Advancing Link Prediction with a Hybrid Graph Neural Network Approach
Abstract
1. Introduction
- Novel Link Prediction Framework: We propose a new method for enhancing link prediction in social networks using Graph Neural Networks (GNNs), specifically addressing complex and dynamic interactions between nodes.
- Graph Representation with GCN: We leverage the Graph Convolutional Network (GCN) model to capture structural and relational information effectively, enabling better node embeddings for link prediction.
- Dual Similarity Measures for Feature Enhancement: We integrate both dot product and cosine similarity to capture complementary relational cues between nodes, improving prediction accuracy.
- Empirical Validation: The proposed approach is extensively evaluated on the Ciao and Epinions datasets, demonstrating superior performance compared to conventional methods, thus confirming its effectiveness.
2. Related Works
3. Methodology
| Algorithm 1: Graph Neural Network Training on Ciao and Epinions Subgraph |
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3.1. Feature Extraction
3.2. Graph Neural Network (GNN)
3.2.1. Graph Convolutional Network (GCN)
3.2.2. GraphSAGE (Graph Sample and Aggregate)
3.2.3. GraphRec (Graph-Based Recommendation)
3.3. Link Prediction via Node Similarity
3.3.1. Cosine Similarity
3.3.2. The Dot Product
3.3.3. Jaccard Similarity
4. Experiments
4.1. Used Dataset
4.2. Experiments Details
Link Prediction
4.3. Results and Discussion
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5. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
- Ma, G.; Ahmed, N.K.; Willke, T.L.; Yu, P.S. Deep graph similarity learning: A survey. Data Min. Knowl. Discov. 2021, 35, 688–725. [Google Scholar] [CrossRef]
- Li, Y.; Zhong, N.; Taniar, D.; Zhang, H. MCGNet+: An improved motor imagery classification based on cosine similarity. Brain Inform. 2022, 9, 3. [Google Scholar] [CrossRef]
- Romanova, A. GNN graph classification method to discover climate change pat-ternsy. In Proceedings of the International Conference on Artificial Neural Networks, Proceedings of the 32nd International Conference on Artificial Neural Networks, Heraklion, Greece, 26–29 September 2023; Springer: Cham, Switzerland, 2023; pp. 388–397. [Google Scholar]
- Zhang, H.; Li, H.; Li, Z.; Chen, P. User preference and social relationship-aware recommendations base on a novel light graph convolutional network. J. Supercomput. 2025, 81, 27. [Google Scholar] [CrossRef]
- Akkaya, B. Current Trends in Recommender Systems: A Survey of Approaches and Future Directions. Comput. Sci. 2025, 10, 53–91. [Google Scholar]
- Li, Y.; Feng, H.; Zeng, Y.; Zhao, X.; Chai, J.; Fu, S.; Ye, C.; Zhang, S. Light disentangled graph learning for social recommendation. World Wide Web 2025, 28, 29. [Google Scholar] [CrossRef]
- Chattopadhyay, S.; Kumar, S.; Kumar, M.S.; Balasubramanian, K.; Pujar, R.P. Novel Method for Predicting Consumer Purchase Behaviour on E-Commerce Platforms through Graph Neural Network Model. In Proceedings of the International Conference on Intelligent Computing and Knowledge Extraction (ICICKE), Bengaluru, India, 6–7 June 2025; pp. 1–6. [Google Scholar]
- Wang, X.; Zhang, H.; Liu, Y.; Zhang, J. Graph neural networks for social recommendation. In Proceedings of the AAAI Conference on Artificial Intelligence, Honolulu, HI, USA, 27 Januray–1 February 2019; Volume 33, pp. 4602–4609. [Google Scholar]
- Dalvi, A.; Honavar, V. Hyperdimensional representation learning for node classification and link prediction. In Proceedings of the Eighteenth ACM International Conference on Web Search and Data Mining, Hannover, Germany, 10–14 March 2025; pp. 88–97. [Google Scholar]
- Wang, L.; Han, M. High-order Graph Neural Networks with Common Neighbor Awareness for Link Prediction. In Proceedings of the 2025 Joint International Conference on Automation-Intelligence-Safety (ICAIS) & International Symposium on Autonomous Systems (ISAS), Xi’an, China, 23–25 May 2025; pp. 1–5. [Google Scholar]
- Ciao. Available online: https://www.ciao.co.uk (accessed on 22 July 2025).
