mlsanityData to 14 Oct 2026

Reification as a Transferable Vocabulary: Zero-Shot Link Prediction with Vanilla GNNs

arXiv 2609.11347 ↗First posted 10 Sep 2026cs.LG cs.AIcited by 0

Not on the map. Why?

Abstract (arXiv)

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 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.

Key facts. No citing papers in the map yet (data through 14 Oct 2026). Builds on 40 of its 45 references that are in the map. First posted on arXiv 10 Sep 2026.

Builds on

40 of 45 references.

References · 40

  1. 2017Graph Attention Networkscited by 8,923
  2. 2017Inductive Representation Learning on Large Graphscited by 6,320
  3. 2018How Powerful are Graph Neural Networks?cited by 4,393
  4. 2019Fast Graph Representation Learning with PyTorch Geometriccited by 2,434
  5. 2017Modeling Relational Data with Graph Convolutional Networkscited by 1,694
  6. 2019Strategies for Pre-training Graph Neural Networkscited by 971
  7. 2022TabPFN: A Transformer That Solves Small Tabular Classification Problems in a Secondcited by 674
  8. 2025TabICL: A Tabular Foundation Model for In-Context Learning on Large Datacited by 289
  9. 2021Neural Bellman-Ford Networks: A General Graph Neural Network Framework for Link Predictioncited by 275
  10. 2019Inductive Relation Prediction by Subgraph Reasoningcited by 239
  11. 2020Labeling Trick: A Theory of Using Graph Neural Networks for Multi-Node Representation Learningcited by 149
  12. 2017Knowledge Transfer for Out-of-Knowledge-Base Entities: A Graph Neural Network Approachcited by 102
28 more
  1. 2024RelBench: A Benchmark for Deep Learning on Relational Databasescited by 96
  2. 2023Towards Foundation Models for Knowledge Graph Reasoningcited by 86
  3. 2024Position: Graph Foundation Models are Already Herecited by 86
  4. 2020Message Passing for Hyper-Relational Knowledge Graphscited by 79
  5. 2020Relational Message Passing for Knowledge Graph Completioncited by 61
  6. 2023Relational Deep Learning: Graph Representation Learning on Relational Databasescited by 56
  7. 2022A*Net: A Scalable Path-based Reasoning Approach for Knowledge Graphscited by 49
  8. 2025Relational Transformer: Toward Zero-Shot Foundation Models for Relational Datacited by 39
  9. 2023A Theory of Link Prediction via Relational Weisfeiler-Leman on Knowledge Graphscited by 32
  10. 2022Relational Message Passing for Fully Inductive Knowledge Graph Completioncited by 30
  11. 2022AdaProp: Learning Adaptive Propagation for Graph Neural Network based Knowledge Graph Reasoningcited by 28
  12. 2022An Open Challenge for Inductive Link Prediction on Knowledge Graphscited by 26
  13. 2024A Prompt-Based Knowledge Graph Foundation Model for Universal In-Context Reasoningcited by 25
  14. 2023A Multi-Task Perspective for Link Prediction with New Relation Types and Nodescited by 24
  15. 2025TRIX: A More Expressive Model for Zero-shot Domain Transfer in Knowledge Graphscited by 24
  16. 2025How Expressive are Knowledge Graph Foundation Models?cited by 23
  17. 2023Double Equivariance for Inductive Link Prediction for Both New Nodes and New Relation Typescited by 21
  18. 2026KumoRFM-2: Scaling Foundation Models for Relational Learningcited by 19
  19. 2024LLM as Prompter: Low-resource Inductive Reasoning on Arbitrary Knowledge Graphscited by 13
  20. 2025Flock: A Knowledge Graph Foundation Model via Learning on Random Walkscited by 9
  21. 2025SEMMA: A Semantic Aware Knowledge Graph Foundation Modelcited by 8
  22. 2025HYPER: A Foundation Model for Inductive Link Prediction with Knowledge Hypergraphscited by 7
  23. 2024Towards Graph Foundation Models: Training on Knowledge Graphs Enables Transferability to General Graphscited by 6
  24. 2025A Survey of Link Prediction in N-ary Knowledge Graphscited by 4
  25. 2023Calibrate and Boost Logical Expressiveness of GNN Over Multi-Relational and Temporal Graphscited by 2
  26. 2026KGPFN: Unlocking the Potential of Knowledge Graph Foundation Model via In-Context Learningcited by 2
  27. 2025Geometric Structural Knowledge Graph Foundation Modelcited by 1
  28. 2026Graphlets as Building Blocks for Structural Vocabulary in Knowledge Graph Foundation Modelscited by 1

Built on by

Not cited yet.