Bringing Light Into the Dark: A Large-scale Evaluation of Knowledge Graph Embedding Models Under a Unified Framework
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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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- 2022A Survey of Knowledge Graph Reasoning on Graph Types: Static, Dynamic, and Multimodalcited by 106
- 2023Towards Foundation Models for Knowledge Graph Reasoningcited by 83
- 2021NodePiece: Compositional and Parameter-Efficient Representations of Large Knowledge Graphscited by 71
- 2023Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarkingcited by 69
- 2022A Decade of Knowledge Graphs in Natural Language Processing: A Surveycited by 40
- 2021A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspectivecited by 37
- 2023Neural Graph Reasoning: Complex Logical Query Answering Meets Graph Databasescited by 35
- 2022Weisfeiler and Leman Go Relationalcited by 28
- 2022An Open Challenge for Inductive Link Prediction on Knowledge Graphscited by 26
- 2022Inductive Logical Query Answering in Knowledge Graphscited by 25
- 2021Query Embedding on Hyper-relational Knowledge Graphscited by 23
- 2021Improving Inductive Link Prediction Using Hyper-Relational Factscited by 21
38 more
- 2023Visual Question Answering: A Survey on Techniques and Common Trends in Recent Literaturecited by 20
- 2021Understanding the Performance of Knowledge Graph Embeddings in Drug Discoverycited by 18
- 2022A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphscited by 14
- 2022Comprehensive Analysis of Negative Sampling in Knowledge Graph Representation Learningcited by 12
- 2023Construction of Knowledge Graphs: State and Challengescited by 12
- 2021Implications of Topological Imbalance for Representation Learning on Biomedical Knowledge Graphscited by 11
- 2021Improving Scene Graph Classification by Exploiting Knowledge from Textscited by 10
- 2023Sem@K: Is my knowledge graph embedding model semantic-aware?cited by 10
- 2021Knowledge Sheaves: A Sheaf-Theoretic Framework for Knowledge Graph Embeddingcited by 9
- 2023Cognitive Semantic Communication Systems Driven by Knowledge Graph: Principle, Implementation, and Performance Evaluationcited by 8
- 2024Comprehensible Artificial Intelligence on Knowledge Graphs: A surveycited by 8
- 2022KGTuner: Efficient Hyper-parameter Search for Knowledge Graph Learningcited by 7
- 2022Re-thinking Knowledge Graph Completion Evaluation from an Information Retrieval Perspectivecited by 7
- 2022A Retrieve-and-Read Framework for Knowledge Graph Link Predictioncited by 6
- 2023KGrEaT: A Framework to Evaluate Knowledge Graphs via Downstream Taskscited by 6
- 2021EAGER: Embedding-Assisted Entity Resolution for Knowledge Graphscited by 5
- 2023Knowledge Graphs Queryingcited by 5
- 2023BioBLP: A Modular Framework for Learning on Multimodal Biomedical Knowledge Graphscited by 5
- 2021Updating Embeddings for Dynamic Knowledge Graphscited by 4
- 2022Relational representation learning with spike trainscited by 4
- 2023Clinical Trial Recommendations Using Semantics-Based Inductive Inference and Knowledge Graph Embeddingscited by 4
- 2023Treat Different Negatives Differently: Enriching Loss Functions with Domain and Range Constraints for Link Predictioncited by 3
- 2023Towards Semantically Enriched Embeddings for Knowledge Graph Completioncited by 3
- 2024Neurosymbolic Methods for Dynamic Knowledge Graphscited by 3
- 2021Prediction of Adverse Biological Effects of Chemicals Using Knowledge Graph Embeddingscited by 2
- 2022LEMON: LanguagE ModeL for Negative Sampling of Knowledge Graph Embeddingscited by 2
- 2024TWIG: Towards pre-hoc Hyperparameter Optimisation and Cross-Graph Generalisation via Simulated KGE Modelscited by 2
- 2024Aligning Multiple Knowledge Graphs in a Single Passcited by 2
- 2024The Role of Graph Topology in the Performance of Biomedical Knowledge Graph Completion Modelscited by 2
