mlsanityData to 7 Oct 2026

BERTMap: A BERT-based Ontology Alignment System

arXiv 2112.02682 ↗First posted 5 Dec 2021cs.AI cs.CL cs.LGcited by 45

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Abstract (arXiv)

Ontology alignment (a.k.a ontology matching (OM)) plays a critical role in knowledge integration. Owing to the success of machine learning in many domains, it has been applied in OM. However, the existing methods, which often adopt ad-hoc feature engineering or non-contextual word embeddings, have not yet outperformed rule-based systems especially in an unsupervised setting. In this paper, we propose a novel OM system named BERTMap which can support both unsupervised and semi-supervised settings. It first predicts mappings using a classifier based on fine-tuning the contextual embedding model BERT on text semantics corpora extracted from ontologies, and then refines the mappings through extension and repair by utilizing the ontology structure and logic. Our evaluation with three alignment tasks on biomedical ontologies demonstrates that BERTMap can often perform better than the leading OM systems LogMap and AML.

Key facts. Cited by 45 papers in the map (data through 7 Oct 2026). Builds on 11 of its 26 references that are in the map. First posted on arXiv 5 Dec 2021.

Builds on

11 of 26 references.

References · 11

  1. 2017Attention Is All You Needcited by 59,932
  2. 2018BERT: Pre-training of Deep Bidirectional Transformers for Language Understandingcited by 40,204
  3. 2019Sentence-BERT: Sentence Embeddings using Siamese BERT-Networkscited by 9,049
  4. 2013Efficient Estimation of Word Representations in Vector Spacecited by 4,346
  5. 2017Decoupled Weight Decay Regularizationcited by 1,722
  6. 2016Enriching Word Vectors with Subword Informationcited by 1,578
  7. 2016Google's Neural Machine Translation System: Bridging the Gap between Human and Machine Translationcited by 1,471
  8. 2019Publicly Available Clinical BERT Embeddingscited by 995
  9. 2020OWL2Vec*: Embedding of OWL Ontologiescited by 63
  10. 2018Ontology Alignment in the Biomedical Domain Using Entity Definitions and Contextcited by 10
  11. 2020Dividing the Ontology Alignment Task with Semantic Embeddings and Logic-based Modulescited by 4

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Cited by year (2026 to 7 Oct)

Citing papers per year: 2021: 1; 2022: 4; 2023: 17; 2024: 7; 2025: 9; 2026: 7.

45 papers.

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  1. 2023Large Language Models and Knowledge Graphs: Opportunities and Challengescited by 71
  2. 2023OLaLa: Ontology Matching with Large Language Modelscited by 35
  3. 2022Contextual Semantic Embeddings for Ontology Subsumption Predictioncited by 31
  4. 2023Exploring Large Language Models for Ontology Alignmentcited by 26
  5. 2023Agent-OM: Leveraging LLM Agents for Ontology Matchingcited by 26
  6. 2023Language Model Analysis for Ontology Subsumption Inferencecited by 25
  7. 2021Zero-shot and Few-shot Learning with Knowledge Graphs: A Comprehensive Surveycited by 23
  8. 2024LLMs4OM: Matching Ontologies with Large Language Modelscited by 22
  9. 2022Machine Learning-Friendly Biomedical Datasets for Equivalence and Subsumption Ontology Matchingcited by 21
  10. 2023DeepOnto: A Python Package for Ontology Engineering with Deep Learningcited by 20
  11. 2024Ontology Embedding: A Survey of Methods, Applications and Resourcescited by 12
  12. 2022Embracing Ambiguity: Improving Similarity-oriented Tasks with Contextual Synonym Knowledgecited by 11
33 more
  1. 2023Exploring the In-context Learning Ability of Large Language Model for Biomedical Concept Linkingcited by 11
  2. 2023Distilling Semantic Concept Embeddings from Contrastively Fine-Tuned Language Modelscited by 8
  3. 2025OntoAligner: A Comprehensive Modular and Robust Python Toolkit for Ontology Alignmentcited by 8
  4. 2023Deep Active Alignment of Knowledge Graph Entities and Schematacited by 6
  5. 2023Truveta Mapper: A Zero-shot Ontology Alignment Frameworkcited by 5
  6. 2025Ontology Matching with Large Language Models and Prioritized Depth-First Searchcited by 5
  7. 2025Language Models as Ontology Encoderscited by 4
  8. 2025Large Language Models as Oracles for Ontology Alignmentcited by 3
  9. 2026The AnIML Ontology: Enabling Semantic Interoperability for Large-Scale Experimental Data in Interconnected Scientific Labscited by 3
  10. 2023Contextualized Structural Self-supervised Learning for Ontology Matchingcited by 2
  11. 2024Ranking Entities along Conceptual Space Dimensions with LLMs: An Analysis of Fine-Tuning Strategiescited by 2
  12. 2025OntologyRAG: Better and Faster Biomedical Code Mapping with Retrieval-Augmented Generation (RAG) Leveraging Ontology Knowledge Graphs and Large Language Modelscited by 2
  13. 2025GenOM: Ontology Matching with Description Generation and Large Language Modelcited by 2
  14. 2026To Neuro-Symbolic Classification and Beyond by Compiling Description Logic Ontologies to Probabilistic Circuitscited by 2
  15. 2026Open Ontologies: Tool-Augmented Ontology Engineering with Stable Matching Alignmentcited by 2
  16. 2023Linking Symptom Inventories using Semantic Textual Similaritycited by 1
  17. 2023RelBERT: Embedding Relations with Language Modelscited by 1
  18. 2023Ontology Revision based on Pre-trained Language Modelscited by 1
  19. 2024Interactive Ontology Matching with Cost-Efficient Learningcited by 1
  20. 2024OWL2Vec4OA: Tailoring Knowledge Graph Embeddings for Ontology Alignmentcited by 1
  21. 2022Exploring Wasserstein Distance across Concept Embeddings for Ontology Matchingcited by 0
  22. 2023Enhancing Data Space Semantic Interoperability through Machine Learning: a Visionary Perspectivecited by 0
  23. 2023An Embedding-based Approach to Inconsistency-tolerant Reasoning with Inconsistent Ontologiescited by 0
  24. 2023What can knowledge graph alignment gain with Neuro-Symbolic learning approaches?cited by 0
  25. 2024How Does A Text Preprocessing Pipeline Affect Ontology Matching?cited by 0
  26. 2024Integration of Contextual Descriptors in Ontology Alignment for Enrichment of Semantic Correspondencecited by 0
  27. 2025Automated Hierarchical Graph Construction for Multi-source Electronic Health Recordscited by 0
  28. 2025CMOMgen: Complex Multi-Ontology Alignment via Pattern-Guided In-Context Learningcited by 0
  29. 2025Leveraging LLMs for Collaborative Ontology Engineering in Parkinson Disease Monitoring and Alertingcited by 0
  30. 2026AgentMap: Joint Equivalence and Subsumption Discovery for Ontology Matchingcited by 0
  31. 2026Improving Interoperability among Defence and National Security Ontologies: Analysis and Evaluation Taskscited by 0
  32. 2026Consistency Is Not Coherence: Orientation Search for Certified Alignments Between 4D Defence Upper Ontologiescited by 0
  33. 2026OntoAligner-Ensemble: Voting-Based Fusion across Heterogeneous Ontology Alignment Techniquescited by 0