Bio-Epidemiology-NER 0.1.3

Recognize bio-medical entities from a text corpus

Bio-Epidemiology-NER is an Python library built on top of biomedical-ner-all model to recognize bio-medical entities from a corpus or a medical report

Feature	Output
Named Entity Recognition	Recognize 84 bio-medical entities
PDF Input	Read Pdf and tabulate the entities
PDF Annotation	Annotate Entities in a medical pdf report

Installation

Use the package manager pip to install Bio-Epidemiology-NER

pip install Bio-Epidemiology-NER

This package has dependency over Pytorch, please install the required configuration from this link https://pytorch.org/get-started/locally/

Usage

NER with Bio-Epidemiology-NER

# load all the functions
from Bio_Epidemiology_NER.bio_recognizer import ner_prediction

# returns the predicted class along with the probability of the actual EnvBert model
doc = """
	CASE: A 28-year-old previously healthy man presented with a 6-week history of palpitations. 
      The symptoms occurred during rest, 2–3 times per week, lasted up to 30 minutes at a time 
      and were associated with dyspnea. Except for a grade 2/6 holosystolic tricuspid regurgitation 
      murmur (best heard at the left sternal border with inspiratory accentuation), physical 
      examination yielded unremarkable findings.
      """

# returns a dataframe output
ner_prediction(corpus=doc, compute='cpu') #pass compute='gpu' if using gpu

Annotate the entities in a Medical Report and export as pdf/csv format

# load all the functions
from Bio_Epidemiology_NER.bio_recognizer import pdf_annotate

# enter pdf file name
pdffile = 'Alhashash-2020-Emergency surgical management.pdf'

# returns a annotated pdf file
pdf_annotate(pdffile,compute='cpu', output_format='pdf') #pass compute='gpu' if using gpu

# returns a csv file with entities
pdf_annotate(pdffile,compute='cpu', output_format='csv') #pass compute='gpu' if using gpu

# return both annotated pdf and csv file
pdf_annotate(pdffile,compute='cpu', output_format='all') #pass compute='gpu' if using gpu

# if you come across any pdf issues, please install PyMuPDF 1.20.1 version

About

This model is part of the Research topic "AI in Biomedical field" conducted by Deepak John Reji, Shaina Raza. If you use this work (code, model or dataset),

Please cite us and star at: https://github.com/dreji18/biomedicalNER

License

MIT License