- Levy, A.; Shalom, B.R.; Chalamish, M. A guide to similarity measures and their data science applications. J. Big Data 2025, 12, 188. [Google Scholar] [CrossRef]
- Firuzbakht, S.; Khansari, M. TwitterTagNet: An extensive graph dataset for node classification in co-occurring hashtag networks. Soc. Netw. Anal. Min. 2025, 15, 17. [Google Scholar] [CrossRef]
- Mishra, A. Graph-Based Methods for e-Commerce Data Science Applications. Ph.D. Thesis, The Pennsylvania State University, University Park, PA, USA, 2025. [Google Scholar]
- Contreras-Velasco, O.; Jones, N.P.; Argomedo, D.W.; Sullivan, J.P.; Callaghan, C. Uncovering hidden alliances in organized crime networks with machine learning: From node similarity to graph neural networks. J. Comput. Soc. Sci. 2025, 8, 101. [Google Scholar] [CrossRef]
- Yu, Z.; Jin, D.; Huo, C.; Wang, Z.; Liu, X.; Qi, H.; Wu, J.; Wu, L. Kgtrust: Evaluating trustworthiness of siot via knowledge enhanced graph neural networks. In Proceedings of the ACM Web Conference 2023, Austin, TX, USA, 30 April–4 May 2023; pp. 727–736. [Google Scholar]
- Velickovic, P.; Cucurull, G.; Casanova, A.; Romero, A.; Lio, P.; Bengio, Y. Graph Attention Networks. arXiv 2018, arXiv:1710.10903. [Google Scholar]
- Wu, F.; Souza, A., Jr.; Zhang, T.; Fifty, C.; Yu, T.; Weinberger, K. Weinberger Simplifying Graph Convolutional Networks. In Proceedings of the 36th International Conference on Machine Learning, ICML, Long Beach, CA, USA, 2–15 June 2019; pp. 6861–6871. [Google Scholar]
- Xu, P.; Hu, W.; Wu, J.; Liu, W.; Du, B.; Yang, J. Social Trust Network Embedding. In Proceedings of the 2019 IEEE International Conference on Data Mining (ICDM), Beijing, China, 8–11 November 2019; pp. 678–687. [Google Scholar]
- Li, Y.; Tian, Y.; Zhang, J.; Chang, Y. Learning Signed Network Embedding via Graph Attention. Proc. AAAI Conf. Artif. Intell. 2020, 34, 4772–4779. [Google Scholar] [CrossRef]
- Wang, Q.; Zhao, W.; Yang, J.; Wu, J.; Hu, W.; Xing, Q. DeepTrust: A Deep User Model of Homophily Effect for Trust Prediction. In Proceedings of the 2019 IEEE International Conference on Data Mining (ICDM), Beijing, China, 8–11 November 2019; pp. 618–627. [Google Scholar]
- Wang, Q.; Zhao, W.; Yang, J.; Wu, J.; Zhou, C.; Xing, Q. DeepTrust: AtNE-Trust: Attributed Trust Network Embedding for Trust Prediction in Online Social Networks. In Proceedings of the 2020 IEEE International Conference on Data Mining (ICDM), Sorrento, Italy, 17–20 November 2020; pp. 601–610. [Google Scholar]
- Han, X.; Xie, X.; Zhao, R.; Li, Y.; Ma, P.; Li, H.; Chen, F.; Zhao, Y.; Tang, Z. Calculating the similarity between prescriptions to find their new indications based on graph neural network. Chin. Med. 2023, 19, 124. [Google Scholar] [CrossRef]
- Wang, Y.; Hu, X.; Gan, Q.; Huang, X.; Qiu, X.; Wipf, D. Efficient link prediction via gnn layers induced by negative sampling. IEEE Trans. Knowl. Data Eng. 2025, 37, 253–264. [Google Scholar] [CrossRef]
- Choudhary, S.; Kumar, G. Enhancing link prediction in dynamic social networks through hybrid GCN-LSTM models. Knowl. Inf. Syst. 2025, 67, 6717–6751. [Google Scholar] [CrossRef]
