{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,25]],"date-time":"2026-01-25T04:26:35Z","timestamp":1769315195115,"version":"3.49.0"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"S13","license":[{"start":{"date-parts":[[2011,11,30]],"date-time":"2011-11-30T00:00:00Z","timestamp":1322611200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1186\/1471-2105-12-s13-s8","type":"journal-article","created":{"date-parts":[[2011,12,2]],"date-time":"2011-12-02T05:03:05Z","timestamp":1322802185000},"source":"Crossref","is-referenced-by-count":17,"title":["Comprehensive evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data"],"prefix":"10.1186","volume":"12","author":[{"given":"Mi Hyeon","family":"Kim","sequence":"first","affiliation":[]},{"given":"Hwa Jeong","family":"Seo","sequence":"additional","affiliation":[]},{"given":"Je-Gun","family":"Joung","sequence":"additional","affiliation":[]},{"given":"Ju Han","family":"Kim","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,11,30]]},"reference":[{"issue":"5","key":"4924_CR1","doi-asserted-by":"publisher","first-page":"571","DOI":"10.1093\/bioinformatics\/btg051","volume":"19","author":"S Bicciato","year":"2003","unstructured":"Bicciato S, Luchini A, Di Bello C: PCA disjoint models for multiclass cancer analysis using gene expression data. Bioinformatics 2003, 19(5):571\u2013578. 10.1093\/bioinformatics\/btg051","journal-title":"Bioinformatics"},{"issue":"4","key":"4924_CR2","doi-asserted-by":"publisher","first-page":"545","DOI":"10.1093\/bioinformatics\/btp009","volume":"25","author":"Q Qi","year":"2009","unstructured":"Qi Q, Zhao Y, Li M, Simon R: Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools. Bioinformatics 2009, 25(4):545\u2013547. 10.1093\/bioinformatics\/btp009","journal-title":"Bioinformatics"},{"issue":"15","key":"4924_CR3","doi-asserted-by":"publisher","first-page":"1688","DOI":"10.1093\/bioinformatics\/btn245","volume":"24","author":"R Schachtner","year":"2008","unstructured":"Schachtner R, Lutter D, Knollmuller P, Tome AM, Theis FJ, Schmitz G, Stetter M, Vilda PG, Lang EW: Knowledge-based gene expression classification via matrix factorization. Bioinformatics 2008, 24(15):1688\u20131697. 10.1093\/bioinformatics\/btn245","journal-title":"Bioinformatics"},{"issue":"3","key":"4924_CR4","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1016\/j.compbiolchem.2004.05.002","volume":"28","author":"Y Tan","year":"2004","unstructured":"Tan Y, Shi L, Tong W, Hwang GT, Wang C: Multi-class tumor classification by discriminant partial least squares using microarray gene expression data and assessment of classification models. Comput Biol Chem 2004, 28(3):235\u2013244. 10.1016\/j.compbiolchem.2004.05.002","journal-title":"Comput Biol Chem"},{"key":"4924_CR5","volume-title":"Brief Bioinform","author":"S Ma","year":"2011","unstructured":"Ma S, Dai Y: Principal component analysis based methods in bioinformatics studies. Brief Bioinform 2011."},{"key":"4924_CR6","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1002\/env.3170050203","volume":"5","author":"P Paatero","year":"1994","unstructured":"Paatero P, Tapper U: Positive matrix factorization: A non-negative factor model with optimal utilization of errorest mates of data values. Environmetrics 1994, 5: 111\u2013126. 10.1002\/env.3170050203","journal-title":"Environmetrics"},{"issue":"6755","key":"4924_CR7","doi-asserted-by":"publisher","first-page":"788","DOI":"10.1038\/44565","volume":"401","author":"DD Lee","year":"1999","unstructured":"Lee DD, Seung HS: Learning the parts of objects by non-negative matrix factorization. Nature 1999, 401(6755):788\u2013791. 10.1038\/44565","journal-title":"Nature"},{"key":"4924_CR8","doi-asserted-by":"publisher","DOI":"10.1002\/0471221317","volume-title":"Independent Component Analysis","author":"A Hyvarinen","year":"2001","unstructured":"Hyvarinen A, Karhunen J, Oja E: Independent Component Analysis. In Edited by: Interscience W. 2001."