# Harnessing Structural Context for Entity Alignment Foundation Models

arXiv: https://arxiv.org/abs/2606.06109 · HTML: https://mlsanity.com/paper/2606.06109/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 25 of its 34 references that are in the map.
- First posted on arXiv 4 Jun 2026.

## Builds on (most cited first, 25 of 25)

- [A Survey on Knowledge Graphs: Representation, Acquisition and Applications](https://mlsanity.com/paper/2002.00388/) (2020)
- [Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Prediction](https://mlsanity.com/paper/2106.06935/) (2021)
- [Multilingual Knowledge Graph Embeddings for Cross-lingual Knowledge Alignment](https://mlsanity.com/paper/1611.03954/) (2016)
- [Cross-lingual Entity Alignment via Joint Attribute-Preserving Embedding](https://mlsanity.com/paper/1708.05045/) (2017)
- [A Benchmarking Study of Embedding-based Entity Alignment for Knowledge Graphs](https://mlsanity.com/paper/2003.07743/) (2020)
- [Knowledge Graph Alignment Network with Gated Multi-hop Neighborhood Aggregation](https://mlsanity.com/paper/1911.08936/) (2019)
- [Knowledge Graph Reasoning with Relational Digraph](https://mlsanity.com/paper/2108.06040/) (2021)
- [Towards Foundation Models for Knowledge Graph Reasoning](https://mlsanity.com/paper/2310.04562/) (2023)
- [Learning to Exploit Long-term Relational Dependencies in Knowledge Graphs](https://mlsanity.com/paper/1905.04914/) (2019)
- [Relational Reflection Entity Alignment](https://mlsanity.com/paper/2008.07962/) (2020)
- [Boosting the Speed of Entity Alignment 10*: Dual Attention Matching Network with Normalized Hard Sample Mining](https://mlsanity.com/paper/2103.15452/) (2021)
- [SelfKG: Self-Supervised Entity Alignment in Knowledge Graphs](https://mlsanity.com/paper/2203.01044/) (2022)
- [A Theory of Link Prediction via Relational Weisfeiler-Leman on Knowledge Graphs](https://mlsanity.com/paper/2302.02209/) (2023)
- [A Benchmark and Comprehensive Survey on Knowledge Graph Entity Alignment via Representation Learning](https://mlsanity.com/paper/2103.15059/) (2021)
- [A Prompt-Based Knowledge Graph Foundation Model for Universal In-Context Reasoning](https://mlsanity.com/paper/2410.12288/) (2024)
- [TRIX: A More Expressive Model for Zero-shot Domain Transfer in Knowledge Graphs](https://mlsanity.com/paper/2502.19512/) (2025)
- [How Expressive are Knowledge Graph Foundation Models?](https://mlsanity.com/paper/2502.13339/) (2025)
- [Entity Alignment with Noisy Annotations from Large Language Models](https://mlsanity.com/paper/2405.16806/) (2024)
- [ClusterEA: Scalable Entity Alignment with Stochastic Training and Normalized Mini-batch Similarities](https://mlsanity.com/paper/2205.10312/) (2022)
- [Informed Multi-context Entity Alignment](https://mlsanity.com/paper/2201.00304/) (2022)
- [Neuro-Symbolic Entity Alignment via Variational Inference](https://mlsanity.com/paper/2410.04153/) (2024)
- [Joint Pre-training and Local Re-training: Transferable Representation Learning on Multi-source Knowledge Graphs](https://mlsanity.com/paper/2306.02679/) (2023)
- [What Makes Entities Similar? A Similarity Flooding Perspective for Multi-sourced Knowledge Graph Embeddings](https://mlsanity.com/paper/2306.02622/) (2023)
- [Lambda: Learning Matchable Prior For Entity Alignment with Unlabeled Dangling Cases](https://mlsanity.com/paper/2403.10978/) (2024)
- [Breaking the Reasoning Horizon in Entity Alignment Foundation Models](https://mlsanity.com/paper/2601.21174/) (2026)

## Abstract (arXiv)

Entity alignment (EA) aims to identify equivalent entities across heterogeneous knowledge graphs (KGs) and is a key component of knowledge fusion and cross-KG reasoning. The recent EA foundation model demonstrates that alignment knowledge, once pretrained, can be directly applied to diverse previously unseen KG pairs. However, it still underuses structural context in two places: cross-KG interaction is weak during encoding, and final candidate ranking still relies too heavily on coarse similarity. We address these limitations with ContextEA, an enhanced encoder-decoder framework for transferable EA. On the encoder side, we introduce a cross-KG interaction encoder that unifies the two KGs with anchor bridges and performs earlier relation-aware cross-graph propagation. On the decoder side, we introduce a structural calibration decoder that calibrates alignment scores with entity-level, neighborhood-level, relation-level, and anchor-aware structural evidence. This design strengthens both structural context construction and structural context exploitation while remaining lightweight. Experiments on 29 EA datasets in OpenEA, SRPRS, and DBP show consistent gains over strong transferable baselines. Notably, the pretrained ContextEA already surpasses the finetuned baselines on all three benchmark groups, demonstrating substantially stronger transfer to unseen KGs. These results suggest that explicitly harnessing structural context is an effective direction for improving EA foundation models.