mlsanityData to 7 Oct 2026

Bringing Light Into the Dark: A Large-scale Evaluation of Knowledge Graph Embedding Models Under a Unified Framework

arXiv 2006.13365 ↗First posted 23 Jun 2020cs.LG cs.AI stat.MLcited by 70

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Abstract (arXiv)

The heterogeneity in recently published knowledge graph embedding models' implementations, training, and evaluation has made fair and thorough comparisons difficult. In order to assess the reproducibility of previously published results, we re-implemented and evaluated 21 interaction models in the PyKEEN software package. Here, we outline which results could be reproduced with their reported hyper-parameters, which could only be reproduced with alternate hyper-parameters, and which could not be reproduced at all as well as provide insight as to why this might be the case. We then performed a large-scale benchmarking on four datasets with several thousands of experiments and 24,804 GPU hours of computation time. We present insights gained as to best practices, best configurations for each model, and where improvements could be made over previously published best configurations. Our results highlight that the combination of model architecture, training approach, loss function, and the explicit modeling of inverse relations is crucial for a model's performances, and not only determined by the model architecture. We provide evidence that several architectures can obtain results competitive to the state-of-the-art when configured carefully. We have made all code, experimental configurations, results, and analyses that lead to our interpretations available at https://github.com/pykeen/pykeen and https://github.com/pykeen/benchmarking

Key facts. Cited by 70 papers in the map (data through 7 Oct 2026). First posted on arXiv 23 Jun 2020.

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Citing papers per year: 2021: 11; 2022: 15; 2023: 21; 2024: 15; 2025: 6; 2026: 2.

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  1. 2022A Survey of Knowledge Graph Reasoning on Graph Types: Static, Dynamic, and Multimodalcited by 106
  2. 2023Towards Foundation Models for Knowledge Graph Reasoningcited by 83
  3. 2021NodePiece: Compositional and Parameter-Efficient Representations of Large Knowledge Graphscited by 71
  4. 2023Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarkingcited by 69
  5. 2022A Decade of Knowledge Graphs in Natural Language Processing: A Surveycited by 40
  6. 2021A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspectivecited by 37
  7. 2023Neural Graph Reasoning: Complex Logical Query Answering Meets Graph Databasescited by 35
  8. 2022Weisfeiler and Leman Go Relationalcited by 28
  9. 2022An Open Challenge for Inductive Link Prediction on Knowledge Graphscited by 26
  10. 2022Inductive Logical Query Answering in Knowledge Graphscited by 25
  11. 2021Query Embedding on Hyper-relational Knowledge Graphscited by 23
  12. 2021Improving Inductive Link Prediction Using Hyper-Relational Factscited by 21
38 more
  1. 2023Visual Question Answering: A Survey on Techniques and Common Trends in Recent Literaturecited by 20
  2. 2021Understanding the Performance of Knowledge Graph Embeddings in Drug Discoverycited by 18
  3. 2022A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphscited by 14
  4. 2022Comprehensive Analysis of Negative Sampling in Knowledge Graph Representation Learningcited by 12
  5. 2023Construction of Knowledge Graphs: State and Challengescited by 12
  6. 2021Implications of Topological Imbalance for Representation Learning on Biomedical Knowledge Graphscited by 11
  7. 2021Improving Scene Graph Classification by Exploiting Knowledge from Textscited by 10
  8. 2023Sem@K: Is my knowledge graph embedding model semantic-aware?cited by 10
  9. 2021Knowledge Sheaves: A Sheaf-Theoretic Framework for Knowledge Graph Embeddingcited by 9
  10. 2023Cognitive Semantic Communication Systems Driven by Knowledge Graph: Principle, Implementation, and Performance Evaluationcited by 8
  11. 2024Comprehensible Artificial Intelligence on Knowledge Graphs: A surveycited by 8
  12. 2022KGTuner: Efficient Hyper-parameter Search for Knowledge Graph Learningcited by 7
  13. 2022Re-thinking Knowledge Graph Completion Evaluation from an Information Retrieval Perspectivecited by 7
  14. 2022A Retrieve-and-Read Framework for Knowledge Graph Link Predictioncited by 6
  15. 2023KGrEaT: A Framework to Evaluate Knowledge Graphs via Downstream Taskscited by 6
  16. 2021EAGER: Embedding-Assisted Entity Resolution for Knowledge Graphscited by 5
  17. 2023Knowledge Graphs Queryingcited by 5
  18. 2023BioBLP: A Modular Framework for Learning on Multimodal Biomedical Knowledge Graphscited by 5
  19. 2021Updating Embeddings for Dynamic Knowledge Graphscited by 4
  20. 2022Relational representation learning with spike trainscited by 4
  21. 2023Clinical Trial Recommendations Using Semantics-Based Inductive Inference and Knowledge Graph Embeddingscited by 4
  22. 2023Treat Different Negatives Differently: Enriching Loss Functions with Domain and Range Constraints for Link Predictioncited by 3
  23. 2023Towards Semantically Enriched Embeddings for Knowledge Graph Completioncited by 3
  24. 2024Neurosymbolic Methods for Dynamic Knowledge Graphscited by 3
  25. 2021Prediction of Adverse Biological Effects of Chemicals Using Knowledge Graph Embeddingscited by 2
  26. 2022LEMON: LanguagE ModeL for Negative Sampling of Knowledge Graph Embeddingscited by 2
  27. 2024TWIG: Towards pre-hoc Hyperparameter Optimisation and Cross-Graph Generalisation via Simulated KGE Modelscited by 2
  28. 2024Aligning Multiple Knowledge Graphs in a Single Passcited by 2
  29. 2024The Role of Graph Topology in the Performance of Biomedical Knowledge Graph Completion Modelscited by 2
  30. 2024A Survey on Knowledge Graph Structure and Knowledge Graph Embeddingscited by 2
  31. 2025ReaLitE: Enrichment of Relation Embeddings in Knowledge Graphs using Numeric Literalscited by 2
  32. 2025On Large-scale Evaluation of Embedding Models for Knowledge Graph Completioncited by 2
  33. 2025Knowledge-augmented Pre-trained Language Models for Biomedical Relation Extractioncited by 2
  34. 2025Understanding Generalization in Node and Link Predictioncited by 2
  35. 2022Start Small, Think Big: On Hyperparameter Optimization for Large-Scale Knowledge Graph Embeddingscited by 1
  36. 2022Embeddings as Epistemic States: Limitations on the Use of Pooling Operators for Accumulating Knowledgecited by 1
  37. 2022Leveraging Wikidata's edit history in knowledge graph refinement taskscited by 1
  38. 2023Can Persistent Homology provide an efficient alternative for Evaluation of Knowledge Graph Completion Methods?cited by 1

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