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SEPIA-paper-final

SEPIA (Simulation-based Evaluation Of PriorIzation Algorithms)

Overview of Contents

  • helper_scripts/make_violinplots.py - creates 9 violin plot figures in figures/, each with with 2 violin plots. Each figure represents an experimental condition, and each of the 2 plots represent either ProACT or HIV-TRACE.
usage: [METRIC]
 METRIC			The number of the metric you want to generate violin plots for with the data
  • figures/ - holds figures used in the SEPIA paper, including the violin plots

Reproducing the SEPIA Paper Results

The SEPIA manuscript utilizes the simulated data used in the ProACT manuscript:

https://github.com/niemasd/ProACT-Paper-Final/tree/master/simulations

Note that SEPIA can use any dataset produced by FAVITES: we just happened to reuse this dataset in the SEPIA manuscript. SEPIA itself is completely generalizable to any simulation conditions.

To redo the analyses conducted in the SEPIA manuscript as well as to reproduce the figures in the manuscript, simply do the following:

  1. Download and extract a zip of the ProACT-Paper-Final repo
  2. Download SEPIA.py and place it within the extracted folder
  3. Download make_violinplots.py and place it within the extracted folder
  4. Run make_violinplots.py: python3 make_violinplots.py <metric>
    • To automate running on all metrics: for m in $(seq 1 6) ; do python3 make_violinplots.py $m ; done