https://github.com/leechristie/antibiotic-optimisation

Source for "Multi-Objective Evolutionary Optimisation of Antibiotic Treatments" (Ochoa, Christie, Brownlee, & Hoyle, 2020).
https://github.com/leechristie/antibiotic-optimisation

antibiotics computer-science java metaheuristics multiobjective-optimization optimization python python3 research

Last synced: 2 months ago
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Source for "Multi-Objective Evolutionary Optimisation of Antibiotic Treatments" (Ochoa, Christie, Brownlee, & Hoyle, 2020).

• Host: GitHub
• URL: https://github.com/leechristie/antibiotic-optimisation
• Owner: leechristie
• Created: 2018-09-09T17:57:25.000Z (about 7 years ago)
• Default Branch: master
• Last Pushed: 2018-11-28T10:54:39.000Z (almost 7 years ago)
• Last Synced: 2025-02-23T18:16:49.258Z (8 months ago)
• Topics: antibiotics, computer-science, java, metaheuristics, multiobjective-optimization, optimization, python, python3, research
• Language: Jupyter Notebook
• Homepage: https://doi.org/10.1016/j.artmed.2019.101759
• Size: 9.28 MB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

          
# Antibiotic Optimisation

## Model (antibiotic-model)

A stochastic model for antibiotic resistance.

Click to see documentation...

### Example Usage (Model)

`AntibioticModel` can be used directly, giving results to compare to the MATLAB

reference implementation. The model constructor accepts additional parameters to

specify initial bacterial load and random number generator for the simulation.

    int samples = 1000;

    AntibioticModel model = new AntibioticModel(samples);

    

    int[] solution = new int[] {10, 10, 10, 10, 10, 10, 10, 10, 10, 10};

    double fitness = model.evaluate(solution);

### Example Usage (Problem)

`AntibioticProblem` is used to create an `IntegerProblem` instance for jMetal

algorithms. Many objectives may be specified.

    int maxIndividualDosage = 60;

    int maxConcentraition = 60;

    AntibioticProblem problem = new AntibioticProblem(

            model,

            maxIndividualDosage,

            AntibioticObjective.totalAntibiotic(),

            AntibioticObjective.overdoseAmount(maxConcentraition),

            AntibioticObjective.uncuredProportion());

    Algorithm> algorithm = ... // jMetal Algorithm usage

## Experiments (antibiotic-model-experiments)

Documentation to follow

## Offline Re-evaluation (antibiotic-offline-reeval)

Documentation to follow

## Results Post-Processing (results-post-processing)

Documentation to follow