Graphlets as Building Blocks for Structural Vocabulary in Knowledge Graph Foundation Models

Knowledge graph (KG) foundation models (KGFMs) are zero-shot generalizers: trained once, they can predict links on unseen graphs without retraining. However, understanding when and how they can robustly generalize across KGs is still an open question. In this paper, we shed some light on their generalization mechanisms highlighting how their performance on unseen KGs is not uniform when it comes to partially seen links, which we call half-links. In fact, we show that to predict a test triple $(h,r,t)$ it might suffice in practice to have observed the half-link $(h,r)$ or $(r,t)$ in the inference graph. This yields a taxonomy of four scenarios when combinations of these half-links are observed or not. In a rigorous stratified analysis over these scenarios, we reveal that SoTA KGFMs use seen half links for predictions, while unseen half-links pose different challenges. As such, our finer-grained taxonomy can be a diagnostic protocol for robust KGFM generalization and highlights where novel KGFMs can improve.

Knowledge graph (KG) foundation models aim to generalize across graphs with unseen entities and relations by learning transferable relational structure. However, most existing methods primarily emphasize relation-level universality, while in-context learning, the other pillar of foundation models remains under-explored for KG reasoning. In KGs, context is inherently structured and heterogeneous: effective prediction requires conditioning on the local context around the query entities as well as the global context that summarizes how a relation behaves across many instances. We propose KGPFN, a KG foundation model using Prior-data Fitted Network that unifies transferable relational regularities with inference-time in-context learning from structured context. KGPFN first learns relation representations via message passing on relation graphs to capture cross-graph relational invariances. For query-specific reasoning, it encodes local neighborhoods using a multi-layer NBFNet as local context. To enable ICL at global scale, it constructs relation-specific global context by retrieving a large set of instances of the query relation together with their local neighborhoods, and aggregates them within a Prior-Data Fitted Network framework that combines feature-level and sample-level attention. Through multi-graph pretraining on diverse KGs, KGPFN learns when to instantiate reusable patterns and when to override them using contextual evidence. Experiments on 57 KG benchmarks demonstrate that KGPFN achieves strong adaptation to previously unseen graphs through in-context learning alone, consistently outperforming competitive fine-tuned KG foundation models. Our code is available at https://github.com/HKUST-KnowComp/KGPFN.

Knowledge graph foundation models such as ULTRA achieve zero-shot link prediction on unseen graphs through dedicated architectures that hard-code a transfer mechanism. In this work we move that mechanism out of the architecture and into the representation, by \emph{reifying} the input graph: every fact becomes a node, connected to its subject, object, and relation type through a fixed vocabulary of six meta-relations, with relation types as anonymous shared nodes rather than model parameters. On this representation, five textbook GNNs (GAT, GINE with sum and with mean+max aggregation, GraphSAGE, R-GCN), each trained on a single knowledge graph of 4,245 triples for 30 minutes on one NVIDIA A100, transfer zero-shot to 40 inductive link-prediction benchmarks. The best of them, an off-the-shelf GAT, matches ULTRA, a dedicated foundation model pretrained on three graphs, across ULTRA's own evaluation suite. The same fixed vocabulary extends to relational databases, a row becoming an entity and a foreign-key column a relation type; a preliminary probe on two unseen databases, with no cell values, schema text or in-context labels, shows a model of this family pretrained on three knowledge graphs ranking foreign-key targets far above random-initialization and degree controls. We release the code, the checkpoints, and the evaluation pipeline for all 40 benchmarks.