Crackovid

Louis Abraham, Gary Bécigneul and Bernhard Schölkopf

For questions and suggestions, join the slack channel: link

Description

Given n people and t testing kits, the characteristics of the test and estimations of the probability for each person to be sick, one wants to optimize the way the tests are used by combining several samples.

We assume the events "the i-th is sick" are independent.

Different metrics can be used. For the moment, the two that are implemented are expected confidence and expected entropy.

Modes of operation

The program supports 2 modes of operation:

• evaluation
• optimization

In the optimization mode, the program tries to find an optimal testing framework.

In the evaluation mode, the program is given a testing framework, test results, and gives the most probable result.

Notations

• n: number of persons
• t: number of tests
• tpr: true positive rate / recall / hit rate of the test
• tnr: true negative rate / specificity / selectivity of the test
• p1,p2,...,pn: prior probabilities for each person to be sick (possibly estimated based on other data)
• threshold: confidence required to make a diagnosis. If threshold=0.9, the probability of being ill must be less than 0.1 or more than 0.1.
• mode: eval or optim

in eval mode:

• test1,test2,...,testt: t binary strings of length n representing tests (1 means testing the person)
• results: binary string of length n representing outcomes (1 means sick)

in optim mode:

• m: samples per person, put 0 if it's infinite or more than t
• metric: confidence, entropy or diagnosed [threshold]
• method: optimization method, can be ga or ga-luby
• mutation_parameter: parameter than controls the search, 1-4 is a good range
• luby_basis: only used with ga-luby, good values are values of epochs that give acceptable results.
• epochs: number of optimization steps

Input format

Eval mode

n t

tpr tnr

p1 p2 ... pn

eval threshold

test1
test2
...
testt

results

Optim mode

n t

tpr tnr

p1 p2 ... pn

optim m metric
method mutation_parameter [luby_basis]
epochs

Examples

Eval mode

Optim mode

Troubleshoot / Feedback

Please report issues and feedback to louis.abraham@yahoo.fr.