{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,16]],"date-time":"2026-06-16T07:28:32Z","timestamp":1781594912492,"version":"3.54.5"},"reference-count":35,"publisher":"Springer Science and Business Media LLC","issue":"S5","license":[{"start":{"date-parts":[[2018,4,1]],"date-time":"2018-04-01T00:00:00Z","timestamp":1522540800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,4]]},"DOI":"10.1186\/s12859-018-2095-4","type":"journal-article","created":{"date-parts":[[2018,4,11]],"date-time":"2018-04-11T06:28:05Z","timestamp":1523428085000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":81,"title":["BCDForest: a boosting cascade deep forest model towards the classification of cancer subtypes based on gene expression data"],"prefix":"10.1186","volume":"19","author":[{"given":"Yang","family":"Guo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuhui","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhanhuai","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuequn","family":"Shang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2018,4,11]]},"reference":[{"issue":"10","key":"2095_CR1","doi-asserted-by":"publisher","first-page":"791","DOI":"10.1038\/nrc2212","volume":"7","author":"J Stingl","year":"2007","unstructured":"Stingl J, Caldas C. Molecular heterogeneity of breast carcinomas and the cancer stem cell hypothesis. Nat Rev Cancer. 2007;7(10):791\u20139.","journal-title":"Nat Rev Cancer"},{"issue":"21","key":"2095_CR2","doi-asserted-by":"publisher","first-page":"8852","DOI":"10.1158\/0008-5472.CAN-10-1039","volume":"70","author":"G Bianchini","year":"2010","unstructured":"Bianchini G, Iwamoto T, Qi Y, Coutant C, Shiang CY, Wang B, Santarpia L, Valero V, Hortobagyi GN, Symmans WF, et al. Prognostic and therapeutic implications of distinct kinase expression patterns in different subtypes of breast cancer. Cancer Res. 2010;70(21):8852\u201362.","journal-title":"Cancer Res"},{"issue":"8","key":"2095_CR3","doi-asserted-by":"publisher","first-page":"2724","DOI":"10.1073\/pnas.1018854108","volume":"109","author":"LM Heiser","year":"2012","unstructured":"Heiser LM, Sadanandam A, Kuo WL, Benz SC, Goldstein TC, Ng S, Gibb WJ, Wang NJ, Ziyad S, Tong F, et al. Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci U S A. 2012;109(8):2724\u20139.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"2095_CR4","doi-asserted-by":"publisher","first-page":"R68","DOI":"10.1186\/bcr2635","volume":"12","author":"A Prat","year":"2010","unstructured":"Prat A, Parker JS, Karginova O, Fan C, Livasy C, Herschkowitz JI, He X, Perou CM. Phenotypic and molecular characterization of the claudin-low intrinsic subtype of breast cancer. Breast Cancer Res. 2010;12(5):R68.","journal-title":"Breast Cancer Res"},{"issue":"13","key":"2095_CR5","doi-asserted-by":"publisher","first-page":"1858","DOI":"10.1093\/bioinformatics\/btu128","volume":"30","author":"MJ Jahid","year":"2014","unstructured":"Jahid MJ, Huang TH, Ruan J. A personalized committee classification approach to improving prediction of breast cancer metastasis. Bioinformatics. 2014;30(13):1858\u201366.","journal-title":"Bioinformatics"},{"issue":"16","key":"2095_CR6","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1186\/s12859-017-1959-3","volume":"18","author":"J Peng","year":"2017","unstructured":"Peng J, Wang H, Lu J, hui W, Wang Y, Shang X. identifying term relations cross different gene ontology categories. BMC Bioinformatics. 2017;18(16):573.","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"2095_CR7","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1504\/IJDMB.2017.084268","volume":"17","author":"JJ Peng","year":"2017","unstructured":"Peng JJ, Xue HS, Shao YK, Shang XQ, Wang YD, Chen J. A novel method to measure the semantic similarity of HPO terms. International Journal of Data Mining and Bioinformatics. 2017;17(2):173\u201388.","journal-title":"International Journal of Data Mining and Bioinformatics"},{"key":"2095_CR8","doi-asserted-by":"crossref","unstructured":"Jiajie P, Zhang X, Hui W, Lu J, Li Q, Shang X. Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach. BMC systems biology. 2018;12(Suppl2)","DOI":"10.1186\/s12918-018-0539-0"},{"issue":"7418","key":"2095_CR9","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1038\/nature11412","volume":"490","author":"DC Koboldt","year":"2012","unstructured":"Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, Fulton LL, Dooling DJ, Ding L, Mardis ER, et al. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490(7418):61\u201370.","journal-title":"Nature"},{"issue":"2","key":"2095_CR10","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1515\/jib-2014-236","volume":"11","author":"M List","year":"2014","unstructured":"List M, Hauschild AC, Tan Q, Kruse TA, Mollenhauer J, Baumbach J, Batra R. Classification of breast cancer subtypes by combining gene expression and DNA methylation data. J Integr Bioinform. 2014;11(2):236.","journal-title":"J Integr Bioinform"},{"key":"2095_CR11","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1016\/j.ymeth.2017.07.024","volume":"131","author":"J Peng","year":"2017","unstructured":"Peng J, Lu J, Shang X, Chen J. Identifying consistent disease subnetworks using DNet. Methods. 