},{"issue":"12","key":"4924_CR9","doi-asserted-by":"publisher","first-page":"4164","DOI":"10.1073\/pnas.0308531101","volume":"101","author":"JP Brunet","year":"2004","unstructured":"Brunet JP, Tamayo P, Golub TR, Mesirov JP: Metagenes and molecular pattern discovery using matrix factorization. Proc Natl Acad Sci U S A 2004, 101(12):4164\u20134169. 10.1073\/pnas.0308531101","journal-title":"Proc Natl Acad Sci U S A"},{"key":"4924_CR10","first-page":"207","volume-title":"Proceedings of IEEE International Conference on Computer Vision and Pattern Recognition: December 2001 2001","author":"SZ Li","year":"2001","unstructured":"Li SZ, Hou XW, Zhang HJ, Cheng QS: Learning spatially localized parts-based representation. Proceedings of IEEE International Conference on Computer Vision and Pattern Recognition: December 2001 2001 2001, 207\u2013212."},{"key":"4924_CR11","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1109\/NNSP.2002.1030067","volume-title":"Neural Networks for Signal Processing XII: 2002; Martigny, Switzerland","author":"PO Hoyer","year":"2002","unstructured":"Hoyer PO: Non-negative sparse coding. Neural Networks for Signal Processing XII: 2002; Martigny, Switzerland 2002, 557\u2013565."},{"key":"4924_CR12","first-page":"1457","volume":"5","author":"PO Hoyer","year":"2004","unstructured":"Hoyer PO, Dayan P: Non-negative Matrix Factorization with sparseness constraints. Journal of Machine Learning Research 2004, 5: 1457\u20131469.","journal-title":"Journal of Machine Learning Research"},{"key":"4924_CR13","first-page":"806","volume-title":"Asian Conference on Computer Vision","author":"Y Wang","year":"2004","unstructured":"Wang Y, Jia Y, Hu C, Turk M: Fisher non-negative matrix factorization for learning local features. In Asian Conference on Computer Vision. Jeju, Korea; 2004:806\u2013811."},{"issue":"21","key":"4924_CR14","doi-asserted-by":"publisher","first-page":"3970","DOI":"10.1093\/bioinformatics\/bti653","volume":"21","author":"Y Gao","year":"2005","unstructured":"Gao Y, Church G: Improving molecular cancer class discovery through sparse non-negative matrix factorization. Bioinformatics 2005, 21(21):3970\u20133975. 10.1093\/bioinformatics\/bti653","journal-title":"Bioinformatics"},{"key":"4924_CR15","volume-title":"Proceedings of the Fourth SIAM International Conference on Data Mining: April 22\u201324 2004; Lake Buena Vista, Florida, USA","author":"P Pauca","year":"2004","unstructured":"Pauca P, Shahnaz F, Berry M, Plemmons R: Text Mining using Non-Negative Matrix Factorizations. Proceedings of the Fourth SIAM International Conference on Data Mining: April 22\u201324 2004; Lake Buena Vista, Florida, USA 2004."},{"key":"4924_CR16","first-page":"1","volume-title":"Classification and Clustering","author":"RR Sokal","year":"1977","unstructured":"Sokal RR: Clustering and classification: background and current directions. In Classification and Clustering. Edited by: Van Ryzin J. Academic Press, London; 1977:1\u201315."},{"key":"4924_CR17","volume-title":"Cluster Analysis","author":"BS Everitt","year":"1933","unstructured":"Everitt BS: Cluster Analysis. Edward Arnold; 1933."},{"issue":"14","key":"4924_CR18","doi-asserted-by":"publisher","first-page":"1787","DOI":"10.1093\/bioinformatics\/btg232","volume":"19","author":"R Sharan","year":"2003","unstructured":"Sharan R, Maron-Katz A, Shamir R: CLICK and EXPANDER: a system for clustering and visualizing gene expression data. Bioinformatics 2003, 19(14):1787\u20131799. 10.1093\/bioinformatics\/btg232","journal-title":"Bioinformatics"},{"issue":"4","key":"4924_CR19","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1093\/bioinformatics\/17.4.309","volume":"17","author":"KY Yeung","year":"2001","unstructured":"Yeung KY, Haynor DR, Ruzzo WL: Validating clustering for gene expression data. Bioinformatics 2001, 17(4):309\u2013318. 10.1093\/bioinformatics\/17.4.309","journal-title":"Bioinformatics"},{"issue":"Suppl 1","key":"4924_CR20","doi-asserted-by":"publisher","first-page":"i144","DOI":"10.1093\/bioinformatics\/bti1041","volume":"21","author":"D Dueck","year":"2005","unstructured":"Dueck D, Morris QD, Frey BJ: Multi-way clustering of microarray data using probabilistic sparse matrix factorization. Bioinformatics 2005, 21(Suppl 1):i144\u2013151. 