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Graph neural networks (GNNs) have demonstrated a significant boost in prediction performance on graph data. At the same time, the predictions made by these models are often hard to interpret. In that regard, many efforts have been made to…

Machine Learning · Computer Science 2023-05-24 Yiqiao Li , Jianlong Zhou , Sunny Verma , Fang Chen

Graph neural networks (GNNs) are powerful tools on graph data. However, their predictions are mis-calibrated and lack interpretability, limiting their adoption in critical applications. To address this issue, we propose a new…

Machine Learning · Computer Science 2025-08-26 Lingkai Kong , Haotian Sun , Yuchen Zhuang , Haorui Wang , Wenhao Mu , Chao Zhang

Graph Neural Network (GNN) has achieved state-of-the-art performance in various high-stake prediction tasks, but multiple layers of aggregations on graphs with irregular structures make GNN a less interpretable model. Prior methods use…

Machine Learning · Computer Science 2021-11-30 Yifei Liu , Chao Chen , Yazheng Liu , Xi Zhang , Sihong Xie

Graph Neural Networks (GNNs) have achieved state-of-the-art performance in solving graph classification tasks. However, most GNN architectures aggregate information from all nodes and edges in a graph, regardless of their relevance to the…

Machine Learning · Statistics 2024-04-19 Pablo Sanchez-Martin , Kinaan Aamir Khan , Isabel Valera

Vulnerability detection is crucial for ensuring the security and reliability of software systems. Recently, Graph Neural Networks (GNNs) have emerged as a prominent code embedding approach for vulnerability detection, owing to their ability…

Software Engineering · Computer Science 2024-07-16 Zhaoyang Chu , Yao Wan , Qian Li , Yang Wu , Hongyu Zhang , Yulei Sui , Guandong Xu , Hai Jin

This paper presents Gem, a model-agnostic approach for providing interpretable explanations for any GNNs on various graph learning tasks. Specifically, we formulate the problem of providing explanations for the decisions of GNNs as a causal…

Machine Learning · Computer Science 2021-06-08 Wanyu Lin , Hao Lan , Baochun Li

Graph Neural Networks (GNNs) achieve outstanding performance across graph-based tasks but remain difficult to interpret. In this paper, we revisit foundational assumptions underlying model-level explanation methods for GNNs, namely: (1)…

Machine Learning · Computer Science 2025-06-10 Hsiao-Ying Lu , Yiran Li , Ujwal Pratap Krishna Kaluvakolanu Thyagarajan , Kwan-Liu Ma

Similarity search is a fundamental task for exploiting information in various applications dealing with graph data, such as citation networks or knowledge graphs. While this task has been intensively approached from heuristics to graph…

Machine Learning · Computer Science 2026-05-12 Daniel Daza , Cuong Xuan Chu , Trung-Kien Tran , Daria Stepanova , Michael Cochez , Paul Groth

Explanations provided by Self-explainable Graph Neural Networks (SE-GNNs) are fundamental for understanding the model's inner workings and for identifying potential misuse of sensitive attributes. Although recent works have highlighted that…

Machine Learning · Computer Science 2026-03-03 Steve Azzolin , Stefano Teso , Bruno Lepri , Andrea Passerini , Sagar Malhotra

Real data collected from different applications that have additional topological structures and connection information are amenable to be represented as a weighted graph. Considering the node labeling problem, Graph Neural Networks (GNNs)…

Social and Information Networks · Computer Science 2020-02-06 Xiaoxiao Li , Joao Saude

Graph Neural Networks (GNNs) are proposed without considering the agnostic distribution shifts between training and testing graphs, inducing the degeneration of the generalization ability of GNNs on Out-Of-Distribution (OOD) settings. The…

Machine Learning · Computer Science 2024-03-12 Shaohua Fan , Xiao Wang , Chuan Shi , Peng Cui , Bai Wang

One significant challenge of exploiting Graph neural networks (GNNs) in real-life scenarios is that they are always treated as black boxes, therefore leading to the requirement of interpretability. To address this, model-level…

Machine Learning · Computer Science 2025-09-22 Xiao Yue , Guangzhi Qu , Lige Gan

Graph Neural Networks (GNNs) are a powerful technique for machine learning on graph-structured data, yet they pose challenges in interpretability. Existing GNN explanation methods usually yield technical outputs, such as subgraphs and…

Machine Learning · Computer Science 2025-04-09 Mateusz Cedro , David Martens

Graph Neural Networks (GNNs) are powerful machine learning prediction models on graph-structured data. However, GNNs lack rigorous uncertainty estimates, limiting their reliable deployment in settings where the cost of errors is…

Machine Learning · Computer Science 2023-11-01 Kexin Huang , Ying Jin , Emmanuel Candès , Jure Leskovec

It has been observed that message-passing graph neural networks (GNN) sometimes struggle to maintain a healthy balance between the efficient/scalable modeling of long-range dependencies across nodes while avoiding unintended consequences…

Machine Learning · Computer Science 2025-05-21 Yongyi Yang , Tang Liu , Yangkun Wang , Zengfeng Huang , David Wipf

Graph neural networks (GNNs) find applications in various domains such as computational biology, natural language processing, and computer security. Owing to their popularity, there is an increasing need to explain GNN predictions since…

Machine Learning · Computer Science 2022-11-14 Mert Kosan , Zexi Huang , Sourav Medya , Sayan Ranu , Ambuj Singh

Graph Neural Networks (GNNs) demonstrate their significance by effectively modeling complex interrelationships within graph-structured data. To enhance the credibility and robustness of GNNs, it becomes exceptionally crucial to bolster…

Machine Learning · Computer Science 2023-12-18 Hang Gao , Chengyu Yao , Jiangmeng Li , Lingyu Si , Yifan Jin , Fengge Wu , Changwen Zheng , Huaping Liu

When engaging in end-to-end graph representation learning with Graph Neural Networks (GNNs), the intricate causal relationships and rules inherent in graph data pose a formidable challenge for the model in accurately capturing authentic…

Machine Learning · Computer Science 2024-06-14 Hang Gao , Peng Qiao , Yifan Jin , Fengge Wu , Jiangmeng Li , Changwen Zheng

Despite the recent progress in Graph Neural Networks (GNNs), it remains challenging to explain the predictions made by GNNs. Existing explanation methods mainly focus on post-hoc explanations where another explanatory model is employed to…

Machine Learning · Computer Science 2021-12-03 Zaixi Zhang , Qi Liu , Hao Wang , Chengqiang Lu , Cheekong Lee

Graph Neural Networks (GNNs) have become a building block in graph data processing, with wide applications in critical domains. The growing needs to deploy GNNs in high-stakes applications necessitate explainability for users in the…