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The main idea of this paper is to take full advantage of the biological observation that neighboring genes in a network tend to function together in biological processes and to embed this information into a formal statistical framework.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We propose a network-based support vector machine for binary classification problems by constructing a penalty term from the<jats:italic>F<\/jats:italic><jats:sub>\u221e<\/jats:sub>-norm being applied to pairwise gene neighbors with the hope to improve predictive performance and gene selection. Simulation studies in both low- and high-dimensional data settings as well as two real microarray applications indicate that the proposed method is able to identify more clinically relevant genes while maintaining a sparse model with either similar or higher prediction accuracy compared with the standard and the<jats:italic>L<\/jats:italic><jats:sub>1<\/jats:sub>penalized support vector machines.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The proposed network-based support vector machine has the potential to be a practically useful classification tool for microarrays and other high-dimensional data.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-10-s1-s21","type":"journal-article","created":{"date-parts":[[2009,1,30]],"date-time":"2009-01-30T20:04:59Z","timestamp":1233345899000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":77,"title":["Network-based support vector machine for classification of microarray samples"],"prefix":"10.1186","volume":"10","author":[{"given":"Yanni","family":"Zhu","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaotong","family":"Shen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Pan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,1,30]]},"reference":[{"key":"3204_CR1","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1038\/msb4100180","volume":"3","author":"HY Chuang","year":"2007","unstructured":"Chuang HY, Lee EJ, Liu YT, Lee DH, Ideker T: Network-based classification of breast cancer metastasis. 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