Installation

It is recommended to use pip for installation. Please make sure the latest version is installed, as PyHealth is updated frequently:

pip install pyhealth            # normal install
pip install --upgrade pyhealth  # or update if needed
pip install --pre pyhealth      # or include pre-release version for new features

Alternatively, you could clone and run setup.py file:

git clone https://github.com/yzhao062/pyhealth.git
cd pyhealth
pip install .

Required Dependencies:

  • Python 3.5, 3.6, or 3.7

  • combo>=0.0.8

  • joblib

  • numpy>=1.13

  • numba>=0.35

  • pandas>=0.25

  • scipy>=0.20

  • scikit_learn>=0.20

  • tqdm

  • torch (this should be installed manually)

  • xgboost (this should be installed manually)

  • xlrd >= 1.0.0

Warning 1: PyHealth has multiple neural network based models, e.g., LSTM, which are implemented in PyTorch. However, PyHealth does NOT install these DL libraries for you. This reduces the risk of interfering with your local copies. If you want to use neural-net based models, please make sure PyTorch is installed. Similarly, models depending on xgboost, would NOT enforce xgboost installation by default.