarchical nature. We introduce a novel framework to seamlessly integrate HDSE into the attention mechanism of existing graph transformers, allowing for simultaneous application with other positional encodings. To apply graph transformers with HDSE to large-scale graphs, we further propose a high-level HDSE that effectively biases the linear transformers towards graph hierarchies. We theoretically prove the superiority of HDSE over shortest path distances in terms of expressivity and generalization. Empirically, we demonstrate that graph transformers with HDSE excel in graph classification, regression on 7 graph-level datasets, and node classification on 11 large-scale graphs, including those with up to a billion nodes.
We analyse the geometric instability of embeddings produced by graph neural networks (GNNs). Existing methods are only applicable for small graphs and lack context in the graph domain. We propose a simple, efficient and graph-native Graph Gram Index (GGI) to measure such instability which is invariant to permutation, orthogonal transformation, translation and order of evaluation. This allows us to study the varying instability behaviour of GNN embeddings on large graphs for both node classification and link prediction.
Graph neural networks (GNNs) are increasingly used in critical human applications for predicting node labels in attributed graphs. Their ability to aggregate features from nodes' neighbors for accurate classification also has the capacity to exacerbate existing biases in data or to introduce new ones towards members from protected demographic groups. Thus, it is imperative to quantify how GNNs may be biased and to what extent their harmful effects may be mitigated. To this end, we propose two new GNN-agnostic interventions namely, (i) PFR-AX which decreases the separability between nodes in protected and non-protected groups, and (ii) PostProcess which updates model predictions based on a blackbox policy to minimize differences between error rates across demographic groups. Through a large set of experiments on four datasets, we frame the efficacies of our approaches (and three variants) in terms of their algorithmic fairness-accuracy tradeoff and benchmark our results against three strong baseline interventions on three state-of-the-art GNN models. Our results show that no single intervention offers a universally optimal tradeoff, but PFR-AX and PostProcess provide granular control and improve model confidence when correctly predicting positive outcomes for nodes in protected groups.
Graph representation learning (GRL) methods, such as graph neural networks and graph transformer models, have been successfully used to analyze graph-structured data, mainly focusing on node classification and link prediction tasks. However, the existing studies mostly only consider local connectivity while ignoring long-range connectivity and the roles of nodes. In this paper, we propose Unified Graph Transformer Networks (UGT) that effectively integrate local and global structural information into fixed-length vector representations. First, UGT learns local structure by identifying the local substructures and aggregating features of the $k$-hop neighborhoods of each node. Second, we construct virtual edges, bridging distant nodes with structural similarity to capture the long-range dependencies. Third, UGT learns unified representations through self-attention, encoding structural distance and $p$-step transition probability between node pairs. Furthermore, we propose a self-supervised learning task that effectively learns transition probability to fuse local and global structural features, which could then be transferred to other downstream tasks. Experimental results on real-world benchmark datasets over various downstream tasks showed that UGT significantly outperformed baselines that consist of state-of-the-art models. In addition, UGT reaches the expressive power of the third-order Weisfeiler-Lehman isomorphism test (3d-WL) in distinguishing non-isomorphic graph pairs. The source code is available at https://github.com/NSLab-CUK/Unified-Graph-Transformer.
Message passing neural networks have shown a lot of success on graph-structured data. However, there are many instances where message passing can lead to over-smoothing or fail when neighboring nodes belong to different classes. In this work, we introduce a simple yet general framework for improving learning in message passing neural networks. Our approach essentially upsamples edges in the original graph by adding "slow nodes" at each edge that can mediate communication between a source and a target node. Our method only modifies the input graph, making it plug-and-play and easy to use with existing models. To understand the benefits of slowing down message passing, we provide theoretical and empirical analyses. We report results on several supervised and self-supervised benchmarks, and show improvements across the board, notably in heterophilic conditions where adjacent nodes are more likely to have different labels. Finally, we show how our approach can be used to generate augmentations for self-supervised learning, where slow nodes are randomly introduced into different edges in the graph to generate multi-scale views with variable path lengths.
Graph Active Learning (GAL), which aims to find the most informative nodes in graphs for annotation to maximize the Graph Neural Networks (GNNs) performance, has attracted many research efforts but remains non-trivial challenges. One major challenge is that existing GAL strategies may introduce semantic confusion to the selected training set, particularly when graphs are noisy. Specifically, most existing methods assume all aggregating features to be helpful, ignoring the semantically negative effect between inter-class edges under the message-passing mechanism. In this work, we present Semantic-aware Active learning framework for Graphs (SAG) to mitigate the semantic confusion problem. Pairwise similarities and dissimilarities of nodes with semantic features are introduced to jointly evaluate the node influence. A new prototype-based criterion and query policy are also designed to maintain diversity and class balance of the selected nodes, respectively. Extensive experiments on the public benchmark graphs and a real-world financial dataset demonstrate that SAG significantly improves node classification performances and consistently outperforms previous methods. Moreover, comprehensive analysis and ablation study also verify the effectiveness of the proposed framework.
