FSBENCHMARK Code

Purpose

These files allow to reproduce results from :
The influence of feature selection methods on the accuracy, stability and interpretability of molecular signatures
Anne-Claire Haury, Pierre Gestraud and Jean-Philippe Vert, 2011. (Technical Report)

Download

The code may be downloaded here: FSBENCHMARK.zip (version 1.0) .

Documentation

HTML Documentation for the code is available here .
Note that you may also access a help file for each function in the MATLAB command window by typing
>> help function_name
or
>> doc function_name

Usage

The main functions are ./Main/compute_accuracy.m, ./Main/compute_stability.m and ./Main/between_setting.m Use the demos provided in ./Demos to get started

Interpretability

Note that GO stability and interpretability were computed using R package GOSemSim, and therefore do not appear here.

Required toolboxes

This code requires the following toolboxes:
  • MATLAB Bioinformatics toolbox (function rankfeatures.m)
  • MATLAB Statistics toolbox
  • SPIDER toolbox (for algorithm svmrfe) that can be dowloaded here . Make sure to replace spider/feat_sel/@rfe/rfe.m by ./Selection/rfe.m
  • SPAMS toolbox (for algorithms Lasso, E-Net and OMP) that can be dowloaded for your specific OS here.
    Any questions regarding this toolbox should be addressed to Julien Mairal