- Ga, S.; Cho, P.H.; Moon, G.E.; Jung, S. Efficient GNN-based social recommender systems through social graph refinement. J. Supercomput. 2025, 81, 215. [Google Scholar] [CrossRef]
- Hamilton, W.; Ying, R.; Leskovec, J. Inductive representation learning on large graphs. arXiv 2017, arXiv:1706.02216. [Google Scholar] [CrossRef]
- Wang, H.; Zhang, F.; Zhang, M.; Leskovec, J.; Zhao, M.; Li, W.; Wang, Z. Knowledge-aware graph neural networks with label smoothness regularization for recommender systems. In Proceedings of the 25th ACM SIGKDD Conference on Knowledge Discovery and Data Mining, Anchorage, AK, USA, 4–8 August 2019; pp. 968–977. [Google Scholar]
- Wang, Y.; Sun, M.; Zhu, X.; Zhang, C. Multi-channel graph neural networks for social recommendation. In Proceedings of the 43rd International ACM SIGIR Conference on Research and Development in Information Retrieval, Virtual, 25–30 June 2020; pp. 135–144. [Google Scholar]
- Zheng, Y.; Zhang, H.; Ma, Y.; Chen, E. Joint deep modeling of users and items using reviews for recommendation. In Proceedings of the Tenth ACM International Conference on Web Search and Data Mining, Cambridge, UK, 6–10 February 2017; Volume 35, pp. 425–434. [Google Scholar]
- Cheng, Q.; Wang, X.; Yin, D.; Niu, Y.; Xiang, X.; Yang, J.; Shen, L. The new similarity measure based on user preference models for collaborative filtering. In Proceedings of the 2015 IEEE International Conference on Information and Automation, Lijiang, China, 8–10 August 2015; pp. 577–582. [Google Scholar]
- Li, D.; Yang, Y.; Cui, Z.; Yin, H.; Hu, P.; Hu, L. LLM-DDI: Leveraging Large Language Models for Drug-Drug Interaction Prediction on Biomedical Knowledge Graph. IEEE J. Biomed. Health Inform. 2025, 1–9. [Google Scholar] [CrossRef] [PubMed]
- Yang, M.-R.; Xu, X.-J. Recent Advances in Hypergraph Neural Networks. J. Oper. Res. Soc. China 2025. [Google Scholar] [CrossRef]
- Tan, G. NAH-GNN: A graph-based framework for multi-behavior and high-hop interaction recommendation. PloS ONE 2025, 20, e0321419. [Google Scholar] [CrossRef] [PubMed]
- Xu, R.; Liu, G.; Wang, Y.; Zhang, X.; Zheng, K.; Zhou, X. Adaptive hypergraph network for trust prediction. In Proceedings of the 2024 IEEE 40th International Conference on Data Engineering (ICDE), Utrecht, The Netherlands, 13–16 May 2024; pp. 2986–2999. [Google Scholar]
- Lee, S.-W.; Tanveer, J.; Rahmani, A.M.; Alinejad-Rokny, H.; Khoshvaght, P.; Zare, G.; Alamdari, P.M.; Hosseinzadeh, M. SFGCN: Synergetic Fusion-based Graph Convolutional Networks Approach for link prediction in social networks. Inf. Fusion 2025, 114, 102684. [Google Scholar] [CrossRef]
- Hassanzadeh, R.; Majidnezhad, V.; Arasteh, B. A novel recommender system using light graph convolutional network and personalized knowledge-aware attention sub-network. Sci. Rep. 2025, 15, 15693. [Google Scholar] [CrossRef]
- Dai, Y.; Yan, M.; Li, J. Granular concept-enhanced relational graph convolution networks for link prediction in knowledge graph. Inf. Sci. 2025, 694, 121698. [Google Scholar] [CrossRef]
- Bansal, S.; Gowda, K.; Kumar, N. Multilingual personalized hashtag recommendation for low-resource Indic languages using graph-based deep neural network. EXpert Syst. Appl. 2024, 236, 121188. [Google Scholar] [CrossRef]
