title: T-ReCS: stable selection of dynamically formed groups of features with application to prediction of clinical outcomes.
abstract: Feature selection is used extensively in biomedical research for biomarker identification and patient classification, both of which are essential steps in developing personalized medicine strategies. However, the structured nature of the biological datasets and high correlation of variables frequently yield multiple equally optimal signatures, thus making traditional feature selection methods unstable. Features selected based on one cohort of patients, may not work as well in another cohort. In addition, biologically important features may be missed due to selection of other co-clustered features We propose a new method, Tree-guided Recursive Cluster Selection (T-ReCS), for efficient selection of grouped features. T-ReCS significantly improves predictive stability while maintains the same level of accuracy. T-ReCS does not require an a priori knowledge of the clusters like group-lasso and also can handle "orphan" features (not belonging to a cluster). T-ReCS can be used with categorical or survival target variables. Tested on simulated and real expression data from breast cancer and lung diseases and survival data, T-ReCS selected stable cluster features without significant loss in classification accuracy.
authors.affiliation: Department of Computational and Systems Biology, and Joint CMU-Pitt PhD Program in computational Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA. tzh4@pitt.edu.
authors.forename: Grace T
authors.initials: GT
authors.lastname: Huang
authors.forename: Ioannis
authors.initials: I
authors.lastname: Tsamardinos
authors.forename: Vineet
authors.initials: V
authors.lastname: Raghu
authors.forename: Naftali
authors.initials: N
authors.lastname: Kaminski
authors.forename: Panayiotis V
authors.initials: PV
authors.lastname: Benos
mesh_terms: D000465:Algorithms; D001943:Breast Neoplasms / Q000235:genetics; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D019295:Computational Biology; D003198:Computer Simulation; D030541:Databases, Genetic / Q000706:statistics & numerical data; D005260:Female; D015870:Gene Expression; D006801:Humans; D008171:Lung Diseases / Q000235:genetics; D057285:Precision Medicine; D011379:Prognosis; D016019:Survival Analysis; D016896:Treatment Outcome