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1. Identity-Aware Graph Neural Networks

   You, Jiaxuan; Gomes-Selman, Jonathan; Ying, Rex; Leskovec, Jure. (January 2021, Conference on Artificial Intelligence (AAAI))

   null (Ed.)

   Message passing Graph Neural Networks (GNNs) provide a powerful modeling framework for relational data. However, the expressive power of existing GNNs is upper-bounded by the 1-Weisfeiler-Lehman (1-WL) graph isomorphism test, which means GNNs that are not able to predict node clustering coefficients and shortest path distances, and cannot differentiate between different d regular graphs. Here we develop a class of message passing GNNs, named Identity-aware Graph Neural Networks (ID-GNNs), with greater expressive power than the 1-WL test. ID-GNN offers a minimal but powerful solution to limitations of existing GNNs. ID-GNN extends existing GNN architectures by inductively considering nodes’ identities during message passing. To embed a given node, IDGNN first extracts the ego network centered at the node, then conducts rounds of heterogeneous message passing, where different sets of parameters are applied to the center node than to other surrounding nodes in the ego network. We further propose a simplified but faster version of ID-GNN that injects node identity information as augmented node features. Altogether, both versions of ID GNN represent general extensions of message passing GNNs, where experiments show that transforming existing GNNs to ID-GNNs yields on average 40% accuracy improvement on challenging node, edge, and graph property prediction tasks; 3% accuracy improvement on node and graph classification benchmarks; and 15% ROC AUC improvement on real-world link prediction tasks. Additionally, ID-GNNs demonstrate improved or comparable performance over other task-specific graph networks. 

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2. Identity-aware Graph Neural Networks

   You, Jiaxuan; Gomes-Selman, Jonathan; Ying, Rex; Leskovec, Jure (January 2021, Proceedings of the AAAI Conference on Artificial Intelligence)

   null (Ed.)

   Message passing Graph Neural Networks (GNNs) provide a powerful modeling framework for relational data. However, the expressive power of existing GNNs is upper-bounded by the 1-Weisfeiler-Lehman (1-WL) graph isomorphism test, which means GNNs that are not able to predict node clustering coefficients and shortest path distances, and cannot differentiate between different d-regular graphs. Here we develop a class of message passing GNNs, named Identity-aware Graph Neural Networks (ID-GNNs), with greater expressive power than the 1-WL test. ID-GNN offers a minimal but powerful solution to limitations of existing GNNs. ID-GNN extends existing GNN architectures by inductively considering nodes’ identities during message passing. To embed a given node, IDGNN first extracts the ego network centered at the node, then conducts rounds of heterogeneous message passing, where different sets of parameters are applied to the center node than to other surrounding nodes in the ego network. We further propose a simplified but faster version of ID-GNN that injects node identity information as augmented node features. Altogether, both versions of ID-GNN represent general extensions of message passing GNNs, where experiments show that transforming existing GNNs to ID-GNNs yields on average 40% accuracy improvement on challenging node, edge, and graph property prediction tasks; 3% accuracy improvement on node and graph classification benchmarks; and 15% ROC AUC improvement on real-world link prediction tasks. Additionally, ID-GNNs demonstrate improved or comparable performance over other task-specific graph networks. 

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3. Adversarial Attacks on Graph Neural Networks via Node Injections: A Hierarchical Reinforcement Learning Approach

   https://doi.org/10.1145/3366423.3380149  

   Sun, Yiwei; Wang, Suhang; Tang, Xianfeng; Hsieh, Tsung-Yu; Honavar, Vasant G. (January 2020, Proceedings of The Web Conference 2020 (WWW '20))

