# Plain Transformers are Surprisingly Powerful Link Predictors

arXiv: https://arxiv.org/abs/2602.01553 · HTML: https://mlsanity.com/paper/2602.01553/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 63 of its 84 references that are in the map.
- First posted on arXiv 2 Feb 2026.

## Builds on (most cited first, 30 of 63)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [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)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [FlashAttention: Fast and Memory-Efficient Exact Attention with IO-Awareness](https://mlsanity.com/paper/2205.14135/) (2022)
- [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)
- [Rethinking Attention with Performers](https://mlsanity.com/paper/2009.14794/) (2020)
- [Deep Sets](https://mlsanity.com/paper/1703.06114/) (2017)
- [Deeper Insights into Graph Convolutional Networks for Semi-Supervised Learning](https://mlsanity.com/paper/1801.07606/) (2018)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)
- [Link Prediction Based on Graph Neural Networks](https://mlsanity.com/paper/1802.09691/) (2018)
- [Exact solutions to the nonlinear dynamics of learning in deep linear neural networks](https://mlsanity.com/paper/1312.6120/) (2013)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [On the Bottleneck of Graph Neural Networks and its Practical Implications](https://mlsanity.com/paper/2006.05205/) (2020)
- [Understanding over-squashing and bottlenecks on graphs via curvature](https://mlsanity.com/paper/2111.14522/) (2021)
- [Rethinking Graph Transformers with Spectral Attention](https://mlsanity.com/paper/2106.03893/) (2021)
- [Invariant and Equivariant Graph Networks](https://mlsanity.com/paper/1812.09902/) (2018)
- [Do Transformers Really Perform Bad for Graph Representation?](https://mlsanity.com/paper/2106.05234/) (2021)
- [Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction](https://mlsanity.com/paper/2106.06935/) (2021)
- [Can Graph Neural Networks Count Substructures?](https://mlsanity.com/paper/2002.04025/) (2020)
- [Weisfeiler and Lehman Go Topological: Message Passing Simplicial Networks](https://mlsanity.com/paper/2103.03212/) (2021)
- [The Surprising Power of Graph Neural Networks with Random Node Initialization](https://mlsanity.com/paper/2010.01179/) (2020)
- [Identity-aware Graph Neural Networks](https://mlsanity.com/paper/2101.10320/) (2021)
- [Representing Long-Range Context for Graph Neural Networks with Global Attention](https://mlsanity.com/paper/2201.08821/) (2022)
- [Structure-Aware Transformer for Graph Representation Learning](https://mlsanity.com/paper/2202.03036/) (2022)
- [Pure Transformers are Powerful Graph Learners](https://mlsanity.com/paper/2207.02505/) (2022)

## Abstract (arXiv)

Link prediction is a core challenge in graph machine learning, demanding models that capture rich and complex topological dependencies. While Graph Neural Networks (GNNs) are the standard solution, state-of-the-art pipelines often rely on explicit structural heuristics or memory-intensive node embeddings -- approaches that struggle to generalize or scale to massive graphs. Emerging Graph Transformers (GTs) offer a potential alternative but often incur significant overhead due to complex structural encodings, hindering their applications to large-scale link prediction. We challenge these sophisticated paradigms with PENCIL, an encoder-only plain Transformer that replaces hand-crafted priors with attention over sampled local subgraphs, retaining the scalability and hardware efficiency of standard Transformers. Through experimental and theoretical analysis, we show that PENCIL extracts richer structural signals than GNNs, implicitly generalizing a broad class of heuristics and subgraph-based expressivity. Empirically, PENCIL outperforms heuristic-informed GNNs and is far more parameter-efficient than ID-embedding--based alternatives, while remaining competitive across diverse benchmarks -- even without node features. Our results challenge the prevailing reliance on complex engineering techniques, demonstrating that simple design choices are potentially sufficient to achieve the same capabilities. Our code is publicly available at https://github.com/quang-truong/pencil.