{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/bertmap-a-bert-based-ontology-alignment","title":"BERTMap: A BERT-based Ontology Alignment System","arxiv_id":"2112.02682","date":"2021-12-05","proceeding":null,"authors":["Yuan He","Jiaoyan Chen","Denvar Antonyrajah","Ian Horrocks"],"abstract":"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.","url_abs":"https://arxiv.org/abs/2112.02682v4","url_pdf":"https://arxiv.org/pdf/2112.02682v4.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"bertmap-a-bert-based-ontology-alignment","repo_url":"https://github.com/KRR-Oxford/DeepOnto","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"Apache-2.0"}}],"tasks":[{"task_slug":"feature-engineering","task_name":"Feature Engineering"},{"task_slug":"ontology-matching","task_name":"Ontology Matching"},{"task_slug":"word-embeddings","task_name":"Word Embeddings"}],"methods":[{"method_slug":"adam","method_name":"Adam"},{"method_slug":"attention","method_name":"Attention"},{"method_slug":"attention-dropout","method_name":"Attention Dropout"},{"method_slug":"bert","method_name":"BERT"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"linear-warmup-with-linear-decay","method_name":"Linear Warmup With Linear Decay"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"repair","method_name":"Repair"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"weight-decay","method_name":"Weight Decay"},{"method_slug":"wordpiece","method_name":"WordPiece"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2112.02682","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}