- Leskovec, J. Graphsage: Inductive representation learning on large graphs. In Proceedings of the 31st International Conference on Neural Information Processing Systems, Long Beach, CA, USA, 4–9 December 2017. [Google Scholar]
- Ramirez, R.; Chiu, Y.C.; Hererra, A.; Mostavi, M.; Ramirez, J.; Chen, Y.; Jin, Y.F. Classification of cancer types using graph convolutional neural networks. Front. Phys. 2020, 8, 203. [Google Scholar] [CrossRef] [PubMed]
- Liu, J.; Ong, G.P.; Chen, X. GraphSAGE-based traffic speed forecasting for segment network with sparse data. IEEE Trans. Intell. Transp. Syst. 2020, 23, 1755–1766. [Google Scholar] [CrossRef]
- Zhang, T.; Shan, H.-R.; Little, M.A. Causal GraphSAGE: A robust graph method for classification based on causal sampling. Pattern Recognit. 2022, 128, 108696. [Google Scholar] [CrossRef]
- Sun, Q.; Wei, X.; Yang, X. GraphSAGE with deep reinforcement learning for financial portfolio optimization. Expert Syst. Appl. 2022, 238, 122027. [Google Scholar] [CrossRef]
- Pompeu, M.L.F.; Holanda Filho, R. Identification Based on GraphSAGE Algorithm. In Proceedings of the Complex Networks & Their Applications XIII, Proceedings of the Thirteenth International Conference on Complex Networks and Their Applications: COMPLEX NETWORKS, Istanbul, Turkey, 10–12 December 2024; Springer Nature: Cham, Switzerland, 2025; Volume 1187, pp. 28–36. [Google Scholar]
- Lee, J.-W.; Kim, J.-H. GraphRec-based Korean expert recommendation using author contribution index and the paper abstracts in marine. Eng. Appl. Artif. Intell. 2024, 133, 108219. [Google Scholar] [CrossRef]
- Liao, D.; Yu, H. PEVGraphRec: A PEV method-based graph neural networks for social recommendations. In Proceedings of the International Conference on Statistics, Data Science, and Computational Intelligence, Qingdao, China, 19–21 August 2022; Volume 12510, pp. 414–420. [Google Scholar]
- Si, G.; Xu, S.; Li, Z.; Zhang, J. Rec-GNN: Research on social recommendation based on graph neural networks. In Proceedings of the 2022 International Conference on Computer Science, Information Engineering and Digital Economy, Guangzhou, China, 28–30 October 2022; pp. 478–485. [Google Scholar]
- Gao, J.; Zhang, Y.; Zhang, Y. Graph Diffusion Social Recommendation. IEEE Trans. Consum. Electron. 2025. [Google Scholar] [CrossRef]
- Zhang, M.; Wu, S.; Gao, M.; Jiang, X.; Xu, K.; Wang, L. Personalized graph neural networks with attention mechanism for session-aware recommendation. IEEE Trans. Knowl. Data Eng. 2023, 34, 3946–3957. [Google Scholar] [CrossRef]
- Lavryk, Y.; Kryvenchuk, Y. Product Recom-mendation System Using Graph Neural Network. In MoMLeT + DS 2023, Proceedings of the 5th International Workshop on Modern Machine Learning Technologies and Data Science, Lviv, Ukraine, 3 June 2023; CEUR: Kyiv, Ukraine, 2023; pp. 182–192. [Google Scholar]




| Statistic | Ciao | Epinions |
|---|---|---|
| Number of Users | 7375 | 75,879 |
| Number of Items | 105,114 | Not specified |
| Number of Ratings | 284,086 | Not specified |
| Rating Density | 0.04% | Not specified |
| Number of Social Links | 111,781 | 508,837 |
