Class Prediction and Feature Selection with Linear Optimization for Metagenomic Count Data |
| |
Authors: | Zhenqiu Liu Dechang Chen Li Sheng Amy Y. Liu |
| |
Affiliation: | 1. University of Maryland Greenebaum Cancer Center, Baltimore, Maryland, United States of America.; 2. Department of Preventive Medicine and Biometrics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America.; 3. Department of Mathematics, Drexel University, Philadelphia, Pennsylvania, United States of America.; 4. Department of Applied Math, Brown University, Providence, Rhode Island, United States of America.; The University of Queensland, Australia, |
| |
Abstract: | The amount of metagenomic data is growing rapidly while the computational methods for metagenome analysis are still in their infancy. It is important to develop novel statistical learning tools for the prediction of associations between bacterial communities and disease phenotypes and for the detection of differentially abundant features. In this study, we presented a novel statistical learning method for simultaneous association prediction and feature selection with metagenomic samples from two or multiple treatment populations on the basis of count data. We developed a linear programming based support vector machine with and joint penalties for binary and multiclass classifications with metagenomic count data (metalinprog). We evaluated the performance of our method on several real and simulation datasets. The proposed method can simultaneously identify features and predict classes with the metagenomic count data. |
| |
Keywords: | |
|
|