Models:
Philip Bordner
philipB/
Med-NLP
0
Downloads: 1
Card

MedNLP

This repository contains code and analysis for ''NLP chatbot for Discharge Summaries'' using MIMIC-III dataset.

The project is aimed at building a system that leverages huge healthcare information available as electronic data and focusses on creating a Human Computer Interaction component in the form of a NLP chatbot. This system answers questions about a patient's discharge summaries primarily based on topic modeling and matching techniques.

Files

  • MED277_bot.ipynb - A jupyter notebook containing code for NLP chatbot.
  • MED277_bot.py - A pyton script for initializing and running the chatbot. Contains same code as MED277_bot.ipynb.
  • data10.pkl - A subset of 50 discharge summaries extracted from MIMIC-II dataset and saved as a python pickle file. The file can be found at location
  • MED277_report.pdf - A pdf report for the project.
  • MED277_presentation.pptx - A power presentation for the project.

Running the chatbot [Complete Data]

The chatbot uses the data from MIMIC-III discharge summaries to train and answer questions. The proper data path of MIMIC-III dataset NOTEEVENTS.csv.gz should be set in base_path. Then navigate to the path of MED277_bot.ipynb run the jupyter notebook using the following command:

jupyter notebook

This should start jupyter and then you can run the notebook MED277_bot.ipynb

To run the python file MED277_bot.py, the code for reading from the file should be uncommented and proper file NOTEEVENTS.csv.gz downloaded from MIMIC-III dataset should be kept at the base_path location, and the code to read from saved data file data10.pkl should be commented in load_data() function. By default the code for reading data is commented out in the MED277_bot.py file. Then the file can be executed using the following command:

python MED277_bot.py

Running the chatbot [Small Subset Data]

We have saved small subset of data to a pickle file data10.pkl.
Just edit the base_path inside MED277_bot.py file load_data() function, and keep this file at the location of base_path. The file MED277_bot.py should then run using the following command:

python MED277_bot.py

Follow the on screen instructions for interacting further with chatbot.

Sample questions for chatbot

  • What is my date of birth?
  • What is my admission date?
  • When was I discharged?
  • What is my gender?
  • What are the services I had?
  • Do I have allergy?
  • Who was my attending?
  • Am I married?
  • What is my social history?
  • How can I make an appointment?
  • Do I need to visit the clinic?
  • How was my MRI?
  • What are the medication I should take?
  • How to take the steroid?
  • What do I do if I have seizures?
  • Is my vision blurry?
  • Is something wrong with my brain?
  • Do I have a cold?
  • Do I have dysphagia?

Required Dependencies & Libraries

  • anaconda 5.2
  • Python 3.x
  • pandas
  • sklearn
  • nltk
  • numpy