10.1093\/bioinformatics\/bti1041","journal-title":"Bioinformatics"},{"issue":"4","key":"4924_CR21","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1093\/bioinformatics\/18.4.536","volume":"18","author":"Y Xu","year":"2002","unstructured":"Xu Y, Olman V, Xu D: Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. Bioinformatics 2002, 18(4):536\u2013545. 10.1093\/bioinformatics\/18.4.536","journal-title":"Bioinformatics"},{"issue":"5439","key":"4924_CR22","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1126\/science.286.5439.531","volume":"286","author":"TR Golub","year":"1999","unstructured":"Golub TR, Slonim DK, Tamayo P, Huard C, Gaasenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, et al.: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 1999, 286(5439):531\u2013537. 10.1126\/science.286.5439.531","journal-title":"Science"},{"issue":"6870","key":"4924_CR23","doi-asserted-by":"publisher","first-page":"436","DOI":"10.1038\/415436a","volume":"415","author":"SL Pomeroy","year":"2002","unstructured":"Pomeroy SL, Tamayo P, Gaasenbeek M, Sturla LM, Angelo M, McLaughlin ME, Kim JY, Goumnerova LC, Black PM, Lau C, et al.: Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 2002, 415(6870):436\u2013442. 10.1038\/415436a","journal-title":"Nature"},{"issue":"5398","key":"4924_CR24","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1126\/science.283.5398.83","volume":"283","author":"VR Iyer","year":"1999","unstructured":"Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JC, Trent JM, Staudt LM, Hudson J Jr., Boguski MS, et al.: The transcriptional program in the response of human fibroblasts to serum. Science 1999, 283(5398):83\u201387. 10.1126\/science.283.5398.83","journal-title":"Science"},{"key":"4924_CR25","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1111\/j.1469-1809.1936.tb02137.x","volume":"7","author":"R Fisher","year":"1936","unstructured":"Fisher R: The use of multiple measurements in taxonomic problem. Ann Eugenics 1936, 7: 179\u2013188. 10.1111\/j.1469-1809.1936.tb02137.x","journal-title":"Ann Eugenics"},{"key":"4924_CR26","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1109\/3477.678624","volume":"28","author":"J Bezdek","year":"1998","unstructured":"Bezdek J, Pal N: Some new indexes of cluster validity. IEEE Trans Syst Man Cybernet 1998, 28: 301\u2013315. 10.1109\/3477.678624","journal-title":"IEEE Trans Syst Man Cybernet"},{"key":"4924_CR27","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1023\/A:1012801612483","volume":"17","author":"M Halkidi","year":"2001","unstructured":"Halkidi M, Batistakis Y, Vazirgiannis M: On clustering validation techniques. Journal of Intelligent Information Systems 2001, 17: 107\u2013145. 10.1023\/A:1012801612483","journal-title":"Journal of Intelligent Information Systems"},{"key":"4924_CR28","first-page":"95","volume-title":"Journal of Cybernetics","author":"J Dunn","year":"1974","unstructured":"Dunn J: Well separated clusters and optimal fuzzy partitions. Journal of Cybernetics 1974, 95\u2013104."},{"key":"4924_CR29","doi-asserted-by":"publisher","first-page":"224","DOI":"10.1109\/TPAMI.1979.4766909","volume":"1","author":"DL Davies","year":"1979","unstructured":"Davies DL, Bouldin DW: Acluster separation measure. IEEE Trans Pattern Anal Machine Intell 1979, 1: 224\u2013227.","journal-title":"IEEE Trans Pattern Anal Machine Intell"},{"key":"4924_CR30","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1016\/0377-0427(87)90125-7","volume":"20","author":"PJ Rousseeuw","year":"1987","unstructured":"Rousseeuw PJ: Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 1987, 20: 53\u201365. 10.1016\/0377-0427(87)90125-7","journal-title":"J Comput Appl Math"},{"key":"4924_CR31","volume-title":"Cluster Analysis for Researchers","author":"HC Romesburg","year":"1984","unstructured":"Romesburg HC: Cluster Analysis for Researchers. Belmont, Calif.: Lifetime Learning Publications; 1984."