Graph Neural Networks

Also known as GNN

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Knowledge Graphs Meet Graph Neural Networks: A Comprehensive Survey
May 12, 2026Chengcheng Sun, Jiayun Tian, Cheng Zhai +5KG Construction Graph Neural Networks
School of Safety Engineering, China University of Mining and Technology, China · School of Computer Science and Technology, China University of Mining and Technology, China · State Key Laboratory of Coal Mine Disaster Prevention and Control, China University of Mining and Technology, China +1
Can Graphs Help Vision SSMs See Better?
May 11, 2026Dhruv Parikh, Anvitha Ramachandran, Haoyang Fan +3Graph Structure Learning Graph Neural Networks
USC · UT Austin · DEVCOM ARL Army Research Office, USA
Oversmoothing as Representation Degeneracy in Neural Sheaf Diffusion
May 11, 2026Arif Dönmez, Axel Mosig, Ellen Fritsche +1Graph Neural Networks Sheaf Neural Networks
IUF – Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany · DNTOX GmbH, Düsseldorf, Germany · Bioinformatics Group, Ruhr University Bochum, Bochum, Germany +1
Debiasing Message Passing to Mitigate Popularity Bias in GNN-based Collaborative Filtering
May 11, 2026Md Aminul Islam, Ahmed Sayeed Faruk, Sourav Medya +1Graph Neural Networks Message Passing Neural Networks
University of Illinois Chicago
On Improving Graph Neural Networks for QSAR by Pre-training on Extended-Connectivity Fingerprints
May 11, 2026Sam Money-Kyrle, Markus Dablander, Thierry Hanser +3Graph Neural Networks OOD Generalization
Department of Statistics, University of Oxford, 24-29 St Giles’, Oxford, OX1 3LB, United Kingdom. · Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford, OX2 6GG, United Kingdom. · Molecular Informatics and AI, Lhasa Limited, Granary Wharf House,May 2 Canal Wharf, Leeds, LS11 5PS, United Kingdom.
Content-Aware Attack Detection in LLM Agent Tool-Call Traffic: An Empirical Study of Features, Architectures, and Evaluation Protocols
May 11, 2026Sultan ZavrakData Leakage Graph Neural Networks
Department of Computer Engineering, Duzce University, Duzce, Turkey
QT-Net: Rethinking Evaluation of AI Models in Atomic Chemical Space
May 11, 2026Pablo Martínez Crespo, Stefano Ribes, Martin Rahm +6Graph Neural Networks Quantum Chemistry
Department of Computer Science and Engineering Chalmers University of Technology and University of Gothenburg · Department of Chemistry and Chemical Engineering Chalmers University of Technology · Technology Research Intel Corporation +3
The Polynomial Counting Capabilities of Message Passing Neural Networks
May 11, 2026Marco Sälzer, Pascal Bergsträßer, Anthony W. LinGraph Neural Networks Message Passing Neural Networks
1RPTU University Kaiserslautern-Landau · 2Max Planck Institute for Software Systems (MPI-SWS)
Efficient Hybrid CNN-GNN Architecture for Monocular Depth Estimation
May 11, 2026Ishan NarayanGraph Neural Networks Depth Estimation
IMCS Lab, CSIR-CSIO · Chandigarh 160030, India
Enabling Structure-Only Initialization and Out-of-Distribution Generalization in GNN-based Molecular Dynamics Simulators
May 10, 2026S. A. Shteingolts, Salman N. Salman, Dan MendelsGraph Neural Networks OOD Generalization
The Wolfson Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
RAwR: Role-Aware Rewiring via Approximate Equitable Partition
May 10, 2026Riccardo Porcedda, Giuseppe Squillace, Bastian Epping +4Graph Structure Learning Graph Neural Networks
Department of Excellence L’EMbeDS, Sant’Anna School of Advanced Studies, Pisa, Italy · Department of Computer Science, University of Pisa, Italy · IMT School for Advanced Studies, Lucca, Italy +4
GravityGraphSAGE: Link Prediction in Directed Attributed Graphs
May 10, 2026Riccardo Porcedda, Francesca Chiaromonte, Fabrizio Lillo +1Graph Neural Networks Graph Representation Learning
Department of Excellence L’EMbeDS, Sant’Anna School of Advanced Studies, Pisa, Italy · Department of Statistics and Huck Institutes of the Life Sciences, The Pennsylvania State University, USA · Class of Science, Scuola Normale Superiore, Pisa, Italy +1
Structural Interpretations of Protein Language Model Representations via Differentiable Graph Partitioning
May 9, 2026Siddhant Dutta, Edward Tan Beng Wai, Soumick Sarker +2Graph Neural Networks Protein Language Models
Nanyang Technological University, Singapore
Attention-based graph neural networks: a survey
May 9, 2026Chengcheng Sun, Chenhao Li, Xiang Lin +4Graph Attention Networks Graph Neural Networks
School of Computer Science and Technology, China University of Mining and Technology, Xuzhou, Jiangsu, 221116, China. · Mine Digitization Engineering Research Center, Ministry of Education of the People’s Republic of China, Xuzhou, Jiangsu, 221116, China.
Hierarchical Multi-Scale Graph Neural Networks: Scalable Heterophilous Learning with Oversmoothing and Oversquashing Mitigation