- 2024A Survey on Knowledge Graph Structure and Knowledge Graph Embeddingscited by 2
- 2025ReaLitE: Enrichment of Relation Embeddings in Knowledge Graphs using Numeric Literalscited by 2
- 2025On Large-scale Evaluation of Embedding Models for Knowledge Graph Completioncited by 2
- 2025Knowledge-augmented Pre-trained Language Models for Biomedical Relation Extractioncited by 2
- 2025Understanding Generalization in Node and Link Predictioncited by 2
- 2022Start Small, Think Big: On Hyperparameter Optimization for Large-Scale Knowledge Graph Embeddingscited by 1
- 2022Embeddings as Epistemic States: Limitations on the Use of Pooling Operators for Accumulating Knowledgecited by 1
- 2022Leveraging Wikidata's edit history in knowledge graph refinement taskscited by 1
- 2023Can Persistent Homology provide an efficient alternative for Evaluation of Knowledge Graph Completion Methods?cited by 1
50 most cited of 70 All 70 (JSON)
- 2026Recipe-Controlled Decoder Audit for Structural Knowledge-Graph Completion12 Jun 2026
- 2026In Data or Invisible: Toward a Better Digital Representation of Low-Resource Languages with Knowledge Graphs7 May 2026
- 2025Geometric Structural Knowledge Graph Foundation Model28 Dec 2025
- 2025Understanding Generalization in Node and Link Prediction1 Jul 2025
- 2025On the Theoretical Limitations of Embedding-based Link Prediction27 Jun 2025
- 2025Knowledge-augmented Pre-trained Language Models for Biomedical Relation Extraction1 May 2025
- 2025On Large-scale Evaluation of Embedding Models for Knowledge Graph Completion11 Apr 2025
- 2025ReaLitE: Enrichment of Relation Embeddings in Knowledge Graphs using Numeric Literals1 Apr 2025
- 2024Extending TWIG: Zero-Shot Predictive Hyperparameter Selection for KGEs based on Graph Structure19 Dec 2024
- 2024A Survey on Knowledge Graph Structure and Knowledge Graph Embeddings13 Dec 2024
- 2024A Pluggable Common Sense-Enhanced Framework for Knowledge Graph Completion6 Oct 2024
- 2024Neurosymbolic Methods for Dynamic Knowledge Graphs6 Sep 2024
38 more
- 2024The Role of Graph Topology in the Performance of Biomedical Knowledge Graph Completion Models6 Sep 2024
- 2024Aligning Multiple Knowledge Graphs in a Single Pass1 Aug 2024
- 2024Predicting Genetic Mutation from Whole Slide Images via Biomedical-Linguistic Knowledge Enhanced Multi-label Classification5 Jun 2024
- 2024From Latent to Lucid: Transforming Knowledge Graph Embeddings into Interpretable Structures with KGEPrisma3 Jun 2024
- 2024Predicting drug-gene relations via analogy tasks with word embeddings3 Jun 2024
- 2024Empowering Small-Scale Knowledge Graphs: A Strategy of Leveraging General-Purpose Knowledge Graphs for Enriched Embeddings17 May 2024
- 2024Comprehensible Artificial Intelligence on Knowledge Graphs: A survey4 Apr 2024
- 2024Infusing Knowledge into Large Language Models with Contextual Prompts3 Mar 2024
- 2024Veni, Vidi, Vici: Solving the Myriad of Challenges before Knowledge Graph Learning8 Feb 2024
- 2024TWIG: Towards pre-hoc Hyperparameter Optimisation and Cross-Graph Generalisation via Simulated KGE Models8 Feb 2024
- 2024Pre-training and Diagnosing Knowledge Base Completion Models27 Jan 2024
- 2023Knowledge Graphs are not Created Equal: Exploring the Properties and Structure of Real KGs10 Nov 2023
- 2023Unlock Reliable Skill Inference for Quadruped Adaptive Behavior by Skill Graph10 Nov 2023
- 2023Towards Foundation Models for Knowledge Graph Reasoning6 Oct 2023
- 2023Clinical Trial Recommendations Using Semantics-Based Inductive Inference and Knowledge Graph Embeddings27 Sep 2023
- 2023A parameterised model for link prediction using node centrality and similarity measure based on graph embedding11 Sep 2023
- 2023Feature Propagation on Knowledge Graphs using Cellular Sheaves7 Sep 2023
- 2023KGrEaT: A Framework to Evaluate Knowledge Graphs via Downstream Tasks21 Aug 2023
- 2023Towards Semantically Enriched Embeddings for Knowledge Graph Completion31 Jul 2023
- 2023Fast Knowledge Graph Completion using Graphics Processing Units22 Jul 2023
