# GNNs Meet Sequence Models Along the Shortest-Path: an Expressive Method for Link Prediction

arXiv: https://arxiv.org/abs/2507.07138 · HTML: https://mlsanity.com/paper/2507.07138/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 26 of its 46 references that are in the map.
- First posted on arXiv 9 Jul 2025.

## Builds on (most cited first, 26 of 26)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Empirical Evaluation of Gated Recurrent Neural Networks on Sequence Modeling](https://mlsanity.com/paper/1412.3555/) (2014)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [node2vec: Scalable Feature Learning for Networks](https://mlsanity.com/paper/1607.00653/) (2016)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Graph Convolutional Neural Networks for Web-Scale Recommender Systems](https://mlsanity.com/paper/1806.01973/) (2018)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)
- [Weisfeiler and Leman Go Neural: Higher-order Graph Neural Networks](https://mlsanity.com/paper/1810.02244/) (2018)
- [Link Prediction Based on Graph Neural Networks](https://mlsanity.com/paper/1802.09691/) (2018)
- [Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction](https://mlsanity.com/paper/2106.06935/) (2021)
- [A Review of Relational Machine Learning for Knowledge Graphs](https://mlsanity.com/paper/1503.00759/) (2015)
- [Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learning](https://mlsanity.com/paper/2010.16103/) (2020)
- [Equivariant and Stable Positional Encoding for More Powerful Graph Neural Networks](https://mlsanity.com/paper/2203.00199/) (2022)
- [Graph Neural Networks for Link Prediction with Subgraph Sketching](https://mlsanity.com/paper/2209.15486/) (2022)
- [APAN: Asynchronous Propagation Attention Network for Real-time Temporal Graph Embedding](https://mlsanity.com/paper/2011.11545/) (2020)
- [Neo-GNNs: Neighborhood Overlap-aware Graph Neural Networks for Link Prediction](https://mlsanity.com/paper/2206.04216/) (2022)
- [Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarking](https://mlsanity.com/paper/2306.10453/) (2023)
- [Neural Common Neighbor with Completion for Link Prediction](https://mlsanity.com/paper/2302.00890/) (2023)
- [Progresses and Challenges in Link Prediction](https://mlsanity.com/paper/2102.11472/) (2021)
- [Line Graph Neural Networks for Link Weight Prediction](https://mlsanity.com/paper/2309.15728/) (2023)
- [Edge Classification on Graphs: New Directions in Topological Imbalance](https://mlsanity.com/paper/2406.11685/) (2024)
- [Simple Path Structural Encoding for Graph Transformers](https://mlsanity.com/paper/2502.09365/) (2025)

## Abstract (arXiv)

Graph Neural Networks (GNNs) often struggle to capture the link-specific structural patterns crucial for accurate link prediction, as their node-centric message-passing schemes overlook the subgraph structures connecting a pair of nodes. Existing methods to inject such structural context either incur high computational cost or rely on simplistic heuristics (e.g., common neighbor counts) that fail to model multi-hop dependencies. We introduce SP4LP (Shortest Path for Link Prediction), a novel framework that combines GNN-based node encodings with sequence modeling over shortest paths. Specifically, SP4LP first applies a GNN to compute representations for all nodes, then extracts the shortest path between each candidate node pair and processes the resulting sequence of node embeddings using a sequence model. This design enables SP4LP to capture expressive multi-hop relational patterns with computational efficiency. Empirically, SP4LP achieves state-of-the-art performance across link prediction benchmarks. Theoretically, we prove that SP4LP is strictly more expressive than standard message-passing GNNs and several state-of-the-art structural features methods, establishing it as a general and principled approach for link prediction in graphs.