Document Type
Article
Publication Date
2011
College/Unit
Eberly College of Arts and Sciences
Department/Program/Center
Statistics
Abstract
Background
Successfully modeling high-dimensional data involving thousands of variables is challenging. This is especially true for gene expression profiling experiments, given the large number of genes involved and the small number of samples available. Random Forests (RF) is a popular and widely used approach to feature selection for such "small n, large p problems." However, Random Forests suffers from instability, especially in the presence of noisy and/or unbalanced inputs.
Results
We present RKNN-FS, an innovative feature selection procedure for "small n, large pproblems." RKNN-FS is based on Random KNN (RKNN), a novel generalization of traditional nearest-neighbor modeling. RKNN consists of an ensemble of base k-nearest neighbor models, each constructed from a random subset of the input variables. To rank the importance of the variables, we define a criterion on the RKNN framework, using the notion of support. A two-stage backward model selection method is then developed based on this criterion. Empirical results on microarray data sets with thousands of variables and relatively few samples show that RKNN-FS is an effective feature selection approach for high-dimensional data. RKNN is similar to Random Forests in terms of classification accuracy without feature selection. However, RKNN provides much better classification accuracy than RF when each method incorporates a feature-selection step. Our results show that RKNN is significantly more stable and more robust than Random Forests for feature selection when the input data are noisy and/or unbalanced. Further, RKNN-FS is much faster than the Random Forests feature selection method (RF-FS), especially for large scale problems, involving thousands of variables and multiple classes.
Conclusions
Given the superiority of Random KNN in classification performance when compared with Random Forests, RKNN-FS's simplicity and ease of implementation, and its superiority in speed and stability, we propose RKNN-FS as a faster and more stable alternative to Random Forests in classification problems involving feature selection for high-dimensional datasets.
Digital Commons Citation
Li, Shengqiao; Harner, E J.; and Adjeroh, Donald A., "Random KNN feature selection - a fast and stable alternative to Random Forests" (2011). Faculty & Staff Scholarship. 2702.
https://researchrepository.wvu.edu/faculty_publications/2702
Source Citation
Li, S., Harner, E.J. & Adjeroh, D.A. Random KNN feature selection - a fast and stable alternative to Random Forests. BMC Bioinformatics 12, 450 (2011). https://doi.org/10.1186/1471-2105-12-450
Comments
© 2011 Li et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.