https://github.com/ur-whitelab/py0

https://github.com/ur-whitelab/py0

Last synced: about 1 month ago
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• Host: GitHub
• URL: https://github.com/ur-whitelab/py0
• Owner: ur-whitelab
• License: gpl-2.0
• Created: 2020-05-01T15:29:40.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2023-03-25T01:33:17.000Z (almost 2 years ago)
• Last Synced: 2024-04-15T15:11:15.137Z (9 months ago)
• Language: Jupyter Notebook
• Homepage: https://ur-whitelab.github.io/py0/
• Size: 234 MB
• Stars: 2
• Watchers: 3
• Forks: 4
• Open Issues: 1
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# Compartmental Epidomiology Modeling

![tests](https://github.com/ur-whitelab/py0/actions/workflows/tests.yml/badge.svg) ![docs](https://github.com/ur-whitelab/py0/actions/workflows/docs.yml/badge.svg)

``py0`` is a python implementation of compartmental disease modeling.

![](docs/source/img/py_0.gif)

## Installation

To install ``py0``:

```sh

pip install py0@git+https://github.com/ur-whitelab/py0.git

```

## Maximum Entropy Biasing

``py0`` can be coupled with [MaxEnt](https://ur-whitelab.github.io/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).

![](docs/source/img/sampling.gif)

### MaxEnt Fit

![](docs/source/img/fit.gif)

### MaxEnt Installation

The package uses Keras (Tensorflow). To install:

```sh

pip install maxent-infer

```

## Citation

[See paper](https://journals.aps.org/pre/abstract/10.1103/PhysRevE.106.014306) and the citation:

```bibtex

@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

[![License: GPL v2](https://img.shields.io/badge/License-GPL%20v2-blue.svg)](https://www.gnu.org/licenses/old-licenses/gpl-2.0.en.html)

## Authors

``py0`` is developed by [Mehrad Ansari]([email protected]), [Rainier Barrett]([email protected]) and [Andrew White]([email protected]).