Deep Learning for Bayesian Inference (dl4bi)

Install

1. Install jax
2. Install numpyro
3. Install the dl4bi package from git:

pip install -U --force-reinstall git+ssh://git@github.com/MLGlobalHealth/dl4bi.git

View Documentation (Locally)

pip install pdoc
git clone git@github.com:MLGlobalHealth/dl4bi.git
cd dl4bi
pdoc --docformat google --math dl4bi

Example scripts can be found here.

Development Setup

• Install Python 3.12 with pyenv:
  • Install pyenv: curl https://pyenv.run | bash
  • Copy the lines it says to your ~/.bashrc and reload source ~/.bashrc
  • Install Python 3.12: pyenv install 3.12
• Create a virtualenv called dl4bi-dev using Python 3.12: pyenv virtualenv 3.12 dl4bi-dev
• Clone the repository and cd into it: git clone git@github.com:MLGlobalHealth/dl4bi.git && cd dl4bi
• Inside the dl4bi repository, tell pyenv to use the dl4bi-dev virtualenv: pyenv local dl4bi-dev
  • pyenv local dl4bi-dev creates a .python-version file that tells pyenv to automatically activate the dl4bi-dev virtualenv whenever you are working in the dl4bi repository, so all python and pip commands will execute within the dl4bi-dev virtualenv
• Inside the dl4bi directory, install the package to the dl4bi-dev virtualenv: pip install -e .
  • Installing this package locally means it is installed "live", i.e. it immediately reflects any changes you make (this only needs to be done once)