May 8, 2026Md Sazzad Hossen, Avimanyu SahooGraph Neural Networks Over-Squashing
University of Alabama in Huntsville, Huntsville, AL, USA.
GRAPHLCP: Structure-Aware Localized Conformal Prediction on Graphs
May 8, 2026Peyman Baghershahi, Fangxin Wang, Debmalya Mandal +1Graph Neural Networks Conformal Prediction
Department of Computer Science, University of Illinois Chicago · Department of Computer Science, University of Warwick
PPI-Net connects molecular protein interactions to functional processes in disease
May 8, 2026Kyle Higgins, Guadalupe Gonzalez, Dennis Veselkov +2Cancer Genomics Graph Neural Networks
Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK. · Prescient Design, Genentech, South San Francisco, CA, USA. · Department of Computing, Imperial College London, U.K.
PhySPRING: Structure-Preserving Reduction of Physics-Informed Twins via GNN
May 8, 2026Yixiong Jing, Xingyuan Chen, Guangming Wang +3Graph Neural Networks Robotics Simulation
University of Cambridge · Shanghai Jiao Tong University
GNN for Structural Displacement Prediction
May 8, 2026Hung-Fu Chang, Tzu-Kang Lin, Yung-Li ChengNeural Surrogate Modeling Graph Neural Networks
R. B. Annis School of Engineering University of Indianapolis Indianapolis United States · Department of Civil Engineering National Yang Ming Chiao Tung University Hsinchu Taiwan
Bilevel Graph Structure Learning, Revisited: Inner-Channel Origins of the Reported Gain
May 8, 2026Minkyoung Kim, Beakcheol JangGraph Structure Learning Graph Neural Networks
Graduate School of Information, Yonsei University
Graph Computation Meets Circuit Algebra: A Task-Aligned Analysis of Graph Neural Networks for Electronic Design Automation
May 8, 2026Hyunmog KimGraph Neural Networks Graph Representation Learning
Independent Researcher.
Trapping Attacker in Dilemma: Examining Internal Correlations and External Influences of Trigger for Defending GNN Backdoors
May 8, 2026Fan Yang, Binyan Xu, Di Tang +1Graph Neural Networks Backdoor Attacks
The Chinese University of Hong Kong · Sun Yat-Sen University
Learning Multi-Relational Graph Representations for DNA Methylation-Based Biological Age Estimation
May 8, 2026Qing Qing, Xikun Zhang, Zhongyuan Zhang +7Graph Neural Networks Graph Representation Learning
Jilin University · RMIT University · The Chinese University of Hong Kong +1
Hierarchical Perfusion Graphs for Tumor Heterogeneity Modeling in Glioma Molecular Subtyping
May 8, 2026Han Jang, Junhyeok Lee, Heeseong Eum +4Graph Neural Networks Magnetic Resonance Imaging
Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea · Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, South Korea · Dept. of Biomedical Sciences, Seoul National University, Seoul, South Korea +4
GAD in the Wild: Benchmarking Graph Anomaly Detection under Realistic Deployment Challenges
May 8, 2026Jingjing Zhou, Shiyu Huang, Qing Qing +7Graph Neural Networks Graph Representation Learning
Zhejiang Gongshang University · Jilin University · Adelaide University +2
Solving Max-Cut to Global Optimality via Feasibility-Preserving Graph Neural Networks
May 8, 2026Hao Chen, Chendi Qian, Christopher Morris +2Semidefinite Programming Graph Neural Networks
1Davidson School of Chemical Engineering, Purdue University · Faculty of Computer Science, RWTH Aachen University · 3Jacobs Technion-Cornell Institute, Cornell Tech
Unlocking High-Fidelity Molecular Generation from Mass Spectra via Dual-Stream Line Graph Diffusion
May 7, 2026Xujun Che, Xiuxia Du, Depeng XuGraph Neural Networks Molecular Graph Generation
Department of Software and Information Systems,2026 University of North Carolina at Charlotte, Charlotte, NC 28223 · Center for Environmental Monitoring and Informatics Technologies for Public Health University of North Carolina at Charlotte, Charlotte, NC 28223 · Department of Bioinformatics and Genomics,May University of North Carolina at Charlotte, Charlotte, NC 28223
Target-Aware Data Augmentation for SAT Prediction
May 7, 2026Eshed Gal, Uri Ascher, Eldad HaberSynthetic Data Augmentation Graph Neural Networks
Department of Computer Science The University of British Columbia Vancouver, Canada · Department of Earth, Ocean and Atmospheric Sciences The University of British Columbia Vancouver, Canada
Model-to-Data Distillation for Graph Neural Networks
May 7, 2026Debolina Halder Lina, Arlei SilvaGraph Structure Learning Graph Neural Networks
Department of Computer Science, Rice University, Houston, TX 77005, USA · Department of Computer Science & Ken Kennedy Institute, Rice University, Houston, TX 77005, USA
Towards Metric-Faithful Neural Graph Matching
May 7, 2026Jyotirmaya Shivottam, Subhankar MishraGraph Neural Networks Neural Representation Geometry
1National Institute of Science Education and Research (NISER), Bhubaneswar, India · 2Homi Bhabha National Institute, Mumbai, India

