Win percentage: a novel measure for assessing the suitability of machine classifiers for biological problems

• Type of Material: Conference Paper
• Authors: R. Mitchell Parry, Georgia Institute of Technology; John Phan, Emory University; Dongmei Wang, Emory University
• Language: English
• Date: 2012-03-21
• Publisher: Emory University Libraries
• Publication Version: Final Published Version
• Copyright Statement: © Parry et al.; licensee BioMed Central Ltd. 2012
• License: Creative Commons Attribution 2.0 Generic
• Final Published Version (URL): http://dx.doi.org/10.1186/1471-2105-13-S3-S7
• Title of Journal or Parent Work: BMC Bioinformatics
• Conference or Event Name: ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB)
• Volume: 13
• Issue: SUPPL.3
• Start Page: S7
• End Page: S7
• Grant/Funding Information: This work was supported in part by grants from National Institutes of Health (Bioengineering Research Partnership R01CA108468, Center for Cancer Nanotechnology Excellence U54CA119338, 1RC2CA148265), and Georgia Cancer Coalition (Distinguished Cancer Scholar Award to Professor MD Wang), Microsoft Research and Hewlett Packard.
• Keywords: Life Sciences & Biomedicine; MODELS; Mathematical & Computational Biology; EXPRESSION; Biotechnology & Applied Microbiology; Biochemical Research Methods; VALIDATION; FEATURE-SELECTION; MATHEMATICAL & COMPUTATIONAL BIOLOGY; CLASSIFICATION; BIOCHEMICAL RESEARCH METHODS; Biochemistry & Molecular Biology; BIOTECHNOLOGY & APPLIED MICROBIOLOGY; Science & Technology
• Research Categories: Biology, Biostatistics; Engineering, Biomedical

Abstract

Background: Selecting an appropriate classifier for a particular biological application poses a difficult problem for researchers and practitioners alike. In particular, choosing a classifier depends heavily on the features selected. For high-throughput biomedical datasets, feature selection is often a preprocessing step that gives an unfair advantage to the classifiers built with the same modeling assumptions. In this paper, we seek classifiers that are suitable to a particular problem independent of feature selection. We propose a novel measure, called "win percentage", for assessing the suitability of machine classifiers to a particular problem. We define win percentage as the probability a classifier will perform better than its peers on a finite random sample of feature sets, giving each classifier equal opportunity to find suitable features.Results: First, we illustrate the difficulty in evaluating classifiers after feature selection. We show that several classifiers can each perform statistically significantly better than their peers given the right feature set among the top 0.001% of all feature sets. We illustrate the utility of win percentage using synthetic data, and evaluate six classifiers in analyzing eight microarray datasets representing three diseases: breast cancer, multiple myeloma, and neuroblastoma. After initially using all Gaussian gene-pairs, we show that precise estimates of win percentage (within 1%) can be achieved using a smaller random sample of all feature pairs. We show that for these data no single classifier can be considered the best without knowing the feature set. Instead, win percentage captures the non-zero probability that each classifier will outperform its peers based on an empirical estimate of performance.Conclusions: Fundamentally, we illustrate that the selection of the most suitable classifier (i.e., one that is more likely to perform better than its peers) not only depends on the dataset and application but also on the thoroughness of feature selection. In particular, win percentage provides a single measurement that could assist users in eliminating or selecting classifiers for their particular application.