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

arXiv: https://arxiv.org/abs/2008.07347 · HTML: https://mlsanity.com/paper/2008.07347/

## Key facts

- Cited by 26 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 17 Aug 2020.

## Built on by (most cited first, 26 of 26)

- [BERN2: an advanced neural biomedical named entity recognition and normalization tool](https://mlsanity.com/paper/2201.02080/) (2022)
- [AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning](https://mlsanity.com/paper/2211.16944/) (2022)
- [LLMs in Biomedicine: A study on clinical Named Entity Recognition](https://mlsanity.com/paper/2404.07376/) (2024)
- [HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools](https://mlsanity.com/paper/2402.12372/) (2024)
- [CLIN-X: pre-trained language models and a study on cross-task transfer for concept extraction in the clinical domain](https://mlsanity.com/paper/2112.08754/) (2021)
- [Inspire the Large Language Model by External Knowledge on BioMedical Named Entity Recognition](https://mlsanity.com/paper/2309.12278/) (2023)
- [A Comprehensive Study of Gender Bias in Chemical Named Entity Recognition Models](https://mlsanity.com/paper/2212.12799/) (2022)
- [Rethinking Document-Level Relation Extraction: A Reality Check](https://mlsanity.com/paper/2306.08953/) (2023)
- [Assigning Species Information to Corresponding Genes by a Sequence Labeling Framework](https://mlsanity.com/paper/2205.03853/) (2022)
- [Keyword Extraction in Scientific Documents](https://mlsanity.com/paper/2207.01888/) (2022)
- [Biomedical Named Entity Recognition via Dictionary-based Synonym Generalization](https://mlsanity.com/paper/2305.13066/) (2023)
- [Exploring Partial Knowledge Base Inference in Biomedical Entity Linking](https://mlsanity.com/paper/2303.10330/) (2023)
- [Partial Annotation Learning for Biomedical Entity Recognition](https://mlsanity.com/paper/2305.13120/) (2023)
- [CSMeD: Bridging the Dataset Gap in Automated Citation Screening for Systematic Literature Reviews](https://mlsanity.com/paper/2311.12474/) (2023)
- [Patience is all you need! An agentic system for performing scientific literature review](https://mlsanity.com/paper/2504.08752/) (2025)
- [Analyzing Research Trends in Inorganic Materials Literature Using NLP](https://mlsanity.com/paper/2106.14157/) (2021)
- [TERMinator: A system for scientific texts processing](https://mlsanity.com/paper/2209.14854/) (2022)
- [Enhancing Label Consistency on Document-level Named Entity Recognition](https://mlsanity.com/paper/2210.12949/) (2022)
- [Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts](https://mlsanity.com/paper/2309.01812/) (2023)
- [Extracting Biomedical Entities from Noisy Audio Transcripts](https://mlsanity.com/paper/2403.17363/) (2024)
- [Privacy Meets Explainability: Managing Confidential Data and Transparency Policies in LLM-Empowered Science](https://mlsanity.com/paper/2504.09961/) (2025)
- [Razmecheno: Named Entity Recognition from Digital Archive of Diaries "Prozhito"](https://mlsanity.com/paper/2201.09997/) (2022)
- [Learning to Discover Medicines](https://mlsanity.com/paper/2202.07096/) (2022)
- [EasyNER: A Customizable Easy-to-Use Pipeline for Deep Learning- and Dictionary-based Named Entity Recognition from Medical and Life Science Text](https://mlsanity.com/paper/2304.07805/) (2023)
- [Korean Bio-Medical Corpus (KBMC) for Medical Named Entity Recognition](https://mlsanity.com/paper/2403.16158/) (2024)
- [FusionDP: Foundation Model-Assisted Differentially Private Learning for Partially Sensitive Features](https://mlsanity.com/paper/2511.03806/) (2025)

## 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