Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease.
BACKGROUND
Feature extraction (FE) is difficult, particularly if there are more features than samples, as small sample numbers often result in biased outcomes or overfitting. Furthermore, multiple sample classes often complicate FE because evaluating performance, which is usual in supervised FE, is generally harder than the two-class problem. Developing sample classification independent unsupervised methods would solve many of these problems.


RESULTS
Two principal component analysis (PCA)-based FE, specifically, variational Bayes PCA (VBPCA) was extended to perform unsupervised FE, and together with conventional PCA (CPCA)-based unsupervised FE, were tested as sample classification independent unsupervised FE methods. VBPCA- and CPCA-based unsupervised FE both performed well when applied to simulated data, and a posttraumatic stress disorder (PTSD)-mediated heart disease data set that had multiple categorical class observations in mRNA/microRNA expression of stressed mouse heart. A critical set of PTSD miRNAs/mRNAs were identified that show aberrant expression between treatment and control samples, and significant, negative correlation with one another. Moreover, greater stability and biological feasibility than conventional supervised FE was also demonstrated. Based on the results obtained, in silico drug discovery was performed as translational validation of the methods.


CONCLUSIONS
Our two proposed unsupervised FE methods (CPCA- and VBPCA-based) worked well on simulated data, and outperformed two conventional supervised FE methods on a real data set. Thus, these two methods have suggested equivalence for FE on categorical multiclass data sets, with potential translational utility for in silico drug discovery.
Department of Physics, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan. tag@granular.com.
Y-h
YH
Taguchi
Department of Biological Science, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan. iwadate@bio.chuo-u.ac.jp.
Mitsuo
M
Iwadate
Department of Biological Science, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan. umeyama@bio.chuo-u.ac.jp.
Hideaki
H
Umeyama
D000465:Algorithms; D000818:Animals; D001499:Bayes Theorem; D015415:Biomarkers; D019295:Computational Biology; D003198:Computer Simulation; D057225:Data Mining / Q000379:methods* / Q000706:statistics & numerical data; D055808:Drug Discovery; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006331:Heart Diseases / Q000188:drug therapy / Q000235:genetics*; D051379:Mice; D035683:MicroRNAs / Q000235:genetics; D025341:Principal Component Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics; D013313:Stress Disorders, Post-Traumatic / Q000188:drug therapy / Q000235:genetics*
D015415:Biomarkers; D035683:MicroRNAs; D012333:RNA, Messenger