   Graph Neural Networks (GNN) offer the powerful approach to node classification in complex networks across many domains including social media, E-commerce, and FinTech. However, recent studies show that GNNs are vulnerable to attacks aimed at adversely impacting their node classification performance. Existing studies of adversarial attacks on GNN focus primarily on manipulating the connectivity between existing nodes, a task that requires greater effort on the part of the attacker in real-world applications. In contrast, it is much more expedient on the part of the attacker to inject adversarial nodes, e.g., fake profiles with forged links, into existing graphs so as to reduce the performance of the GNN in classifying existing nodes. Hence, we consider a novel form of node injection poisoning attacks on graph data. We model the key steps of a node injection attack, e.g., establishing links between the injected adversarial nodes and other nodes, choosing the label of an injected node, etc. by a Markov Decision Process. We propose a novel reinforcement learning method for Node Injection Poisoning Attacks (NIPA), to sequentially modify the labels and links of the injected nodes, without changing the connectivity between existing nodes. Specifically, we introduce a hierarchical Q-learning network to manipulate the labels of the adversarial nodes and their links with other nodes in the graph, and design an appropriate reward function to guide the reinforcement learning agent to reduce the node classification performance of GNN. The results of the experiments show that NIPA is consistently more effective than the baseline node injection attack methods for poisoning graph data on three benchmark datasets. 

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4. Edge Prompt Tuning for Graph Neural Networks

   Fu, Xingbo; He, Yinhan; Li, Jundong (April 2025, International Conference on Learning Representations)

   Pre-training powerful Graph Neural Networks (GNNs) with unlabeled graph data in a self-supervised manner has emerged as a prominent technique in recent years. However, inevitable objective gaps often exist between pre-training and downstream tasks. To bridge this gap, graph prompt tuning techniques design and learn graph prompts by manipulating input graphs or reframing downstream tasks as pre-training tasks without fine-tuning the pre-trained GNN models. While recent graph prompt tuning methods have proven effective in adapting pre-trained GNN models for downstream tasks, they overlook the crucial role of edges in graph prompt design, which can significantly affect the quality of graph representations for downstream tasks. In this study, we propose EdgePrompt, a simple yet effective graph prompt tuning method from the perspective of edges. Unlike previous studies that design prompt vectors on node features, EdgePrompt manipulates input graphs by learning additional prompt vectors for edges and incorporates the edge prompts through message passing in the pre-trained GNN models to better embed graph structural information for downstream tasks. Our method is compatible with prevalent GNN architectures pre-trained under various pre-training strategies and is universal for different downstream tasks. We provide comprehensive theoretical analyses of our method regarding its capability of handling node classification and graph classification as downstream tasks. Extensive experiments on ten graph datasets under four pre-training strategies demonstrate the superiority of our proposed method against six baselines. 

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5. Subgraph Structure Membership Inference Attacks against Graph Neural Networks

   https://doi.org/10.56553/popets-2024-0116  

   Wang, Xiuling; Wang, Wendy Hui (October 2024, Proceedings on Privacy Enhancing Technologies)

   Graph Neural Networks (GNNs) have been widely applied to various applications across different domains. However, recent studies have shown that GNNs are susceptible to the membership inference attacks (MIAs) which aim to infer if some particular data samples were included in the model’s training data. While most previous MIAs have focused on inferring the membership of individual nodes and edges within the training graph, we introduce a novel form of membership inference attack called the Structure Membership Inference Attack (SMIA) which aims to determine whether a given set of nodes corresponds to a particular target structure, such as a clique or a multi-hop path, within the original training graph. To address this issue, we present novel black-box SMIA attacks that leverage the prediction outputs generated by the target GNN model for inference. Our approach involves training a three-label classifier, which, in combination with shadow training, aids in enabling the inference attack. Our extensive experimental evaluation of three representative GNN models and three real-world graph datasets demonstrates that our proposed attacks consistently outperform three baseline methods, including the one that employs the conventional link membership inference attacks to infer the subgraph structure. Additionally, we design a defense mechanism that introduces perturbations to the node embeddings thus influencing the corresponding prediction outputs by the target model. Our defense selectively perturbs dimensions within the node embeddings that have the least impact on the model's accuracy. Our empirical results demonstrate that the defense effectiveness of our approach is comparable with two established defense techniques that employ differential privacy. Moreover, our method achieves a better trade-off between defense strength and the accuracy of the target model compared to the two existing defense methods. 

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