mlsanityData to 7 Oct 2026

HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition

arXiv 2008.07347 ↗First posted 17 Aug 2020cs.CLcited by 26

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Abstract (arXiv)

Summary: Named Entity Recognition (NER) is an important step in biomedical information extraction pipelines. Tools for NER should be easy to use, cover multiple entity types, highly accurate, and robust towards variations in text genre and style. To this end, we propose HunFlair, an NER tagger covering multiple entity types integrated into the widely used NLP framework Flair. HunFlair outperforms other state-of-the-art standalone NER tools with an average gain of 7.26 pp over the next best tool, can be installed with a single command and is applied with only four lines of code. Availability: HunFlair is freely available through the Flair framework under an MIT license: https://github.com/flairNLP/flair and is compatible with all major operating systems. Contact:{weberple,saengema,alan.akbik}@informatik.hu-berlin.de

Key facts. Cited by 26 papers in the map (data through 7 Oct 2026). First posted on arXiv 17 Aug 2020.

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Citing papers per year: 2021: 2; 2022: 9; 2023: 8; 2024: 4; 2025: 3.

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  1. 2022BERN2: an advanced neural biomedical named entity recognition and normalization toolcited by 42
  2. 2022AIONER: All-in-one scheme-based biomedical named entity recognition using deep learningcited by 12
  3. 2024LLMs in Biomedicine: A study on clinical Named Entity Recognitioncited by 12
  4. 2024HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization toolscited by 8
  5. 2021CLIN-X: pre-trained language models and a study on cross-task transfer for concept extraction in the clinical domaincited by 7
  6. 2023Inspire the Large Language Model by External Knowledge on BioMedical Named Entity Recognitioncited by 6
  7. 2022A Comprehensive Study of Gender Bias in Chemical Named Entity Recognition Modelscited by 4
  8. 2023Rethinking Document-Level Relation Extraction: A Reality Checkcited by 4
  9. 2022Assigning Species Information to Corresponding Genes by a Sequence Labeling Frameworkcited by 3
  10. 2022Keyword Extraction in Scientific Documentscited by 3
  11. 2023Biomedical Named Entity Recognition via Dictionary-based Synonym Generalizationcited by 3
  12. 2023Exploring Partial Knowledge Base Inference in Biomedical Entity Linkingcited by 2
14 more
  1. 2023Partial Annotation Learning for Biomedical Entity Recognitioncited by 2
  2. 2023CSMeD: Bridging the Dataset Gap in Automated Citation Screening for Systematic Literature Reviewscited by 2
  3. 2025Patience is all you need! An agentic system for performing scientific literature reviewcited by 2
  4. 2021Analyzing Research Trends in Inorganic Materials Literature Using NLPcited by 1
  5. 2022TERMinator: A system for scientific texts processingcited by 1
  6. 2022Enhancing Label Consistency on Document-level Named Entity Recognitioncited by 1
  7. 2023Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Textscited by 1
  8. 2024Extracting Biomedical Entities from Noisy Audio Transcriptscited by 1
  9. 2025Privacy Meets Explainability: Managing Confidential Data and Transparency Policies in LLM-Empowered Sciencecited by 1
  10. 2022Razmecheno: Named Entity Recognition from Digital Archive of Diaries "Prozhito"cited by 0
  11. 2022Learning to Discover Medicinescited by 0
  12. 2023EasyNER: A Customizable Easy-to-Use Pipeline for Deep Learning- and Dictionary-based Named Entity Recognition from Medical and Life Science Textcited by 0
  13. 2024Korean Bio-Medical Corpus (KBMC) for Medical Named Entity Recognitioncited by 0
  14. 2025FusionDP: Foundation Model-Assisted Differentially Private Learning for Partially Sensitive Featurescited by 0