# Enhancing Graph Transformers with Hierarchical Distance Structural Encoding

arXiv: https://arxiv.org/abs/2308.11129 · HTML: https://mlsanity.com/paper/2308.11129/

## Key facts

- Cited by 16 papers in the map (data through 14 Oct 2026).
- Builds on 65 of its 97 references that are in the map.
- First posted on arXiv 22 Aug 2023.

## Builds on (most cited first, 30 of 65)

- [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)
- [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)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (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)
- [Simplifying Graph Convolutional Networks](https://mlsanity.com/paper/1902.07153/) (2019)
- [Linformer: Self-Attention with Linear Complexity](https://mlsanity.com/paper/2006.04768/) (2020)
- [Geometric Deep Learning: Grids, Groups, Graphs, Geodesics, and Gauges](https://mlsanity.com/paper/2104.13478/) (2021)
- [Predict then Propagate: Graph Neural Networks meet Personalized PageRank](https://mlsanity.com/paper/1810.05997/) (2018)
- [Representation Learning on Graphs with Jumping Knowledge Networks](https://mlsanity.com/paper/1806.03536/) (2018)
- [Geom-GCN: Geometric Graph Convolutional Networks](https://mlsanity.com/paper/2002.05287/) (2020)
- [Hierarchical Graph Representation Learning with Differentiable Pooling](https://mlsanity.com/paper/1806.08804/) (2018)
- [Recipe for a General, Powerful, Scalable Graph Transformer](https://mlsanity.com/paper/2205.12454/) (2022)
- [Benchmarking Graph Neural Networks](https://mlsanity.com/paper/2003.00982/) (2020)
- [A Generalization of Transformer Networks to Graphs](https://mlsanity.com/paper/2012.09699/) (2020)
- [On the Bottleneck of Graph Neural Networks and its Practical Implications](https://mlsanity.com/paper/2006.05205/) (2020)
- [Adaptive Universal Generalized PageRank Graph Neural Network](https://mlsanity.com/paper/2006.07988/) (2020)
- [Multi-scale Attributed Node Embedding](https://mlsanity.com/paper/1909.13021/) (2019)
- [Graph U-Nets](https://mlsanity.com/paper/1905.05178/) (2019)
- [Principal Neighbourhood Aggregation for Graph Nets](https://mlsanity.com/paper/2004.05718/) (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)
- [Self-Attention Graph Pooling](https://mlsanity.com/paper/1904.08082/) (2019)
- [GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models](https://mlsanity.com/paper/1802.08773/) (2018)
- [Residual Gated Graph ConvNets](https://mlsanity.com/paper/1711.07553/) (2017)
- [Graph Neural Networks with Learnable Structural and Positional Representations](https://mlsanity.com/paper/2110.07875/) (2021)

## Built on by (most cited first, 16 of 16)

- [Classic GNNs are Strong Baselines: Reassessing GNNs for Node Classification](https://mlsanity.com/paper/2406.08993/) (2024)
- [When is Task Vector Provably Effective for Model Editing? A Generalization Analysis of Nonlinear Transformers](https://mlsanity.com/paper/2504.10957/) (2025)
- [How Do Nonlinear Transformers Learn and Generalize in In-Context Learning?](https://mlsanity.com/paper/2402.15607/) (2024)
- [Can Classic GNNs Be Strong Baselines for Graph-level Tasks? Simple Architectures Meet Excellence](https://mlsanity.com/paper/2502.09263/) (2025)
- [Spatio-Spectral Graph Neural Networks](https://mlsanity.com/paper/2405.19121/) (2024)
- [What Improves the Generalization of Graph Transformers? A Theoretical Dive into the Self-attention and Positional Encoding](https://mlsanity.com/paper/2406.01977/) (2024)
- [A Survey of Graph Transformers: Architectures, Theories and Applications](https://mlsanity.com/paper/2502.16533/) (2025)
- [Best of Both Worlds: Advantages of Hybrid Graph Sequence Models](https://mlsanity.com/paper/2411.15671/) (2024)
- [Molecular Fingerprints Are Strong Models for Peptide Function Prediction](https://mlsanity.com/paper/2501.17901/) (2025)
- [DualEquiNet: A Dual-Space Hierarchical Equivariant Network for Large Biomolecules](https://mlsanity.com/paper/2506.19862/) (2025)
- [How Can Mamba Learn In Context with Outliers and Generalize Provably?](https://mlsanity.com/paper/2510.00399/) (2025)
- [Simple Path Structural Encoding for Graph Transformers](https://mlsanity.com/paper/2502.09365/) (2025)
- [ReSSFormer: A Recursive Sparse Structured Transformer for Scalable and Long-Context Reasoning](https://mlsanity.com/paper/2510.01585/) (2025)
- [Heterogeneous Graph Alignment for Joint Reasoning and Interpretability](https://mlsanity.com/paper/2601.22593/) (2026)
- [Transformers Learn the Optimal DDPM Denoiser for Multi-Token GMMs](https://mlsanity.com/paper/2604.10074/) (2026)
- [Adaptive Multi-Agent Feature Selection for Personalized Fall Risk Prevention](https://mlsanity.com/paper/2608.18450/) (2026)

## Abstract (arXiv)

Graph transformers need strong inductive biases to derive meaningful attention scores. Yet, current methods often fall short in capturing longer ranges, hierarchical structures, or community structures, which are common in various graphs such as molecules, social networks, and citation networks. This paper presents a Hierarchical Distance Structural Encoding (HDSE) method to model node distances in a graph, focusing on its multi-level, hierarchical nature. We introduce a novel framework to seamlessly integrate HDSE into the attention mechanism of existing graph transformers, allowing for simultaneous application with other positional encodings. To apply graph transformers with HDSE to large-scale graphs, we further propose a high-level HDSE that effectively biases the linear transformers towards graph hierarchies. We theoretically prove the superiority of HDSE over shortest path distances in terms of expressivity and generalization. Empirically, we demonstrate that graph transformers with HDSE excel in graph classification, regression on 7 graph-level datasets, and node classification on 11 large-scale graphs, including those with up to a billion nodes.