Graph Representation Learning

Overview

Graph representation learning studies how to turn relational data into useful representations while preserving information about connectivity, node and edge attributes, and sometimes time or geometry. Common approaches include message-passing graph neural networks, spectral and positional encodings, graph Transformers, and self-supervised methods such as contrastive learning and masked prediction. These representations support tasks including node classification, link prediction, graph comparison, clustering, and molecular or social prediction; newer work also explores higher-order structure and foundation models that transfer across graphs. A central challenge is balancing expressive, scalable models with reliable generalization across graph sizes, domains, feature types, and structural shifts, while establishing when graph structure helps beyond simpler baselines.

Latest papers

CardsList

305 papers33 papers in the last four weeks, up 3% on the four weeks before. 0.2% of all new papers.

  1. EpiFormer: Learning Antigen-Antibody Interactions for Epitope Prediction via Geometric Deep Learning

    Jun 2, 2026Mansoor Ahmed, Huirong Chai, Haoxin Wang +2Graph Representation LearningCross-Attention

  2. Contrastive Neural Algorithmic Reasoning for Graph Coloring

    Jun 2, 2026Thien Le, Tianyu Zhao, Melanie WeberGraph Neural NetworksGraph Representation Learning

  3. Learn When and Where to Connect: Adaptive Virtual Nodes for Dynamic Message Passing on Graphs

    Jun 2, 2026Jaejun Lee, Joyce Jiyoung WhangGraph Structure LearningGraph Neural Networks

  4. Scaling Higher-Order Graph Learning with Maximal Clique Complexes

    May 29, 2026Antoine Vialle, Aref Einizade, Fragkiskos D. Malliaros +1Graph Neural NetworksGraph Representation Learning

  5. Graph Neural Networks Are Not Continuous Across Graph Resolutions

    May 29, 2026Christian Koke, Yuesong Shen, Abhishek Saroha +4Neural Network GeneralizationGraph Neural Networks

  6. When Do Graph Foundation Models Transfer? A Data-Centric Theory

    May 28, 2026Jiajun Zhu, Ying Chen, Peihao Wang +4Graph Positional EncodingGraphon Theory

  7. Forget Less, Generalize More: Unifying Temporal and Structural Adaptation for Dynamic Graphs

    May 28, 2026Qian Chang, Ciprian Doru Giurcaneanu, Runsong Jia +6Temporal GNNsGraph Representation Learning

  8. Traditional machine learning vs. deep learning from dynamic graph representations of proteins' 3D folds in the task of protein structure classification

    May 28, 2026Aydin Wells, Francis A. Gatsi, Aaron Striegel +1Protein Structure PredictionGraph Representation Learning

  9. Let Relations Speak: An End-to-End LLM-GNN Soft Prompt Framework for Fraud Detection

    May 27, 2026Zhixing Zuo, Huilin He, Jiasheng Wu +1Graph Neural NetworksGraph Representation Learning

  10. T-GINEE: A Tensor-Based Multilayer Graph Representation Learning

    May 27, 2026Maolin Wang, Ziting Mai, Xuhui Chen +9Graph Representation Learning

  11. Robust Contrastive Graph Clustering with Adaptive Local-Global Integration

    May 27, 2026Lei Zhang, Fubo Sun, Haipeng Yang +2Graph Representation LearningMulti-Scale Feature Fusion

  12. GraD-IBD: Graph Representation Learning from Diagnosis Trajectories for Early Detection of Inflammatory Bowel Disease

    May 27, 2026Leo Y. Li-Han, Ellen L. Larson, Elizabeth B. Habermann +2Temporal GNNsGraph Representation Learning

  13. Closed-Form Node Classification with Exact Graph Unlearning

    May 25, 2026Aditya Gaur, Charu SharmaGraph Representation LearningPrivacy-Preserving ML

  14. SiST-GNN: Simultaneous Spatial-Temporal Message Passing for Dynamic Graph Representation Learning

    May 25, 2026Shubhajit Roy, Anirban DasguptaGraph Representation LearningTemporal Link Prediction

  15. Clustering as Reasoning: A kk-Means Interpretation of Chain-of-Thought Graph Learning

    May 24, 2026Xuanting Xie, Zhaochen Guo, Bingheng Li +4Graph Representation LearningText-Attributed Graph Learning

  16. Knowledge Graph Modulated Deep Learning for Limited-Sample Clinical Data Analysis

    May 22, 2026Yuwei Xue, Sakib Mostafa, James Zou +5Graph Representation LearningMedical Diagnosis

  17. S3^3GNN: Efficient Global Mixing and Local Message Passing for Long-Range Graph Learning

    May 22, 2026Dai Shi, Luke Thompson, Linhan Luo +4Long-Range Graph LearningGraph Neural Networks

  18. Generative Representation Learning on Hyper-relational Knowledge Graphs via Masked Discrete Diffusion

    May 22, 2026Jaejun Lee, Seheon Kim, Joyce Jiyoung WhangGraph Representation LearningKnowledge Representation

  19. Lost in Tokenization: Fundamental Trade-offs in Graph Tokenization for Transformers

    May 21, 2026Maya Bechler-Speicher, Gilad Yehudai, Gil Harari +3Transformer ExpressivityGraph Representation Learning

  20. Fast and Featureless Node Representation Learning with Partial Pairwise Supervision

    May 19, 2026Sujan Chakraborty, Saptarshi BejGraph Representation LearningGraph Contrastive Learning

  21. TERGAD: Structure-Aware Text-Enhanced Representations for Graph Anomaly Detection

    May 19, 2026Wen Shi, Zhe Wang, Huafei Huang +6Graph Representation LearningText-Attributed Graph Learning

  22. Graph Hierarchical Recurrence for Long-Range Generalization

    May 18, 2026Stefano Carotti, Marco Pacini, Alessio Gravina +3Long-Range Graph LearningGraph Neural Networks

  23. Learning over Positive and Negative Edges with Contrastive Message Passing

    May 18, 2026Peter Pao-Huang, Charilaos I. Kanatsoulis, Michael Bereket +1Graph Neural NetworksGraph Representation Learning

  24. Position: Graph Condensation Needs a Reset -- Move Beyond Full-dataset Training and Model-Dependence

    May 17, 2026Mridul Gupta, Samyak Jain, Vansh Ramani +2Graph Neural NetworksGraph Representation Learning

  25. Multi-hop Relational Contrastive Learning: Extending Spatial Contrastive Pre-training Beyond Pairwise Relations

    May 15, 2026Sheikh Tanvir Ahmed, Md. Tanvir RaihanContrastive LearningVisual Spatial Reasoning

  26. Gaussian Relational Graph Transformer

    May 15, 2026Zezhong Ding, Jin Li, Xugang Wang +1Graph Attention NetworksGraph Representation Learning

  27. OgBench: A Framework for Evaluating Graph Neural Networks on Omics Data

    May 15, 2026Louisa Cornelis, Johan Mathe, Louis Van Langendonck +2Graph Neural NetworksGraph Representation Learning

  28. A Unified Non-Parametric and Interpretable Point Cloud Analysis via t-FCW Graph Representation

    May 14, 2026Haijian Lai, Bowen Liu, Man Xu +43D Point Cloud Segmentation3D Part Segmentation

  29. Rethinking Graph Convolution for 2D-to-3D Hand Pose Lifting

    May 13, 2026Chanyoung Kim, Donghyun Kim, Dong-Hyun Sim +2Graph Positional EncodingGraph Attention Networks