{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,12]],"date-time":"2026-05-12T15:20:36Z","timestamp":1778599236968,"version":"3.51.4"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Gene\u2013gene interactions are important contributors to complex biological traits. Multifactor dimensionality reduction (MDR) is a method to analyze gene\u2013gene interactions and has been applied to many genetics studies of complex diseases. In order to identify the best interaction model associated with disease susceptibility, MDR classifiers corresponding to interaction models has been constructed and evaluated as a predictor of disease status via a certain measure such as balanced accuracy (BA). It has been shown that the performance of MDR tends to depend on the choice of the evaluation measures.<\/jats:p>\n               <jats:p>Results: In this article, we introduce two types of new evaluation measures. First, we develop weighted BA (wBA) that utilizes the quantitative information on the effect size of each multi-locus genotype on a trait. Second, we employ ordinal association measures to assess the performance of MDR classifiers. Simulation studies were conducted to compare the proposed measures with BA, a current measure. Our results showed that the wBA and \u03c4b improved the power of MDR in detecting gene\u2013gene interactions. Noticeably, the power increment was higher when data contains the greater number of genetic markers. Finally, we applied the proposed evaluation measures to real data.<\/jats:p>\n               <jats:p>Contact: \u00a0tspark@stats.snu.ac.kr<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn629","type":"journal-article","created":{"date-parts":[[2009,1,23]],"date-time":"2009-01-23T01:13:55Z","timestamp":1232673235000},"page":"338-345","source":"Crossref","is-referenced-by-count":56,"title":["New evaluation measures for multifactor dimensionality reduction classifiers in gene\u2013gene interaction analysis"],"prefix":"10.1093","volume":"25","author":[{"given":"Junghyun","family":"Namkung","sequence":"first","affiliation":[{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"},{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"},{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kyunga","family":"Kim","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"},{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"},{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sungon","family":"Yi","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"},{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"},{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wonil","family":"Chung","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"},{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"},{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Min-Seok","family":"Kwon","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"},{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"},{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taesung","family":"Park","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"},{"name":"1 Bioinformatics Program and 2Department of Statistics, Seoul National University, Seoul 151-747, Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2009,1,22]]},"reference":[{"key":"2023013110003360100_B1","doi-asserted-by":"crossref","DOI":"10.1002\/0471249688","volume-title":"Categorical Data Analysis.","author":"Agresti","year":"2002"},{"key":"2023013110003360100_B2","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/1471-2105-9-238","article-title":"Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction","volume":"9","author":"Bush","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023013110003360100_B3","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1093\/bioinformatics\/btl557","article-title":"Odds ratio based multifactor-dimensionality reduction method for detecting gene-gene interactions","volume":"23","author":"Chung","year":"2007","journal-title":"Bioinformatics"},{"key":"2023013110003360100_B4","doi-asserted-by":"crossref","first-page":"2463","DOI":"10.1093\/hmg\/11.20.2463","article-title":"Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans","volume":"11","author":"Cordell","year":"2002","journal-title":"Hum. 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