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Knowledge Graphs Meet Graph Neural Networks: A Comprehensive Survey

Chengcheng Sun, Jiayun Tian, Cheng Zhai, Zhixiao Wang+4

School of Safety Engineering, China University of Mining and Technology, China · School of Computer Science and Technology, China University of Mining and Technology, China · State Key Laboratory of Coal Mine Disaster Prevention and Control, China University of Mining and Technology, China+1

KG Construction Graph Neural Networks Graph Representation Learning KG Embedding Knowledge Graphs

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Graph Neural Networks (GNNs) have emerged as a powerful paradigm in Knowledge Graphs (KGs) due to their intrinsic ability to model graph-structured data. However, there remains a lack of a systematic review about GNN-based methodologies across the entire knowledge graph technologies pipeline. To address this gap, we first propose a novel two-level taxonomy framework for GNN-based knowledge graph technologies: the KG technologies pipeline and GNN-based perspective. Specifically, the knowledge graph technologies pipeline covers knowledge graph construction, knowledge graph embedding, knowledge reasoning and knowledge graph applications. Meanwhile, the GNN-based perspective provides a new categorization of knowledge graph technologies with GNN models, such as GCN, GAT, and HGNN. Then, we analyze the advantages of GNN technology based on the characteristics of different tasks in the knowledge graph lifecycle. Furthermore, we detailed review various GNN-based models for knowledge graph following the proposed taxonomy, and summarize strengths and limitations. Finally, we discuss unresolved challenges and outline promising directions for future research.