Towards Effective Federated Graph Foundation Model via Mitigating Knowledge Entanglement

Recent advances in graph machine learning have shifted to data-centric paradigms, driven by two emerging research fields: (1) Federated graph learning (FGL) facilitates multi-client collaboration but struggles with data and task heterogeneity, resulting in limited practicality; (2) Graph foundation model (GFM) enables desirable domain generalization but is typically confined to single-machine training, neglecting the potential of cross-silo data and computational resources. It is evident that these two paradigms are complementary, and their integration offers substantial advantages. Motivated by this, we present a pioneering study about the federated graph foundation model (FedGFM), a novel decentralized GFM training paradigm. Despite the promising vision of FedGFM, knowledge entanglement has emerged as a critical challenge, where multi-domain knowledge is encoded into indistinguishable representations, thereby limiting downstream adaptation. To this end, we propose FedGFM+, an effective FedGFM framework with two key modules to mitigate knowledge entanglement in a dual-pronged manner. (1) AncDAI: From a global perspective, we introduce a novel anchor-based domain-aware initialization strategy. Before pre-training, each client encodes its local graph into a domain-specific prototypes, which serve as semantic anchors in the representation space. Around each anchor, we construct synthetic embeddings to initialize the global model. We theoretically show that these prototypes are distinguishable across domains, and the initialization provides a strong inductive bias that facilitates disentanglement of domain-specific knowledge. (2) AdaDPP: From a local perspective, during pre-training, each client independently learns a lightweight graph prompt that captures domain semantic preferences. During fine-tuning, prompts from all clients are aggregated into an adaptive domain-sensitive prompt pool, from which the GFM selects relevant prompts to augment the target graph’s attributes, thereby improving the downstream adaptation. FedGFM+ is extensively evaluated on 8 diverse benchmarks spanning multiple domains and tasks, outperforming 20 baselines from isolated supervised learning, FGL, and federated variants of centralized GFM paradigms.