Framework for healthcare ML implementation
Project description
cyclops
is a framework for facilitating research and deployment of ML models
in the health (or clinical) setting. It provides a few high-level APIs namely:
query
- Querying EHR databases (such as MIMIC-IV)process
- Process static and temporal EHR dataevaluate
- Evaluate models on clinical prediction tasksmonitor
- Detect data drift relevant for clinical use cases
cyclops
also provides a library of use-cases on clinical datasets. The implemented
use cases include:
- Mortality decompensation prediction
🐣 Getting Started
Installing the core cyclops package using pip
python3 -m pip install pycyclops
Setup Python virtual environment and install dependencies for development
The development environment has been tested on python = 3.9.7
.
The python virtual environment can be set up using poetry. Hence, make sure it is installed and then run:
poetry install
source $(poetry env info --path)/bin/activate
📚 Documentation
🎓 Notebooks
To use jupyter notebooks, the python virtual environment can be installed and used inside an IPython kernel. After activating the virtual environment, run:
python3 -m ipykernel install --user --name <name_of_kernel>
Now, you can navigate to the notebook's Kernel
tab and set it as
<name_of_kernel>
.
Tutorial notebooks in tutorials
can be useful to view the
functionality of the framework.
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