On the Ambiguity of Rank-Based Evaluation of Entity Alignment or Link Prediction Methods
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Abstract (arXiv)
In this work, we take a closer look at the evaluation of two families of methods for enriching information from knowledge graphs: Link Prediction and Entity Alignment. In the current experimental setting, multiple different scores are employed to assess different aspects of model performance. We analyze the informativeness of these evaluation measures and identify several shortcomings. In particular, we demonstrate that all existing scores can hardly be used to compare results across different datasets. Moreover, we demonstrate that varying size of the test size automatically has impact on the performance of the same model based on commonly used metrics for the Entity Alignment task. We show that this leads to various problems in the interpretation of results, which may support misleading conclusions. Therefore, we propose adjustments to the evaluation and demonstrate empirically how this supports a fair, comparable, and interpretable assessment of model performance. Our code is available at https://github.com/mberr/rank-based-evaluation.
Key facts. Cited by 13 papers in the map (data through 14 Oct 2026). First posted on arXiv 17 Feb 2020.
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Citing papers per year: 2021: 4; 2022: 4; 2023: 2; 2024: 1; 2025: 1; 2026: 1.
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- 2021A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspectivecited by 38
- 2022An Open Challenge for Inductive Link Prediction on Knowledge Graphscited by 26
- 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 15
- 2023Sem@K: Is my knowledge graph embedding model semantic-aware?cited by 10
- 2021Explainable Biomedical Recommendations via Reinforcement Learning Reasoning on Knowledge Graphscited by 7
- 2022Re-thinking Knowledge Graph Completion Evaluation from an Information Retrieval Perspectivecited by 7
- 2022Knowledge Graph Embedding Methods for Entity Alignment: An Experimental Reviewcited by 5
- 2021Rule Induction in Knowledge Graphs Using Linear Programmingcited by 4
- 2024Improving Molecule Generation and Drug Discovery with a Knowledge-enhanced Generative Modelcited by 3
- 2025DuetGraph: Coarse-to-Fine Knowledge Graph Reasoning with Dual-Pathway Global-Local Fusioncited by 2
- 2023PDPK: A Framework to Synthesise Process Data and Corresponding Procedural Knowledge for Manufacturingcited by 0
- 2026Generalized Rank-based Evaluation for Knowledge Graph Completion: Perspectives, Framework, and Analyses8 Jun 2026
- 2025DuetGraph: Coarse-to-Fine Knowledge Graph Reasoning with Dual-Pathway Global-Local Fusion15 Jul 2025
- 2024Improving Molecule Generation and Drug Discovery with a Knowledge-enhanced Generative Model13 Feb 2024
- 2023PDPK: A Framework to Synthesise Process Data and Corresponding Procedural Knowledge for Manufacturing16 Aug 2023
- 2023Sem@K: Is my knowledge graph embedding model semantic-aware?13 Jan 2023
- 2022Re-thinking Knowledge Graph Completion Evaluation from an Information Retrieval Perspective9 May 2022
- 2022Knowledge Graph Embedding Methods for Entity Alignment: An Experimental Review17 Mar 2022
- 2022A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphs14 Mar 2022
- 2022An Open Challenge for Inductive Link Prediction on Knowledge Graphs3 Mar 2022
- 2021Explainable Biomedical Recommendations via Reinforcement Learning Reasoning on Knowledge Graphs20 Nov 2021
- 2021Rule Induction in Knowledge Graphs Using Linear Programming15 Oct 2021
- 2021Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery17 May 2021
- 2021A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspectivecited by 38
- 2022An Open Challenge for Inductive Link Prediction on Knowledge Graphscited by 26
- 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 15
- 2023Sem@K: Is my knowledge graph embedding model semantic-aware?cited by 10
- 2021Explainable Biomedical Recommendations via Reinforcement Learning Reasoning on Knowledge Graphscited by 7
- 2022Re-thinking Knowledge Graph Completion Evaluation from an Information Retrieval Perspectivecited by 7
- 2022Knowledge Graph Embedding Methods for Entity Alignment: An Experimental Reviewcited by 5
- 2021Rule Induction in Knowledge Graphs Using Linear Programmingcited by 4
- 2024Improving Molecule Generation and Drug Discovery with a Knowledge-enhanced Generative Modelcited by 3
- 2025DuetGraph: Coarse-to-Fine Knowledge Graph Reasoning with Dual-Pathway Global-Local Fusioncited by 2
- 2023PDPK: A Framework to Synthesise Process Data and Corresponding Procedural Knowledge for Manufacturingcited by 0
- 2025DuetGraph: Coarse-to-Fine Knowledge Graph Reasoning with Dual-Pathway Global-Local Fusion15 Jul 2025
- 2024Improving Molecule Generation and Drug Discovery with a Knowledge-enhanced Generative Model13 Feb 2024
- 2023PDPK: A Framework to Synthesise Process Data and Corresponding Procedural Knowledge for Manufacturing16 Aug 2023
- 2023Sem@K: Is my knowledge graph embedding model semantic-aware?13 Jan 2023
- 2022Re-thinking Knowledge Graph Completion Evaluation from an Information Retrieval Perspective9 May 2022
- 2022Knowledge Graph Embedding Methods for Entity Alignment: An Experimental Review17 Mar 2022
- 2022A Unified Framework for Rank-based Evaluation Metrics for Link Prediction in Knowledge Graphs14 Mar 2022
- 2022An Open Challenge for Inductive Link Prediction on Knowledge Graphs3 Mar 2022
- 2021Explainable Biomedical Recommendations via Reinforcement Learning Reasoning on Knowledge Graphs20 Nov 2021
- 2021Rule Induction in Knowledge Graphs Using Linear Programming15 Oct 2021
- 2021Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery17 May 2021
- 2021A Review of Biomedical Datasets Relating to Drug Discovery: A Knowledge Graph Perspective19 Feb 2021