peustr / heparin-research

This is the code to support my MSc thesis: Predictive Modeling of Heparin Dosing in Critical Care.

heparin-research

Install the dependencies

Navigate to the root of the project and run:

pip install -r requirements.txt

Generate the MIMIC dataset

This tutorial assumes you have a PosgreSQL instance with the MIMIC database running.

First run the query in mimic-data/mimic-sql/lab_measurements.sql. This will give you a result set. Export it to CSV and name it mimic_lab_measurements.csv.

Then run the script in mimic-data/build_query_for_features.py like:

python build_query_for_features.py

This will generate a SQL file: mimic-data/mimic-sql/patient_features.sql. Run this SQL file in your local PostgreSQL instance. Export its results to mimic_patient_featrures.csv.

Then run the script in mimic-data/join_measurements_and_features.py like:

python join_measurements_and_features.py

This will generate a CSV file: mimic_data.csv. This is the MIMIC dataset used for training.