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BioMed Research International
Volume 2015, Article ID 713953, 7 pages
http://dx.doi.org/10.1155/2015/713953
Research Article

Network-Based Logistic Classification with an Enhanced Solver Reveals Biomarker and Subnetwork Signatures for Diagnosing Lung Cancer

Faculty of Information Technology & State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Avenida Wai Long, Taipa 999078, Macau

Received 24 October 2014; Revised 5 April 2015; Accepted 30 April 2015

Academic Editor: Jennifer Wu

Copyright © 2015 Hai-Hui Huang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Identifying biomarker and signaling pathway is a critical step in genomic studies, in which the regularization method is a widely used feature extraction approach. However, most of the regularizers are based on -norm and their results are not good enough for sparsity and interpretation and are asymptotically biased, especially in genomic research. Recently, we gained a large amount of molecular interaction information about the disease-related biological processes and gathered them through various databases, which focused on many aspects of biological systems. In this paper, we use an enhanced penalized solver to penalize network-constrained logistic regression model called an enhanced net, where the predictors are based on gene-expression data with biologic network knowledge. Extensive simulation studies showed that our proposed approach outperforms regularization, the old penalized solver, and the Elastic net approaches in terms of classification accuracy and stability. Furthermore, we applied our method for lung cancer data analysis and found that our method achieves higher predictive accuracy than regularization, the old penalized solver, and the Elastic net approaches, while fewer but informative biomarkers and pathways are selected.