Recently, Zero-Shot Node Classification (ZNC) has been an emerging and crucial task in graph data analysis. This task aims to predict nodes from unseen classes which are unobserved in the training process. Existing work mainly utilizes Graph Neural Networks (GNNs) to associate features' prototypes and labels' semantics thus enabling knowledge transfer from seen to unseen classes. However, the multi-faceted semantic orientation in the feature-semantic alignment has been neglected by previous work, i.e. the content of a node usually covers diverse topics that are relevant to the semantics of multiple labels. It's necessary to separate and judge the semantic factors that tremendously affect the cognitive ability to improve the generality of models. To this end, we propose a Knowledge-Aware Multi-Faceted framework (KMF) that enhances the richness of label semantics via the extracted KG (Knowledge Graph)-based topics. And then the content of each node is reconstructed to a topic-level representation that offers multi-faceted and fine-grained semantic relevancy to different labels. Due to the particularity of the graph's instance (i.e., node) representation, a novel geometric constraint is developed to alleviate the problem of prototype drift caused by node information aggregation. Finally, we conduct extensive experiments on several public graph datasets and design an application of zero-shot cross-domain recommendation. The quantitative results demonstrate both the effectiveness and generalization of KMF with the comparison of state-of-the-art baselines.
In the past, the dichotomy between homophily and heterophily has inspired research contributions toward a better understanding of Deep Graph Networks' inductive bias. In particular, it was believed that homophily strongly correlates with better node classification predictions of message-passing methods. More recently, however, researchers pointed out that such dichotomy is too simplistic as we can construct node classification tasks where graphs are completely heterophilic but the performances remain high. Most of these works have also proposed new quantitative metrics to understand when a graph structure is useful, which implicitly or explicitly assume the correlation between node features and target labels. Our work empirically investigates what happens when this strong assumption does not hold, by formalising two generative processes for node classification tasks that allow us to build and study ad-hoc problems. To quantitatively measure the influence of the node features on the target labels, we also use a metric we call Feature Informativeness. We construct six synthetic tasks and evaluate the performance of six models, including structure-agnostic ones. Our findings reveal that previously defined metrics are not adequate when we relax the above assumption. Our contribution to the workshop aims at presenting novel research findings that could help advance our understanding of the field.
Learning graph embeddings is a crucial task in graph mining tasks. An effective graph embedding model can learn low-dimensional representations from graph-structured data for data publishing benefiting various downstream applications such as node classification, link prediction, etc. However, recent studies have revealed that graph embeddings are susceptible to attribute inference attacks, which allow attackers to infer private node attributes from the learned graph embeddings. To address these concerns, privacy-preserving graph embedding methods have emerged, aiming to simultaneously consider primary learning and privacy protection through adversarial learning. However, most existing methods assume that representation models have access to all sensitive attributes in advance during the training stage, which is not always the case due to diverse privacy preferences. Furthermore, the commonly used adversarial learning technique in privacy-preserving representation learning suffers from unstable training issues. In this paper, we propose a novel approach called Private Variational Graph AutoEncoders (PVGAE) with the aid of independent distribution penalty as a regularization term. Specifically, we split the original variational graph autoencoder (VGAE) to learn sensitive and non-sensitive latent representations using two sets of encoders. Additionally, we introduce a novel regularization to enforce the independence of the encoders. We prove the theoretical effectiveness of regularization from the perspective of mutual information. Experimental results on three real-world datasets demonstrate that PVGAE outperforms other baselines in private embedding learning regarding utility performance and privacy protection.