| Feature/Model | GCN (Graph Convolutional Network) | GraphSAGE | GraphRec |
|---|---|---|---|
| Learning Type | Transductive | Inductive | Task-specific (Recommender Systems) |
| Aggregation | Full neighborhood (mean) | Sampled neighbors (mean, LSTM, pooling) | Attention-based + interaction modeling |
| Scalability | Limited for large graphs | Scalable (sampling) | Moderate (depends on graph size) |
| Use Case | Node classification, link prediction | Node classification, embeddings | Rating prediction, personalized recommendation |
| Accuracy on ciao dataset (%) | 87.6 | 74.2 | 76.5 |
| Precision on ciao dataset (%) | 84.3 | 71.5 | 73.8 |
| Recall on ciao dataset (%) | 86.9 | 73.2 | 75.1 |
| F1-score on ciao dataset (%) | 85.6 | 72.3 | 74.4 |
| Accuracy on epinions dataset (%) | 67.31 | 53.85 | 67.31 |
| Precision on epinions dataset (%) | 65.2 | 51.4 | 66.0 |
| Recall on epinions dataset (%) | 66.8 | 52.0 | 67.5 |
| F1-score on epinions dataset (%) | 66.0 | 51.7 | 66.7 |
| Strengths | Simplicity, strong baseline performance | Scalability, flexibility | High performance in recommendation tasks |
| Limitations | Not scalable, transductive only | Sensitive to sampling strategy | Less generalizable to other tasks |
| Similarity Techniques | Results on Ciao Dataset (%) | Results on Epinions Dataset (%) | ||||||
|---|---|---|---|---|---|---|---|---|
| Accuracy | Precision | Recall | F1-Score | Accuracy | Precision | Recall | F1-Score | |
| Jaccard similarity | 45.33 | 27.3 | 50.0 | 35.0 | 45.00 | 27.3 | 50.0 | 35.0 |
| Jaccard + Cosine similarity | 53.36 | 33.6 | 40.0 | 34.0 | 50.98 | 28.9 | 43.3 | 34.6 |
| Cosine + Jaccard + Dot similarity | 55.37 | 33.3 | 50.0 | 40.0 | 55.21 | 33.3 | 50.0 | 40.0 |
| Dot similarity | 55.42 | 33.3 | 50.0 | 40.0 | 57.59 | 36.4 | 53.3 | 43.5 |
| Jaccard + Dot similarity | 61.90 | 40.9 | 60.0 | 48.7 | 48.53 | 25.6 | 36.7 | 30.0 |
| Cosine similarity | 72.78 | 54.1 | 66.7 | 59.8 | 52.63 | 29.3 | 40.0 | 34.0 |
| Cosine + Dot similarity | 90.15 | 83.3 | 83.3 | 83.3 | 73.33 | 53.8 | 70.0 | 61.0 |
| Method | Ciao Accuracy in % | Epinions Accuracy % |
|---|---|---|
| GAT | 64.28 | 72.05 |
| SGC | 69.93 | 78.62 |
| STNE | 71.33 | 79.51 |
| SNEA | 68.97 | 74.63 |
| DeepTrust | 50.17 | 58.38 |
| AtNE-Trust | 68.23 | 74.35 |
| NALP | 90.15 | 73.33 |
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Gharsallah, S.; Yahia, S.; Bouchelligua, W.; Bouchrika, T. Advancing Link Prediction with a Hybrid Graph Neural Network Approach. Mathematics 2025, 13, 3594. https://doi.org/10.3390/math13223594
Gharsallah S, Yahia S, Bouchelligua W, Bouchrika T. Advancing Link Prediction with a Hybrid Graph Neural Network Approach. Mathematics. 2025; 13(22):3594. https://doi.org/10.3390/math13223594
Chicago/Turabian StyleGharsallah, Siwar, Samah Yahia, Wided Bouchelligua, and Tahani Bouchrika. 2025. "Advancing Link Prediction with a Hybrid Graph Neural Network Approach" Mathematics 13, no. 22: 3594. https://doi.org/10.3390/math13223594
APA StyleGharsallah, S., Yahia, S., Bouchelligua, W., & Bouchrika, T. (2025). Advancing Link Prediction with a Hybrid Graph Neural Network Approach. Mathematics, 13(22), 3594. https://doi.org/10.3390/math13223594


