Benchmarking transformer models with named entity recognition in clinical trial eligibility criteria

Chia dataset can be downloaded here: https://figshare.com/articles/dataset/Chia_Annotated_Datasets/11855817/2

Facebook Research Data can be downloaded here: https://github.com/facebookresearch/Clinical-Trial-Parser/blob/master/data/ner/medical_ner.tsv

All the Transformer based NER models can be found here: https://github.com/uf-hobi-informatics-lab/ClinicalTransformerNER

Reference:
1. Kury, Fabrício, et al. “Chia, a Large Annotated Corpus of Clinical Trial Eligibility Criteria.” Nature News, Nature Publishing Group, 27 Aug. 2020, www.nature.com/articles/s41597-020-00620-0.

1. Tseo, Yitong, et al. “Information Extraction of Clinical Trial Eligibility Criteria.” ArXiv.org, 28 July 2020, https://arxiv.org/pdf/2006.07296.pdf

2. Yang, Xi, et al. “Clinical Concept Extraction Using Transformers.” OUP Academic, Oxford University Press, 29 Oct. 2020, https://academic.oup.com/jamia/article/27/12/1935/5943218