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Collection of bio-medical and clinical ner models in spacy, stanza, flair with some utility files

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magesh-technovator/bio-medical-clinical-ner

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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

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