Existing studies for applying the mixup technique on graphs mainly focus on graph classification tasks, while the research in node classification is still under-explored. In this paper, we propose a novel mixup augmentation for node classification called Structural Mixup (S-Mixup). The core idea is to take into account the structural information while mixing nodes. Specifically, S-Mixup obtains pseudo-labels for unlabeled nodes in a graph along with their prediction confidence via a Graph Neural Network (GNN) classifier. These serve as the criteria for the composition of the mixup pool for both inter and intra-class mixups. Furthermore, we utilize the edge gradient obtained from the GNN training and propose a gradient-based edge selection strategy for selecting edges to be attached to the nodes generated by the mixup. Through extensive experiments on real-world benchmark datasets, we demonstrate the effectiveness of S-Mixup evaluated on the node classification task. We observe that S-Mixup enhances the robustness and generalization performance of GNNs, especially in heterophilous situations. The source code of S-Mixup can be found at \url{https://github.com/SukwonYun/S-Mixup}
Recently, Graph Neural Networks (GNNs) have shown promising performance in tasks on dynamic graphs such as node classification, link prediction and graph regression. However, few work has studied the temporal edge regression task which has important real-world applications. In this paper, we explore the application of GNNs to edge regression tasks in both static and dynamic settings, focusing on predicting food and agriculture trade values between nations. We introduce three simple yet strong baselines and comprehensively evaluate one static and three dynamic GNN models using the UN Trade dataset. Our experimental results reveal that the baselines exhibit remarkably strong performance across various settings, highlighting the inadequacy of existing GNNs. We also find that TGN outperforms other GNN models, suggesting TGN is a more appropriate choice for edge regression tasks. Moreover, we note that the proportion of negative edges in the training samples significantly affects the test performance. The companion source code can be found at: https://github.com/scylj1/GNN_Edge_Regression.
Semi-Supervised image classification is one of the most fundamental problem in computer vision, which significantly reduces the need for human labor. In this paper, we introduce a new semi-supervised learning algorithm - SimMatchV2, which formulates various consistency regularizations between labeled and unlabeled data from the graph perspective. In SimMatchV2, we regard the augmented view of a sample as a node, which consists of a label and its corresponding representation. Different nodes are connected with the edges, which are measured by the similarity of the node representations. Inspired by the message passing and node classification in graph theory, we propose four types of consistencies, namely 1) node-node consistency, 2) node-edge consistency, 3) edge-edge consistency, and 4) edge-node consistency. We also uncover that a simple feature normalization can reduce the gaps of the feature norm between different augmented views, significantly improving the performance of SimMatchV2. Our SimMatchV2 has been validated on multiple semi-supervised learning benchmarks. Notably, with ResNet-50 as our backbone and 300 epochs of training, SimMatchV2 achieves 71.9\% and 76.2\% Top-1 Accuracy with 1\% and 10\% labeled examples on ImageNet, which significantly outperforms the previous methods and achieves state-of-the-art performance. Code and pre-trained models are available at \href{https://github.com/mingkai-zheng/SimMatchV2}{https://github.com/mingkai-zheng/SimMatchV2}.
Representing nodes in a network as dense vectors node embeddings is important for understanding a given network and solving many downstream tasks. In particular, for weighted homophilous graphs where similar nodes are connected with larger edge weights, we desire node embeddings where node pairs with strong weights have closer embeddings. Although random walk based node embedding methods like node2vec and node2vec+ do work for weighted networks via including edge weights in the walk transition probabilities, our experiments show that the embedding result does not adequately reflect edge weights. In this paper, we propose ARGEW (Augmentation of Random walks by Graph Edge Weights), a novel augmentation method for random walks that expands the corpus in such a way that nodes with larger edge weights end up with closer embeddings. ARGEW can work with any random walk based node embedding method, because it is independent of the random sampling strategy itself and works on top of the already-performed walks. With several real-world networks, we demonstrate that with ARGEW, compared to not using it, the desired pattern that node pairs with larger edge weights have closer embeddings is much clearer. We also examine ARGEW's performance in node classification: node2vec with ARGEW outperforms pure node2vec and is not sensitive to hyperparameters (i.e. consistently good). In fact, it achieves similarly good results as supervised GCN, even without any node feature or label information during training. Finally, we explain why ARGEW works consistently well by exploring the coappearance distributions using a synthetic graph with clear structural roles.
Node classification is the task of predicting the labels of unlabeled nodes in a graph. State-of-the-art methods based on graph neural networks achieve excellent performance when all labels are available during training. But in real-life, models are often applied on data with new classes, which can lead to massive misclassification and thus significantly degrade performance. Hence, developing open-set classification methods is crucial to determine if a given sample belongs to a known class. Existing methods for open-set node classification generally use transductive learning with part or all of the features of real unseen class nodes to help with open-set classification. In this paper, we propose a novel generative open-set node classification method, i.e. $\mathcal{G}^2Pxy$, which follows a stricter inductive learning setting where no information about unknown classes is available during training and validation. Two kinds of proxy unknown nodes, inter-class unknown proxies and external unknown proxies are generated via mixup to efficiently anticipate the distribution of novel classes. Using the generated proxies, a closed-set classifier can be transformed into an open-set one, by augmenting it with an extra proxy classifier. Under the constraints of both cross entropy loss and complement entropy loss, $\mathcal{G}^2Pxy$ achieves superior effectiveness for unknown class detection and known class classification, which is validated by experiments on benchmark graph datasets. Moreover, $\mathcal{G}^2Pxy$ does not have specific requirement on the GNN architecture and shows good generalizations.
