title: Ordinal response prediction using bootstrap aggregation, with application to a high-throughput methylation data set.
abstract: Many investigators conducting translational research are performing high-throughput genomic experiments and then developing multigenic classifiers using the resulting high-dimensional data set. In a large number of applications, the class to be predicted may be inherently ordinal. Examples of ordinal outcomes include tumor-node-metastasis (TNM) stage (I, II, III, IV); drug toxicity evaluated as none, mild, moderate, or severe; and response to treatment classified as complete response, partial response, stable disease, or progressive disease. While one can apply nominal response classification methods to ordinal response data, in doing so some information is lost that may improve the predictive performance of the classifier. This study examined the effectiveness of alternative ordinal splitting functions combined with bootstrap aggregation for classifying an ordinal response. We demonstrate that the ordinal impurity and ordered twoing methods have desirable properties for classifying ordinal response data and both perform well in comparison to other previously described methods. Developing a multigenic classifier is a common goal for microarray studies, and therefore application of the ordinal ensemble methods is demonstrated on a high-throughput methylation data set.
authors.affiliation: Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298-0032, USA. kjarcher@vcu.edu
authors.forename: K J
authors.initials: KJ
authors.lastname: Archer
authors.forename: V R
authors.initials: VR
authors.lastname: Mas
mesh_terms: D001185:Artificial Intelligence; D003198:Computer Simulation; D018899:CpG Islands / Q000502:physiology; D003627:Data Interpretation, Statistical; D006801:Humans; D008745:Methylation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D057170:Translational Research, Biomedical / Q000379:methods*
references.citation: Nat Genet. 2000 Feb;24(2):101-2
references.pmid: 10655046
references.citation: Artif Intell Med. 2003 Jan;27(1):65-79
references.pmid: 12473392
references.citation: J Chem Inf Comput Sci. 2003 Nov-Dec;43(6):1947-58
references.pmid: 14632445
references.citation: Nat Genet. 1999 Feb;21(2):163-7
references.pmid: 9988266