Bio-medical and Clinical NER: spacy, stanza, sciSpacy, HunFlair(flair)

This repository contains various templates / utilities to run bio-medical and clinical ner using spacy, sciSpacy, stanza and flair.

Dependencies

pip install -r requirements.txt

Usage: Refer to framework specific documentation(Readme.md)

1. stanza -State Of The Art (Tokenizer, Tagger, Parser, NER)
2. med7NER -Tagger, Parser, 7 Clinical NER(Dosage, drug, duration, form, frequeny, route, strength)
3. sciSpacy -NER, Abbrevation detector and Entity linker
4. HunFlair -Bio-medical NER based on flair framework, achieves SOTA(comparison without fine-tuning), Easy framework for biomedical fine-tuning, training and pre-training
5. PubMedBERT -Domain Specific pre-training of BioMed from scratch