{"doi":"10.18653/v1/2021.bionlp-1.2","title":"Triplet-Trained Vector Space and Sieve-Based Search Improve Biomedical Concept Normalization","abstract":"Concept normalization, the task of linking textual mentions of concepts to concepts in an ontology, is critical for mining and analyzing biomedical texts. We propose a vector-space model for concept normalization, where mentions and concepts are encoded via transformer networks that are trained via a triplet objective with online hard triplet mining. The transformer networks refine existing pre-trained models, and the online triplet mining makes training efficient even with hundreds of thousands of concepts by sampling training triples within each mini-batch. We introduce a variety of strategies for searching with the trained vector-space model, including approaches that incorporate domain-specific synonyms at search time with no model retraining. Across five datasets, our models that are trained only once on their corresponding ontologies are within 3 points of state-of-the-art models that are retrained for each new domain. Our models can also be trained for each domain, achieving new state-of-the-art on multiple datasets.","journal":"UA Campus Repository (The University of Arizona)","year":2021,"id":215114,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9512,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":318128,"name":"Steven Bethard","orcid":"0000-0001-9560-6491","position":1,"is_corresponding":false},{"id":488870,"name":"Dongfang Xu","orcid":"0000-0003-0828-1102","position":0,"is_corresponding":true}],"reference_count":43,"raw_metadata":null,"created_at":"2026-07-18T23:52:51.201033Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}