Training Graph Neural Networks (GNNs) on real-world graphs consisting of billions of nodes and edges is quite challenging, primarily due to the substantial memory needed to store the graph and its intermediate node and edge features, and there is a pressing need to speed up the training process. A common approach to achieve speed up is to divide the graph into many smaller subgraphs, which are then distributed across multiple GPUs in one or more machines and processed in parallel. However, existing distributed methods require frequent and substantial cross-GPU communication, leading to significant time overhead and progressively diminishing scalability. Here, we introduce CoFree-GNN, a novel distributed GNN training framework that significantly speeds up the training process by implementing communication-free training. The framework utilizes a Vertex Cut partitioning, i.e., rather than partitioning the graph by cutting the edges between partitions, the Vertex Cut partitions the edges and duplicates the node information to preserve the graph structure. Furthermore, the framework maintains high model accuracy by incorporating a reweighting mechanism to handle a distorted graph distribution that arises from the duplicated nodes. We also propose a modified DropEdge technique to further speed up the training process. Using an extensive set of experiments on real-world networks, we demonstrate that CoFree-GNN speeds up the GNN training process by up to 10 times over the existing state-of-the-art GNN training approaches.
Textual graphs (TGs) are graphs whose nodes correspond to text (sentences or documents), which are widely prevalent. The representation learning of TGs involves two stages: (i) unsupervised feature extraction and (ii) supervised graph representation learning. In recent years, extensive efforts have been devoted to the latter stage, where Graph Neural Networks (GNNs) have dominated. However, the former stage for most existing graph benchmarks still relies on traditional feature engineering techniques. More recently, with the rapid development of language models (LMs), researchers have focused on leveraging LMs to facilitate the learning of TGs, either by jointly training them in a computationally intensive framework (merging the two stages), or designing complex self-supervised training tasks for feature extraction (enhancing the first stage). In this work, we present SimTeG, a frustratingly Simple approach for Textual Graph learning that does not innovate in frameworks, models, and tasks. Instead, we first perform supervised parameter-efficient fine-tuning (PEFT) on a pre-trained LM on the downstream task, such as node classification. We then generate node embeddings using the last hidden states of finetuned LM. These derived features can be further utilized by any GNN for training on the same task. We evaluate our approach on two fundamental graph representation learning tasks: node classification and link prediction. Through extensive experiments, we show that our approach significantly improves the performance of various GNNs on multiple graph benchmarks.
Traditional Graph Neural Network (GNN), as a graph representation learning method, is constrained by label information. However, Graph Contrastive Learning (GCL) methods, which tackle the label problem effectively, mainly focus on the feature information of the global graph or small subgraph structure (e.g., the first-order neighborhood). In the paper, we propose a Local Structure-aware Graph Contrastive representation Learning method (LS-GCL) to model the structural information of nodes from multiple views. Specifically, we construct the semantic subgraphs that are not limited to the first-order neighbors. For the local view, the semantic subgraph of each target node is input into a shared GNN encoder to obtain the target node embeddings at the subgraph-level. Then, we use a pooling function to generate the subgraph-level graph embeddings. For the global view, considering the original graph preserves indispensable semantic information of nodes, we leverage the shared GNN encoder to learn the target node embeddings at the global graph-level. The proposed LS-GCL model is optimized to maximize the common information among similar instances at three various perspectives through a multi-level contrastive loss function. Experimental results on five datasets illustrate that our method outperforms state-of-the-art graph representation learning approaches for both node classification and link prediction tasks.
Federated learning enables collaborative training of machine learning models by keeping the raw data of the involved workers private. Three of its main objectives are to improve the models' privacy, security, and scalability. Vertical Federated Learning (VFL) offers an efficient cross-silo setting where a few parties collaboratively train a model without sharing the same features. In such a scenario, classification labels are commonly considered sensitive information held exclusively by one (active) party, while other (passive) parties use only their local information. Recent works have uncovered important flaws of VFL, leading to possible label inference attacks under the assumption that the attacker has some, even limited, background knowledge on the relation between labels and data. In this work, we are the first (to the best of our knowledge) to investigate label inference attacks on VFL using a zero-background knowledge strategy. To formulate our proposal, we focus on Graph Neural Networks (GNNs) as a target model for the underlying VFL. In particular, we refer to node classification tasks, which are widely studied, and GNNs have shown promising results. Our proposed attack, BlindSage, provides impressive results in the experiments, achieving nearly 100% accuracy in most cases. Even when the attacker has no information about the used architecture or the number of classes, the accuracy remains above 90% in most instances. Finally, we observe that well-known defenses cannot mitigate our attack without affecting the model's performance on the main classification task.