{"ID":2887242,"CreatedAt":"2026-06-01T04:54:23.091178241Z","UpdatedAt":"2026-06-01T04:54:23.091178241Z","DeletedAt":null,"paper_url":"https://arxiv.org/abs/2508.01630","arxiv_id":"2508.01630","title":"OpenMed NER: Open-Source, Domain-Adapted State-of-the-Art Transformers for Biomedical NER Across 12 Public Datasets","abstract":"Named-entity recognition (NER) is fundamental to extracting structured information from the \u003e80% of healthcare data that resides in unstructured clinical notes and biomedical literature. Despite recent advances with large language models, achieving state-of-the-art performance across diverse entity types while maintaining computational efficiency remains a significant challenge. We introduce OpenMed NER, a suite of open-source, domain-adapted transformer models that combine lightweight domain-adaptive pre-training (DAPT) with parameter-efficient Low-Rank Adaptation (LoRA). Our approach performs cost-effective DAPT on a 350k-passage corpus compiled from ethically sourced, publicly available research repositories and de-identified clinical notes (PubMed, arXiv, and MIMIC-III) using DeBERTa-v3, PubMedBERT, and BioELECTRA backbones. This is followed by task-specific fine-tuning with LoRA, which updates less than 1.5% of model parameters. We evaluate our models on 12 established biomedical NER benchmarks spanning chemicals, diseases, genes, and species. OpenMed NER achieves new state-of-the-art micro-F1 scores on 10 of these 12 datasets, with substantial gains across diverse entity types. Our models advance the state-of-the-art on foundational disease and chemical benchmarks (e.g., BC5CDR-Disease, +2.70 pp), while delivering even larger improvements of over 5.3 and 9.7 percentage points on more specialized gene and clinical cell line corpora. This work demonstrates that strategically adapted open-source models can surpass closed-source solutions. This performance is achieved with remarkable efficiency: training completes in under 12 hours on a single GPU with a low carbon footprint (\u003c 1.2 kg CO2e), producing permissively licensed, open-source checkpoints designed to help practitioners facilitate compliance with emerging data protection and AI regulations, such as the EU AI Act.","short_abstract":"Named-entity recognition (NER) is fundamental to extracting structured information from the \u003e80% of healthcare data that resides in unstructured clinical notes and biomedical literature. Despite recent advances with large language models, achieving state-of-the-art performance across diverse entity types while maintain...","url_abs":"https://arxiv.org/abs/2508.01630","url_pdf":"https://arxiv.org/pdf/2508.01630v1","authors":"[\"Maziyar Panahi\"]","published":"2025-08-03T07:33:28Z","proceeding":"cs.CL","tasks":"[\"cs.CL\",\"cs.AI\"]","methods":"[\"Transformer\",\"Language Model\",\"LoRA\"]","has_code":false}