Token Classification
GLiNER
PyTorch
English
NER
GLiNER
information extraction
encoder
entity recognition
biomed
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  1. README.md +14 -10
README.md CHANGED
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  # GLiNER-BioMed
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- The model was presented in the paper [GLiNER-BioMed: A Suite of Efficient Models for Open Biomedical Named Entity Recognition](https://arxiv.org/abs/2504.00676).
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  The code is available at [https://github.com/ds4dh/GLiNER-biomed](https://github.com/ds4dh/GLiNER-biomed).
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  **GLiNER** is a Named Entity Recognition (NER) model capable of identifying any entity type using a bidirectional transformer encoders (BERT-like). It provides a practical alternative to traditional NER models, which are limited to predefined entities, and Large Language Models (LLMs) that, despite their flexibility, are costly and large for resource-constrained scenarios.
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- **GLiNER-biomed**, developed in collaboration with [DS4DH](https://www.unige.ch/medecine/radio/en/research-groups/1035teodoro) from the University of Geneva, introduces a specialized suite of efficient open biomedical NER models based on the GLiNER framework. GLiNER-biomed leverages synthetic annotations distilled from large generative biomedical language models to achieve state-of-the-art zero-shot and few-shot performance in biomedical entity recognition tasks.
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  ### How to Use
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  Install the official GLiNER library with pip:
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  If you use GLiNER-biomed models in your work, please cite:
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  ```bibtex
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- @misc{yazdani2025glinerbiomedsuiteefficientmodels,
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- title={GLiNER-BioMed: A Suite of Efficient Models for Open Biomedical Named Entity Recognition},
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- author={Anthony Yazdani and Ihor Stepanov and Douglas Teodoro},
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- year={2025},
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- eprint={2504.00676},
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- archivePrefix={arXiv},
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- primaryClass={cs.CL},
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- url={https://arxiv.org/abs/2504.00676},
 
 
 
 
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  }
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  ```
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  # GLiNER-BioMed
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+ The model was presented in the paper [GLiNER-BioMed: a suite of efficient models for open biomedical named entity recognition](https://doi.org/10.1093/bioinformatics/btag322).
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  The code is available at [https://github.com/ds4dh/GLiNER-biomed](https://github.com/ds4dh/GLiNER-biomed).
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  **GLiNER** is a Named Entity Recognition (NER) model capable of identifying any entity type using a bidirectional transformer encoders (BERT-like). It provides a practical alternative to traditional NER models, which are limited to predefined entities, and Large Language Models (LLMs) that, despite their flexibility, are costly and large for resource-constrained scenarios.
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+ **GLiNER-biomed**, developed in collaboration with [DS4DH](https://ds4dh.unige.ch/) from the University of Geneva, introduces a specialized suite of efficient open biomedical NER models based on the GLiNER framework. GLiNER-biomed leverages synthetic annotations distilled from large generative biomedical language models to achieve state-of-the-art zero-shot and few-shot performance in biomedical entity recognition tasks.
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  ### How to Use
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  Install the official GLiNER library with pip:
 
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  If you use GLiNER-biomed models in your work, please cite:
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  ```bibtex
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+ @article{yazdani2026gliner,
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+ author = {Yazdani, Anthony and Stepanov, Ihor and Teodoro, Douglas},
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+ title = {{GLiNER-BioMed}: a suite of efficient models for open biomedical named entity recognition},
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+ journal = {Bioinformatics},
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+ volume = {42},
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+ number = {6},
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+ pages = {btag322},
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+ year = {2026},
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+ month = jun,
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+ issn = {1367-4811},
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+ doi = {10.1093/bioinformatics/btag322},
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+ url = {https://doi.org/10.1093/bioinformatics/btag322}
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  }
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  ```
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