title: Network-Based Logistic Classification with an Enhanced L 1/2 Solver Reveals Biomarker and Subnetwork Signatures for Diagnosing Lung Cancer.
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 L 1-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 L 1/2 penalized solver to penalize network-constrained logistic regression model called an enhanced L 1/2 net, where the predictors are based on gene-expression data with biologic network knowledge. Extensive simulation studies showed that our proposed approach outperforms L 1 regularization, the old L 1/2 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 L 1 regularization, the old L 1/2 penalized solver, and the Elastic net approaches, while fewer but informative biomarkers and pathways are selected.
authors.affiliation: 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.
authors.forename: Hai-Hui
authors.initials: HH
authors.lastname: Huang
authors.affiliation: 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.
authors.forename: Yong
authors.initials: Y
authors.lastname: Liang
authors.affiliation: 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.
authors.forename: Xiao-Ying
authors.initials: XY
authors.lastname: Liu
mesh_terms: D000465:Algorithms; D014408:Biomarkers, Tumor / Q000378:metabolism*; D003936:Diagnosis, Computer-Assisted / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D008175:Lung Neoplasms / Q000175:diagnosis* / Q000378:metabolism*; D015233:Models, Statistical; D010363:Pattern Recognition, Automated / Q000379:methods; D025941:Protein Interaction Mapping / Q000379:methods; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D015398:Signal Transduction
chemical_list: D014408:Biomarkers, Tumor