},{"key":"4924_CR32","volume-title":"An Introduction to Linear Regression and Correlation","author":"AL Edwards","year":"1976","unstructured":"Edwards AL: The Correlation Coefficient. In An Introduction to Linear Regression and Correlation. San Francisco, CA: W. H. Freeman; 1976."},{"key":"4924_CR33","volume-title":"Nonparametrics: Statistical Methods Based on Ranks","author":"EL Lehmann","year":"1998","unstructured":"Lehmann EL, D'Abrera HJM: Nonparametrics: Statistical Methods Based on Ranks. Upper Saddle River, N.J. : Prentice Hall; 1998."},{"issue":"2","key":"4924_CR34","doi-asserted-by":"publisher","first-page":"411","DOI":"10.1111\/1467-9868.00293","volume":"63","author":"R Tibshirani","year":"2001","unstructured":"Tibshirani R, Walther G, Hastie T: Estimating the number of clusters in a data set via the gap statistic. Journal of the Royal Statistical Society: Series B (Statistical Methodology) 2001, 63(2):411\u2013423. 10.1111\/1467-9868.00293","journal-title":"Journal of the Royal Statistical Society: Series B (Statistical Methodology)"},{"issue":"336","key":"4924_CR35","doi-asserted-by":"publisher","first-page":"846","DOI":"10.1080\/01621459.1971.10482356","volume":"66","author":"WM Rand","year":"1971","unstructured":"Rand WM: Objective criteria for the evaluation of clustering methods. Journal of the American Statistical Association 1971, 66(336):846\u2013850. 10.2307\/2284239","journal-title":"Journal of the American Statistical Association"},{"key":"4924_CR36","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1007\/BF01908075","volume":"2","author":"A Hubert","year":"1985","unstructured":"Hubert A: Comparing partitions. J Classif 1985, 2: 193\u2013198. 10.1007\/BF01908075","journal-title":"J Classif"},{"key":"4924_CR37","first-page":"223","volume":"44","author":"S Jaccard","year":"1908","unstructured":"Jaccard S: Nouvelles recherches sur la distribution florale. Bull Soc Vandoise des Sci Nat 1908, 44: 223\u2013270.","journal-title":"Bull Soc Vandoise des Sci Nat"},{"key":"4924_CR38","volume-title":"Mathematical Taxonomy","author":"N Jardine","year":"1971","unstructured":"Jardine N, Sibson R: Mathematical Taxonomy. Wiley, London. Kangas; 1971."},{"key":"4924_CR39","first-page":"267","volume-title":"Proceedings of the 26th annual international ACM SIGIR conference on Research and development in informaion retrieval July 28- August 1 2003; Toronto, CA","author":"W Xu","year":"2003","unstructured":"Xu W, Liu X, Gong Y: Document-clustering based on non-negative matrix factorization. Proceedings of the 26th annual international ACM SIGIR conference on Research and development in informaion retrieval July 28- August 1 2003; Toronto, CA 2003, 267\u2013273."},{"issue":"Web Server issu","key":"4924_CR40","doi-asserted-by":"publisher","first-page":"W460","DOI":"10.1093\/nar\/gkh476","volume":"32","author":"HJ Chung","year":"2004","unstructured":"Chung HJ, Kim M, Park CH, Kim J, Kim JH: ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res 2004, 32(Web Server issue):W460\u2013464.","journal-title":"Nucleic Acids Res"},{"issue":"Web Server issu","key":"4924_CR41","doi-asserted-by":"publisher","first-page":"W621","DOI":"10.1093\/nar\/gki450","volume":"33","author":"HJ Chung","year":"2005","unstructured":"Chung HJ, Park CH, Han MR, Lee S, Ohn JH, Kim J, Kim JH: ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics. Nucleic Acids Res 2005, 33(Web Server issue):W621\u2013626.","journal-title":"Nucleic Acids Res"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S13-S8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-12-S13-S8\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-12-S13-S8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,23]],"date-time":"2019-01-23T10:47:47Z","timestamp":1548240467000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-12-S13-S8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,11,30]]},"references-count":41,"journal-issue":{"issue":"S13","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["4924"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-12-s13-s8","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,11,30]]},"article-number":"S8"}}