CS685FinalProject

Configure Python Environment

1. Install conda
   • https://docs.conda.io/projects/conda/en/latest/user-guide/getting-started.html
2. Create and activate conda environment

   conda init
   conda create -n CS685FinalProject
   conda activate CS685FinalProject
   

3. Install Dependencies

   conda install -y -c anaconda python=3.9 scikit-learn nbconvert jinja2==3.0.3
   conda install -y -c conda-forge evaluate matplotlib pyppeteer
   conda install -y -c huggingface transformers datasets
   pip install torch torchvision torchaudio
   

4. If Using CUDA, Install GPU support
   • Install drivers: https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html
   • Install Python CUDA support

   conda install -y -c conda-forge cudatoolkit
   

Download raw data

• you must have username/password on physionet.org with access to the MIMIC IV dataset

mkdir -p data
export MIMIC_USER=
export MIMIC_PW=
wget -P data -N -c -r -np --user $MIMIC_USER --password $MIMIC_PW https://physionet.org/files/mimiciv/2.2/hosp/diagnoses_icd.csv.gz https://physionet.org/files/mimic-iv-note/2.2/note/discharge.csv.gz