hhchang0210 / mimic_code

Classifications and regressions on ICU hospital data (MIMIC III database).

MIMIC_Code

In this repo I present how I

• access data from the MIMIC III database
• how I perform classification and regressions with it

Setup

Clone the repo from https://github.com/mar-volk/MIMIC_Code .

conda env create --file environment.yml
source activate MIMIC_Code

Request access for the MIMIC III database as explained on https://mimic.physionet.org

Copy unzipped MIMIC-data into 'data/all/raw'

Copy unzipped MIMIC-demo-data (smaller files for testing) into 'data/demo_data/all/raw'

Usage

conda env update --file environment.yml
source activate MIMIC_Code
jupyter notebook
pytest

Run the following script to split the data into training, validation and test data

src/prep/train_test_split.py

Click through following jupyter notebook to get an overview: exp/Examples_on_how_to_prepare_predictors_and_targets.ipynb exp/Evaluate_NN_Classifier_07.ipynb