Population Disease Occurrence Models

This project generates populations according to statistics about the population using Evolutionary Computation Techniques The technique is summarized in the paper 2019 paper: "Population Disease Occurrence Models Using Evolutionary Computation" by: Olaf Dammann, Anselm Blumer, Jacob Barhak, Aaron Garrett

USAGE:

python PopDOM.py <InstructionsFile.yaml | PAPER>

• InstructionsFile.yaml - Optional instructions file containing the problem definitions
• PAPER - if using this key word, the program will reproduce paper results - High Performance Computing is advised after setting up a dask scheduler and dask workers
• If the user specifies no keyword, the program will look for the instructions file PopDOM.yaml to define the problem to solve

INSTALLATION & DEPENDENCIES:

To install:

1. Copy the files in this repository to a directory of choice - you may omit the Results.zip file
2. Install Anaconda from https://www.anaconda.com/download/
3. install Inspyred: pip install inspyred

Dependant libraries are: Inspyred, numpy, pandas, sklearn, dask, bokeh, holoviews

It is recommended you use Anaconda, yet other python environments should work as well This code was tested on Windows 10 Python 2.7.14 and Linux 18.04 Python 2.7.15 and Anaconda (64-bit) with Inspyred 1.0.

EXAMPLES:

To reproduce the results in the paper results type the following: python PopDOM.py PAPER

To solve the problem defined in the file PopDOM.yaml python ModelCombine.py

To solve the problem defined in the file MyProblem.yaml python MyProblem.yaml

FILES:

• PopDOM.py : Main file with calculations
• CreatePlots.py : A file used to create holoviews plots when generating results to reproduce the paper
• PopDOM1.yaml : A problem definitions file to define step 1 parameters in the paper
• PopDOM2.yaml : A A problem definitions template file to generate step 2 parameters for different strategies used in the paper
• Results.zip : Archived results created running the command python PopDOM.py PAPER
• Readme.md : The file that you are reading now

VERSION HISTORY:

Development started on 7-Apr-2018 when Aaron sent the first code draft.

DEVELOPER CONTACT INFO:

Please pass questions to:

Aaron Garrett aaron.lee.garrett@gmail.com http://sites.wofford.edu/garrettal/

Jacob Barhak Ph.D. jacob.barhak@gmail.com http://sites.google.com/site/jacobbarhak/

ACKNOWLEDGEMENTS:

Thanks to Olaf Dammann and Anselm Blumer for useful discussions that led to development of this code.

LICENSE

Copyright (C) 2018-2019 Jacob Barhak, Aaron Garrett

This file is part of the Population Disease Occurrence Models . The Population Disease Occurrence Models is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

The Population Disease Occurrence Models is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

See the GNU General Public License for more details.