# Link Prediction without Graph Neural Networks

arXiv: https://arxiv.org/abs/2305.13656 · HTML: https://mlsanity.com/paper/2305.13656/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Builds on 58 of its 99 references that are in the map.
- First posted on arXiv 23 May 2023.

## Builds on (most cited first, 30 of 58)

- [Adam: A Method for Stochastic Optimization](https://mlsanity.com/paper/1412.6980/) (2014)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [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)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [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)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [Simplifying Graph Convolutional Networks](https://mlsanity.com/paper/1902.07153/) (2019)
- [Variational Graph Auto-Encoders](https://mlsanity.com/paper/1611.07308/) (2016)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [Pitfalls of Graph Neural Network Evaluation](https://mlsanity.com/paper/1811.05868/) (2018)
- [Predict then Propagate: Graph Neural Networks meet Personalized PageRank](https://mlsanity.com/paper/1810.05997/) (2018)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)
- [Embedding Entities and Relations for Learning and Inference in Knowledge Bases](https://mlsanity.com/paper/1412.6575/) (2014)
- [RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space](https://mlsanity.com/paper/1902.10197/) (2019)
- [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)
- [Hierarchical Graph Representation Learning with Differentiable Pooling](https://mlsanity.com/paper/1806.08804/) (2018)
- [Image-based Recommendations on Styles and Substitutes](https://mlsanity.com/paper/1506.04757/) (2015)
- [GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models](https://mlsanity.com/paper/1802.08773/) (2018)
- [Hyperbolic Graph Convolutional Neural Networks](https://mlsanity.com/paper/1910.12933/) (2019)
- [Graph Convolutional Networks for Text Classification](https://mlsanity.com/paper/1809.05679/) (2018)
- [KGAT: Knowledge Graph Attention Network for Recommendation](https://mlsanity.com/paper/1905.07854/) (2019)
- [Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction](https://mlsanity.com/paper/2106.06935/) (2021)
- [Graph networks as learnable physics engines for inference and control](https://mlsanity.com/paper/1806.01242/) (2018)
- [Learning Discrete Structures for Graph Neural Networks](https://mlsanity.com/paper/1903.11960/) (2019)
- [Learning Deep Generative Models of Graphs](https://mlsanity.com/paper/1803.03324/) (2018)
- [Iterative Deep Graph Learning for Graph Neural Networks: Better and Robust Node Embeddings](https://mlsanity.com/paper/2006.13009/) (2020)

## Built on by (most cited first, 3 of 3)

- [Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarking](https://mlsanity.com/paper/2306.10453/) (2023)
- [Enhancing Graph Representation Learning with Localized Topological Features](https://mlsanity.com/paper/2501.09178/) (2025)
- [PersonalizedRouter: Personalized LLM Routing via Graph-based User Preference Modeling](https://mlsanity.com/paper/2511.16883/) (2025)

## Abstract (arXiv)

Link prediction, which consists of predicting edges based on graph features, is a fundamental task in many graph applications. As for several related problems, Graph Neural Networks (GNNs), which are based on an attribute-centric message-passing paradigm, have become the predominant framework for link prediction. GNNs have consistently outperformed traditional topology-based heuristics, but what contributes to their performance? Are there simpler approaches that achieve comparable or better results? To answer these questions, we first identify important limitations in how GNN-based link prediction methods handle the intrinsic class imbalance of the problem -- due to the graph sparsity -- in their training and evaluation. Moreover, we propose Gelato, a novel topology-centric framework that applies a topological heuristic to a graph enhanced by attribute information via graph learning. Our model is trained end-to-end with an N-pair loss on an unbiased training set to address class imbalance. Experiments show that Gelato is 145% more accurate, trains 11 times faster, infers 6,000 times faster, and has less than half of the trainable parameters compared to state-of-the-art GNNs for link prediction.