PY0
py0 is a python implementation of compartmental disease modeling.
Installation
To install py0:
pip install py0@git+https://github.com/ur-whitelab/py0.git
Maximum Entropy Biasing
py0 can be coupled with MaxEnt to modify epidomiology parameters to find the best fit to disease trajectory given a set of observations and also infer the true origin of the outbreak (patient-zero). These observations are time-averaged fractional values that can come from different compartments (S, E, A, I and R) of a known synthetic reference trajectory or real pandemic spread data.
Creating an Ensemble of Trajectories
We try to explore the disease trajectory space over a distribution of epidomiology parameters, while changing the infection origin to different nodes (counties).
MaxEnt Fit
MaxEnt Installation
The package uses Keras (Tensorflow). To install:
pip install maxent-infer
Citation
See paper and the citation:
@article{ansari2022inferring,
title={Inferring spatial source of disease outbreaks using maximum entropy},
author={Ansari, Mehrad and Soriano-Pa{\~n}os, David and Ghoshal, Gourab and White, Andrew D},
journal={Physical Review E},
volume={106},
number={1},
pages={014306},
year={2022},
publisher={APS}
}
License
