Genetic test bed for feature selection.
BACKGROUND
Given a large set of potential features, such as the set of all gene-expression values from a microarray, it is necessary to find a small subset with which to classify. The task of finding an optimal feature set of a given size is inherently combinatoric because to assure optimality all feature sets of a given size must be checked. Thus, numerous suboptimal feature-selection algorithms have been proposed. There are strong impediments to evaluate feature-selection algorithms using real data when data are limited, a common situation in genetic classification. The difficulty is compound. First, there are no class-conditional distributions from which to draw data points, only a single small labeled sample. Second, there are no test data with which to estimate the feature-set errors, and one must depend on a training-data-based error estimator. Finally, there is no optimal feature set with which to compare the feature sets found by the algorithms.


RESULTS
This paper describes a genetic test bed for the evaluation of feature-selection algorithms. It begins with a large biological feature-label dataset that is used as an empirical distribution and, using massively parallel computation, finds the top feature sets of various sizes based on a given sample size and classification rule. The user can draw random samples from the data, apply a proposed algorithm, and evaluate the proficiency of the proposed algorithm via three different measures (code provided). A key feature of the test bed is that, once a dataset is input, a single command creates the entire test bed relative to the dataset. The particular dataset used for the first version of the test bed comes from a microarray-based classification study that analyzes a large number of microarrays, prepared with RNA from breast tumor samples from each of 295 patients.


BACKGROUND
The software and supplementary material are available at http://public.tgen.org/tgen-cb/support/testbed/


BACKGROUND
edward@ece.tamu.edu.
Choudhary
Ashish
A
Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843, USA.
Brun
Marcel
M
Hua
Jianping
J
Lowey
James
J
Suh
Ed
E
Dougherty
Edward R
ER
D000465:Algorithms; D001943:Breast Neoplasms; D003198:Computer Simulation; D003625:Data Collection; D030541:Databases, Genetic; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D015233:Models, Statistical; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods