# HeterSEED: Semantics-Structure Decoupling for Heterogeneous Graph Learning under Heterophily

arXiv: https://arxiv.org/abs/2605.04594 · HTML: https://mlsanity.com/paper/2605.04594/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 36 references that are in the map.
- First posted on arXiv 6 May 2026.

## Builds on (most cited first, 21 of 21)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Modeling Relational Data with Graph Convolutional Networks](https://mlsanity.com/paper/1703.06103/) (2017)
- [Geom-GCN: Geometric Graph Convolutional Networks](https://mlsanity.com/paper/2002.05287/) (2020)
- [Heterogeneous Graph Attention Network](https://mlsanity.com/paper/1903.07293/) (2019)
- [Heterogeneous Graph Transformer](https://mlsanity.com/paper/2003.01332/) (2020)
- [Graph Transformer Networks](https://mlsanity.com/paper/1911.06455/) (2019)
- [Beyond Low-frequency Information in Graph Convolutional Networks](https://mlsanity.com/paper/2101.00797/) (2021)
- [Large Scale Learning on Non-Homophilous Graphs: New Benchmarks and Strong Simple Methods](https://mlsanity.com/paper/2110.14446/) (2021)
- [MAGNN: Metapath Aggregated Graph Neural Network for Heterogeneous Graph Embedding](https://mlsanity.com/paper/2002.01680/) (2020)
- [Are we really making much progress? Revisiting, benchmarking, and refining heterogeneous graph neural networks](https://mlsanity.com/paper/2112.14936/) (2021)
- [Graph Neural Networks for Graphs with Heterophily: A Survey](https://mlsanity.com/paper/2202.07082/) (2022)
- [Revisiting Heterophily For Graph Neural Networks](https://mlsanity.com/paper/2210.07606/) (2022)
- [A Survey on Heterogeneous Graph Embedding: Methods, Techniques, Applications and Sources](https://mlsanity.com/paper/2011.14867/) (2020)
- [HINormer: Representation Learning On Heterogeneous Information Networks with Graph Transformer](https://mlsanity.com/paper/2302.11329/) (2023)
- [When Heterophily Meets Heterogeneous Graphs: Latent Graphs Guided Unsupervised Representation Learning](https://mlsanity.com/paper/2409.00687/) (2024)
- [DiffGraph: Heterogeneous Graph Diffusion Model](https://mlsanity.com/paper/2501.02313/) (2025)
- [Seq-HGNN: Learning Sequential Node Representation on Heterogeneous Graph](https://mlsanity.com/paper/2305.10771/) (2023)
- [GRAIN: Multi-Granular and Implicit Information Aggregation Graph Neural Network for Heterophilous Graphs](https://mlsanity.com/paper/2504.06649/) (2025)
- [Adaptive Heterogeneous Graph Neural Networks: Bridging Heterophily and Heterogeneity](https://mlsanity.com/paper/2508.06034/) (2025)
- [On the Cross-type Homophily of Heterogeneous Graphs: Understanding and Unleashing](https://mlsanity.com/paper/2501.14600/) (2025)

## Abstract (arXiv)

Many real-world heterogeneous graphs exhibit pronounced heterophily, where connected nodes often have dissimilar labels or play different semantic roles. In such settings, standard heterogeneous graph neural networks that aggregate messages along metapaths or meta-relations primarily based on feature similarity can propagate misleading information, since feature similarity may be misaligned with underlying relational semantics. In this paper, we propose HeterSEED, a semantics-structure decoupling framework for heterogeneous graph learning under heterophily. HeterSEED decouples representation learning into a heterogeneous semantic channel that captures type- and relation-aware local semantics and a structure-aware heterophily channel that separates homophilic and heterophilic neighborhoods via pseudo-label-guided partitioning and aggregates them using metapath-based structural weights. A node-level adaptive fusion mechanism then combines the two channels to produce context-dependent node representations. Theoretically, we establish that, on heterogeneous graphs under heterophily, HeterSEED is strictly more expressive than standard heterogeneous graph neural networks that rely primarily on feature similarity and provably reduces the prediction bias introduced by heterophilic neighbors. Experiments on five real-world heterogeneous graphs, including two large-scale networks at the million-node and hundred-million-edge scale, demonstrate that HeterSEED consistently outperforms representative heterogeneous graph neural networks and recent heterophily-aware baselines, especially in strongly heterophilic regimes.