- 2023Anticipating Technical Expertise and Capability Evolution in Research Communities using Dynamic Graph Transformers18 Jul 2023
- 2023Multi-Dialectal Representation Learning of Sinitic Phonology30 Jun 2023
- 2023Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarking18 Jun 2023
- 2023BioBLP: A Modular Framework for Learning on Multimodal Biomedical Knowledge Graphs6 Jun 2023
- 2023Knowledge Graphs Querying23 May 2023
- 2023Visual Question Answering: A Survey on Techniques and Common Trends in Recent Literature18 May 2023
- 2023Neural Graph Reasoning: Complex Logical Query Answering Meets Graph Databases26 Mar 2023
- 2023Cognitive Semantic Communication Systems Driven by Knowledge Graph: Principle, Implementation, and Performance Evaluation15 Mar 2023
- 2023Treat Different Negatives Differently: Enriching Loss Functions with Domain and Range Constraints for Link Prediction1 Mar 2023
- 2023Construction of Knowledge Graphs: State and Challenges22 Feb 2023
- 2023Can Persistent Homology provide an efficient alternative for Evaluation of Knowledge Graph Completion Methods?30 Jan 2023
- 2023Sem@K: Is my knowledge graph embedding model semantic-aware?13 Jan 2023
- 2022A Retrieve-and-Read Framework for Knowledge Graph Link Prediction19 Dec 2022
- 2022A Survey of Knowledge Graph Reasoning on Graph Types: Static, Dynamic, and Multimodal12 Dec 2022
- 2022Weisfeiler and Leman Go Relational30 Nov 2022
- 2022Leveraging Wikidata's edit history in knowledge graph refinement tasks27 Oct 2022
- 2022Inductive Logical Query Answering in Knowledge Graphs13 Oct 2022
- 2022Embeddings as Epistemic States: Limitations on the Use of Pooling Operators for Accumulating Knowledge11 Oct 2022
50 newest of 70 All 70 (JSON)
- 2022A Survey of Knowledge Graph Reasoning on Graph Types: Static, Dynamic, and Multimodalcited by 106
- 2023Towards Foundation Models for Knowledge Graph Reasoningcited by 83
- 2021NodePiece: Compositional and Parameter-Efficient Representations of Large Knowledge Graphscited by 71
- 2023Evaluating Graph Neural Networks for Link Prediction: Current Pitfalls and New Benchmarkingcited by 69
- 2022A Decade of Knowledge Graphs in Natural Language Processing: A Surveycited by 40
- 2021A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspectivecited by 37
- 2022An Open Challenge for Inductive Link Prediction on Knowledge Graphscited by 26
- 2022Inductive Logical Query Answering in Knowledge Graphscited by 25
- 2021Query Embedding on Hyper-relational Knowledge Graphscited by 23
- 2021Improving Inductive Link Prediction Using Hyper-Relational Factscited by 21
- 2023Visual Question Answering: A Survey on Techniques and Common Trends in Recent Literaturecited by 20
- 2021Understanding the Performance of Knowledge Graph Embeddings in Drug Discoverycited by 18
12 most cited of 67 All 67 (JSON)
- 2026Recipe-Controlled Decoder Audit for Structural Knowledge-Graph Completion12 Jun 2026
- 2026In Data or Invisible: Toward a Better Digital Representation of Low-Resource Languages with Knowledge Graphs7 May 2026
- 2025Geometric Structural Knowledge Graph Foundation Model28 Dec 2025
- 2025Understanding Generalization in Node and Link Prediction1 Jul 2025
- 2025On the Theoretical Limitations of Embedding-based Link Prediction27 Jun 2025
- 2025Knowledge-augmented Pre-trained Language Models for Biomedical Relation Extraction1 May 2025
- 2025On Large-scale Evaluation of Embedding Models for Knowledge Graph Completion11 Apr 2025
- 2025ReaLitE: Enrichment of Relation Embeddings in Knowledge Graphs using Numeric Literals1 Apr 2025
- 2024Extending TWIG: Zero-Shot Predictive Hyperparameter Selection for KGEs based on Graph Structure19 Dec 2024
- 2024A Survey on Knowledge Graph Structure and Knowledge Graph Embeddings13 Dec 2024
- 2024A Pluggable Common Sense-Enhanced Framework for Knowledge Graph Completion6 Oct 2024
- 2024Neurosymbolic Methods for Dynamic Knowledge Graphs6 Sep 2024
12 newest of 67 All 67 (JSON)