# Towards Effective Federated Graph Foundation Model via Mitigating Knowledge Entanglement

arXiv: https://arxiv.org/abs/2505.12684 · HTML: https://mlsanity.com/paper/2505.12684/

## Key facts

- Cited by 14 papers in the map (data through 14 Oct 2026).
- Builds on 55 of its 66 references that are in the map.
- First posted on arXiv 19 May 2025.

## Builds on (most cited first, 30 of 55)

- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Llama 2: Open Foundation and Fine-Tuned Chat Models](https://mlsanity.com/paper/2307.09288/) (2023)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Communication-Efficient Learning of Deep Networks from Decentralized Data](https://mlsanity.com/paper/1602.05629/) (2016)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [PaLM: Scaling Language Modeling with Pathways](https://mlsanity.com/paper/2204.02311/) (2022)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [A Comprehensive Survey on Graph Neural Networks](https://mlsanity.com/paper/1901.00596/) (2019)
- [Optuna: A Next-generation Hyperparameter Optimization Framework](https://mlsanity.com/paper/1907.10902/) (2019)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Estimating or Propagating Gradients Through Stochastic Neurons for Conditional Computation](https://mlsanity.com/paper/1308.3432/) (2013)
- [Graph Neural Networks: A Review of Methods and Applications](https://mlsanity.com/paper/1812.08434/) (2018)
- [Spectral Networks and Locally Connected Networks on Graphs](https://mlsanity.com/paper/1312.6203/) (2013)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)
- [Model-Contrastive Federated Learning](https://mlsanity.com/paper/2103.16257/) (2021)
- [Convolutional 2D Knowledge Graph Embeddings](https://mlsanity.com/paper/1707.01476/) (2017)
- [Wiki-CS: A Wikipedia-Based Benchmark for Graph Neural Networks](https://mlsanity.com/paper/2007.02901/) (2020)
- [One for All: Towards Training One Graph Model for All Classification Tasks](https://mlsanity.com/paper/2310.00149/) (2023)
- [Subgraph Federated Learning with Missing Neighbor Generation](https://mlsanity.com/paper/2106.13430/) (2021)
- [Federated Graph Classification over Non-IID Graphs](https://mlsanity.com/paper/2106.13423/) (2021)
- [Federated Learning on Non-IID Graphs via Structural Knowledge Sharing](https://mlsanity.com/paper/2211.13009/) (2022)
- [GFT: Graph Foundation Model with Transferable Tree Vocabulary](https://mlsanity.com/paper/2411.06070/) (2024)
- [OpenGraph: Towards Open Graph Foundation Models](https://mlsanity.com/paper/2403.01121/) (2024)
- [UniGraph: Learning a Unified Cross-Domain Foundation Model for Text-Attributed Graphs](https://mlsanity.com/paper/2402.13630/) (2024)
- [Augmenting Low-Resource Text Classification with Graph-Grounded Pre-training and Prompting](https://mlsanity.com/paper/2305.03324/) (2023)
- [SAMGPT: Text-free Graph Foundation Model for Multi-domain Pre-training and Cross-domain Adaptation](https://mlsanity.com/paper/2502.05424/) (2025)

## Built on by (most cited first, 14 of 14)

- [FedBook: A Unified Federated Graph Foundation Codebook with Intra-domain and Inter-domain Knowledge Modeling](https://mlsanity.com/paper/2510.07755/) (2025)
- [A Comprehensive Data-centric Overview of Federated Graph Learning](https://mlsanity.com/paper/2507.16541/) (2025)
- [TMTE: Effective Multimodal Graph Learning with Task-aware Modality and Topology Co-evolution](https://mlsanity.com/paper/2603.27723/) (2026)
- [Rethinking Federated Graph Foundation Models: A Graph-Language Alignment-based Approach](https://mlsanity.com/paper/2601.21369/) (2026)
- [GRM: Utility-Aware Jailbreak Attacks on Audio LLMs via Gradient-Ratio Masking](https://mlsanity.com/paper/2604.09222/) (2026)
- [Riemannian Geometry Speaks Louder Than Words: From Graph Foundation Model to Next-Generation Graph Intelligence](https://mlsanity.com/paper/2603.21601/) (2026)
- [FedLAB: Traceable Semantic Codebooks for Federated Multimodal Graph Foundation Learning](https://mlsanity.com/paper/2606.32016/) (2026)
- [Toward Federated Multimodal Graph Foundation Models: A Topology-Aware Multimodal Alignment Framework](https://mlsanity.com/paper/2607.15687/) (2026)
- [Towards Effective Federated Multimodal Graph Learning via Navigating Multifaceted Heterogeneity](https://mlsanity.com/paper/2608.00623/) (2026)
- [DANCE: Dynamic, Available, Neighbor-gated Condensation for Federated Text-Attributed Graphs](https://mlsanity.com/paper/2601.16519/) (2026)
- [A Unified Graph Language Model for Multi-Domain Multi-Task Graph Alignment Instruction Tuning](https://mlsanity.com/paper/2605.12197/) (2026)
- [MMFGU: Multimodal Federated Graph Unlearning](https://mlsanity.com/paper/2607.28708/) (2026)
- [Towards Adaptive Federated Graph Clustering: A Global Community-aware Contrastive Learning-based Approach](https://mlsanity.com/paper/2609.26063/) (2026)
- [Coupling Perception and Reasoning in Federated Multimodal Graph Foundation Models](https://mlsanity.com/paper/2610.00277/) (2026)

## Abstract (arXiv)

Recent advances in graph machine learning have shifted to data-centric paradigms, driven by two emerging fields: (1) Federated graph learning (FGL) enables multi-client collaboration but faces challenges from data and task heterogeneity, limiting its practicality; (2) Graph foundation models (GFM) offer strong domain generalization but are usually trained on single machines, missing out on cross-silo data and resources. These paradigms are complementary, and their integration brings notable benefits. Motivated by this, we propose FedGFM, a novel decentralized GFM training paradigm. However, a key challenge is knowledge entanglement, where multi-domain knowledge merges into indistinguishable representations, hindering downstream adaptation. To address this, we present FedGFM+, an enhanced framework with two core modules to reduce knowledge entanglement: (1) AncDAI: A global anchor-based domain-aware initialization strategy. Before pre-training, each client encodes its local graph into domain-specific prototypes that serve as semantic anchors. Synthetic embeddings around these anchors initialize the global model. We theoretically prove these prototypes are distinguishable across domains, providing a strong inductive bias to disentangle domain-specific knowledge. (2) AdaDPP: A local adaptive domain-sensitive prompt pool. Each client learns a lightweight graph prompt capturing domain semantics during pre-training. During fine-tuning, prompts from all clients form a pool from which the GFM selects relevant prompts to augment target graph attributes, improving downstream adaptation. FedGFM+ is evaluated on 8 diverse benchmarks across multiple domains and tasks, outperforming 20 baselines from supervised learning, FGL, and federated GFM variants.