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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

Graph neural networks (GNNs) provide important prospective insights in applications such as social behavior analysis and financial risk analysis based on their powerful learning capabilities on graph data. Nevertheless, GNNs' predictive…

Machine Learning · Computer Science 2024-12-23 Yuecen Wei , Xingcheng Fu , Lingyun Liu , Qingyun Sun , Hao Peng , Chunming Hu

While graph neural networks (GNNs) have been shown to perform well on graph-based data from a variety of fields, they suffer from a lack of transparency and accountability, which hinders trust and consequently the deployment of such models…

Machine Learning · Computer Science 2021-07-27 Lucie Charlotte Magister , Dmitry Kazhdan , Vikash Singh , Pietro Liò

Interpretable brain network models for disease prediction are of great value for the advancement of neuroscience. GNNs are promising to model complicated network data, but they are prone to overfitting and suffer from poor interpretability,…

Machine Learning · Computer Science 2021-07-13 Hejie Cui , Wei Dai , Yanqiao Zhu , Xiaoxiao Li , Lifang He , Carl Yang

Graph Neural Networks (GNNs) are deep learning models that take graph data as inputs, and they are applied to various tasks such as traffic prediction and molecular property prediction. However, owing to the complexity of the GNNs, it has…

Machine Learning · Computer Science 2021-11-02 Tetsu Kasanishi , Xueting Wang , Toshihiko Yamasaki

Deep neural networks (DNNs) are increasingly being deployed in high-stakes applications, from self-driving cars to biometric authentication. However, their unpredictable and unreliable behaviors in real-world settings require new approaches…

Cryptography and Security · Computer Science 2025-10-01 Firas Ben Hmida , Abderrahmen Amich , Ata Kaboudi , Birhanu Eshete

Control Flow Graphs (CFGs) are critical for analyzing program execution and characterizing malware behavior. With the growing adoption of Graph Neural Networks (GNNs), CFG-based representations have proven highly effective for malware…

Cryptography and Security · Computer Science 2025-08-22 Hossein Shokouhinejad , Griffin Higgins , Roozbeh Razavi-Far , Hesamodin Mohammadian , Ali A. Ghorbani

Data-driven surrogate modeling has surged in capability in recent years with the emergence of graph neural networks (GNNs), which can operate directly on mesh-based representations of data. The goal of this work is to introduce an…

Machine Learning · Computer Science 2024-10-25 Shivam Barwey , Hojin Kim , Romit Maulik

Graph Neural Networks (GNNs) achieve strong performance on node classification tasks but remain difficult to interpret, particularly with respect to which input features drive their predictions. Existing global GNN explainers operate at the…

Machine Learning · Computer Science 2026-05-06 Rishi Raj Sahoo , Subhankar Mishra

Graph Neural Networks (GNNs) have emerged as an efficient alternative to convolutional approaches for vision tasks such as image classification, leveraging patch-based representations instead of raw pixels. These methods construct graphs…

Computer Vision and Pattern Recognition · Computer Science 2025-04-29 Nikolaos Chaidos , Angeliki Dimitriou , Nikolaos Spanos , Athanasios Voulodimos , Giorgos Stamou

Graph Neural Networks (GNNs) have emerged as a dominant paradigm for learning on graph-structured data, thanks to their ability to jointly exploit node features and relational information encoded in the graph topology. This joint modeling,…

Machine Learning · Computer Science 2025-12-30 Yongyu Wang

Explainability is crucial for the application of black-box Graph Neural Networks (GNNs) in critical fields such as healthcare, finance, cybersecurity, and more. Various feature attribution methods, especially the perturbation-based methods,…

Machine Learning · Computer Science 2024-12-31 Xingping Xian , Jianlu Liu , Chao Wang , Tao Wu , Shaojie Qiao , Xiaochuan Tang , Qun Liu

This study explores the effectiveness of graph neural networks (GNNs) for vulnerability detection in software code, utilizing a real-world dataset of Java vulnerability-fixing commits. The dataset's structure, based on the number of…

Cryptography and Security · Computer Science 2024-06-19 Ravil Mussabayev

Graph Neural Networks (GNNs) are increasingly adopted across domains such as molecular biology and social network analysis, yet their black-box nature hinders interpretability and trust. This is especially problematic in high-stakes…

Machine Learning · Computer Science 2026-03-05 Matteo De Sanctis , Riccardo De Sanctis , Stefano Faralli , Paola Velardi , Bardh Prenkaj

Despite the recent success of graph neural networks (GNN), common architectures often exhibit significant limitations, including sensitivity to oversmoothing, long-range dependencies, and spurious edges, e.g., as can occur as a result of…

Machine Learning · Computer Science 2021-12-06 Yongyi Yang , Tang Liu , Yangkun Wang , Jinjing Zhou , Quan Gan , Zhewei Wei , Zheng Zhang , Zengfeng Huang , David Wipf

Trust evaluation assesses trust relationships between entities and facilitates decision-making. Machine Learning (ML) shows great potential for trust evaluation owing to its learning capabilities. In recent years, Graph Neural Networks…

Machine Learning · Computer Science 2024-02-06 Jie Wang , Zheng Yan , Jiahe Lan , Elisa Bertino , Witold Pedrycz

Graph Neural Networks (GNNs) have shown remarkable effectiveness in capturing abundant information in graph-structured data. However, the black-box nature of GNNs hinders users from understanding and trusting the models, thus leading to…

Machine Learning · Computer Science 2022-07-25 Jiaxuan Xie , Yezi Liu , Yanning Shen

Advances in machine learning have led to graph neural network-based methods for drug discovery, yielding promising results in molecular design, chemical synthesis planning, and molecular property prediction. However, current graph neural…

Quantitative Methods · Quantitative Biology 2021-07-13 Jiahua Rao , Shuangjia Zheng , Yuedong Yang

Detecting security vulnerabilities in source code remains challenging, particularly due to class imbalance in real-world datasets where vulnerable functions are under-represented. Existing learning-based methods often optimise for recall,…

Cryptography and Security · Computer Science 2025-07-24 Radowanul Haque , Aftab Ali , Sally McClean , Naveed Khan

The rapid expansion of Internet of Things (IoT) ecosystems has led to increasingly complex and heterogeneous network topologies. Traditional network monitoring and visualization tools rely on aggregated metrics or static representations,…