- Conference Article
- 10.1109/ijcnn64981.2025.11228419
TopoLink: Topology-enhanced Graph Transformer with Extended Persistent Homology For Link Prediction
- Jun 30, 2025
- Lizhi Liu
Despite being a groundbreaking research that has achieved phenomenal success in various graph learning tasks, graph convolutional network (GCN) falters in link prediction (LP). This is primarily due to its inherent message-passing mechanism. On one hand, GCN has limited expressive power and cannot identify topological patterns such as counting 3-cycles, which is a cornerstone of LP heuristics. On the other hand, GCN restricts message flow to hardwired interactions, while in LP scenarios, many edges in the graph are missing. This contradiction hinders GCN from learning ideal node representations. To tackle these challenges, we propose TopoLink, a topology-enhanced graph Transformer for LP. We design a Simplified Graph Transformer that integrates classical GCN with a global attention module with linear complexity to simultaneously capture local and global information. Besides, we introduce extended persistent homology (EPH) to enrich the ability to detect topological features such as cycles. Specifically, to deeply understand abstract and complex topological information, we transform EPH into persistence images and, for the first time, apply computer vision techniques to refine them into vectorized topological fingerprints. Extensive experiments on real-world datasets demonstrate that TopoLink outperforms state-of-the-art methods with 0.55-18.84% improvements. The code is available at https://github.com/liulizhi1996/TopoLink.
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