# EasyNER: A Customizable Easy-to-Use Pipeline for Deep Learning- and Dictionary-based Named Entity Recognition from Medical and Life Science Text

arXiv: https://arxiv.org/abs/2304.07805 · HTML: https://mlsanity.com/paper/2304.07805/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 21 of its 50 references that are in the map.
- First posted on arXiv 16 Apr 2023.

## Builds on (most cited first, 21 of 21)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Efficient Estimation of Word Representations in Vector Space](https://mlsanity.com/paper/1301.3781/) (2013)
- [HuggingFace's Transformers: State-of-the-art Natural Language Processing](https://mlsanity.com/paper/1910.03771/) (2019)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Accurate, Large Minibatch SGD: Training ImageNet in 1 Hour](https://mlsanity.com/paper/1706.02677/) (2017)
- [Google's Neural Machine Translation System: Bridging the Gap between Human and Machine Translation](https://mlsanity.com/paper/1609.08144/) (2016)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [Publicly Available Clinical BERT Embeddings](https://mlsanity.com/paper/1904.03323/) (2019)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [One Billion Word Benchmark for Measuring Progress in Statistical Language Modeling](https://mlsanity.com/paper/1312.3005/) (2013)
- [Transfer Learning in Biomedical Natural Language Processing: An Evaluation of BERT and ELMo on Ten Benchmarking Datasets](https://mlsanity.com/paper/1906.05474/) (2019)
- [ScispaCy: Fast and Robust Models for Biomedical Natural Language Processing](https://mlsanity.com/paper/1902.07669/) (2019)
- [BioRED: A Rich Biomedical Relation Extraction Dataset](https://mlsanity.com/paper/2204.04263/) (2022)
- [MedMentions: A Large Biomedical Corpus Annotated with UMLS Concepts](https://mlsanity.com/paper/1902.09476/) (2019)
- [BioMegatron: Larger Biomedical Domain Language Model](https://mlsanity.com/paper/2010.06060/) (2020)
- [BERN2: an advanced neural biomedical named entity recognition and normalization tool](https://mlsanity.com/paper/2201.02080/) (2022)
- [HunFlair: An Easy-to-Use Tool for State-of-the-Art Biomedical Named Entity Recognition](https://mlsanity.com/paper/2008.07347/) (2020)
- [Scattertext: a Browser-Based Tool for Visualizing how Corpora Differ](https://mlsanity.com/paper/1703.00565/) (2017)
- [AIONER: All-in-one scheme-based biomedical named entity recognition using deep learning](https://mlsanity.com/paper/2211.16944/) (2022)
- [tmVar 3.0: an improved variant concept recognition and normalization tool](https://mlsanity.com/paper/2204.03637/) (2022)
- [Predicting and interpreting embeddings for out of vocabulary words in downstream tasks](https://mlsanity.com/paper/1903.00724/) (2019)

## Abstract (arXiv)

Background Medical and life science research generates millions of publications, and it is a great challenge for researchers to utilize this information in full since its scale and complexity greatly surpasses human reading capabilities. Automated text mining can help extract and connect information spread across this large body of literature, but this technology is not easily accessible to life scientists. Methods and Results Here, we developed an easy-to-use end-to-end pipeline for deep learning- and dictionary-based named entity recognition (NER) of typical entities found in medical and life science research articles, including diseases, cells, chemicals, genes/proteins, species and others. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. In addition, we provide two accessory scripts which allow processing of files in PubTator format and rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19. Conclusions The NER pipeline we present is applicable in a variety of medical research settings and makes customizable text mining accessible to life scientists.