2017;131:104\u201310.","journal-title":"Methods"},{"issue":"2","key":"2095_CR12","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1109\/TNB.2011.2144998","volume":"10","author":"CH Zheng","year":"2011","unstructured":"Zheng CH, Ng TY, Zhang L, Shiu CK, Wang HQ. Tumor classification based on non-negative matrix factorization using gene expression data. Ieee Transactions on Nanobioscience. 2011;10(2):86\u201393.","journal-title":"Ieee Transactions on Nanobioscience"},{"key":"2095_CR13","doi-asserted-by":"crossref","unstructured":"Marisa L, de Reynies A, Duval A, Selves J, Gaub MP, Vescovo L, Etienne-Grimaldi MC, Schiappa R, Guenot D, Ayadi M, et al. Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value. PLoS Med. 2013;10(5)","DOI":"10.1371\/journal.pmed.1001453"},{"issue":"3","key":"2095_CR14","doi-asserted-by":"publisher","first-page":"272","DOI":"10.1002\/path.4536","volume":"236","author":"HS Leong","year":"2015","unstructured":"Leong HS, Galletta L, Etemadmoghadam D, George J, Australian Ovarian Cancer S, Kobel M, Ramus SJ, Bowtell D. Efficient molecular subtype classification of high-grade serous ovarian cancer. J Pathol. 2015;236(3):272\u20137.","journal-title":"J Pathol"},{"key":"2095_CR15","doi-asserted-by":"crossref","unstructured":"Hu Y, Zhou M, Shi H, Ju H, Jiang Q, Cheng L. Measuring disease similarity and predicting disease-related ncRNAs by a novel method. BMC Medical Genomics. 2017;10(Suppl 5)","DOI":"10.1186\/s12920-017-0315-9"},{"issue":"Suppl 1","key":"2095_CR16","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1186\/s13326-017-0140-2","volume":"8","author":"Y Hu","year":"2017","unstructured":"Hu Y, Zhao L, Liu Z, Ju H, Shi H, Xu P, Wang Y, Liang L. DisSetSim: an online system for calculating similarity between disease sets. Journal of Biomedical Semantics. 2017;8(Suppl 1):28.","journal-title":"Journal of Biomedical Semantics"},{"key":"2095_CR17","doi-asserted-by":"publisher","DOI":"10.1038\/srep30024","volume":"6","author":"L Cheng","year":"2016","unstructured":"Cheng L, Jiang Y, Wang Z, Shi H, Sun J, Yang H, Zhang S, Hu Y, Zhou M. DisSim: an online system for exploring significant similar diseases and exhibiting potential therapeutic drugs. Sci Rep. 2016;6:30024.","journal-title":"Sci Rep"},{"issue":"3","key":"2095_CR18","doi-asserted-by":"publisher","first-page":"900","DOI":"10.1021\/ci0256438","volume":"43","author":"HX Liu","year":"2003","unstructured":"Liu HX, Zhang RS, Luan F, Yao XJ, Liu MC, Hu ZD, Fan BT. Diagnosing breast cancer based on support vector machines. J Chem Inf Comput Sci. 2003;43(3):900\u20137.","journal-title":"J Chem Inf Comput Sci"},{"key":"2095_CR19","doi-asserted-by":"crossref","unstructured":"Okun O, Priisalu H: Random forest for gene expression based cancer classification: Overlooked issues. Pattern Recognition and Image Analysis, Pt 2, Proceedings 2007, 4478:483\u2212+.","DOI":"10.1007\/978-3-540-72849-8_61"},{"key":"2095_CR20","doi-asserted-by":"crossref","unstructured":"Statnikov A, Wang L, Aliferis CF. A comprehensive comparison of random forests and support vector machines for microarray-based cancer classification. Bmc Bioinformatics. 2008;9","DOI":"10.1186\/1471-2105-9-319"},{"key":"2095_CR21","doi-asserted-by":"crossref","unstructured":"Ali HR, Rueda OM, Chin SF, Curtis C, Dunning MJ, Aparicio SAJR, Caldas C. Genome-driven integrated classification of breast cancer validated in over 7,500 samples. Genome Biol. 2014;15(8)","DOI":"10.1186\/s13059-014-0431-1"},{"issue":"2","key":"2095_CR22","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1093\/bioinformatics\/btu618","volume":"31","author":"H Saddiki","year":"2015","unstructured":"Saddiki H, McAuliffe J, Flaherty P. GLAD: a mixed-membership model for heterogeneous tumor subtype classification. Bioinformatics. 2015;31(2):225\u201332.","journal-title":"Bioinformatics"},{"key":"2095_CR23","doi-asserted-by":"crossref","unstructured":"Zhou Z-H, Feng J. Deep Forest: towards an alternative to deep neural networks. In: ArXiv e-prints vol. 1702.08835v1: 2017","DOI":"10.24963\/ijcai.2017\/497"},{"issue":"6","key":"2095_CR24","doi-asserted-by":"publisher","first-page":"82","DOI":"10.1109\/MSP.2012.2205597","volume":"29","author":"G Hinton","year":"2012","unstructured":"Hinton G, Deng L, Yu D, dahl GE, Mohamed AR, Jaitly N, senior a, Vanhoucke V, Nguyen P, Sainath TN, et al. deep neural networks for acoustic modeling in speech recognition. IEEE Signal Process Mag. 2012;29(6):82\u201397.","journal-title":"IEEE Signal Process Mag"},{"issue":"4","key":"2095_CR25","doi-asserted-by":"publisher","first-page":"928","DOI":"10.1109\/TCBB.2014.2377729","volume":"12","author":"MX Liang","year":"2015","unstructured":"Liang MX, Li ZZ, Chen T, Zeng JY. Integrative data analysis of multi-platform cancer data with a multimodal deep learning approach. Ieee-Acm Transactions on Computational Biology and Bioinformatics. 2015;12(4):928\u201337.","journal-title":"Ieee-Acm Transactions on Computational Biology and Bioinformatics"},{"key":"2095_CR26","doi-asserted-by":"crossref","unstructured":"Litjens G, Sanchez CI, Timofeeva N, Hermsen M, Nagtegaal I, Kovacs I, Hulsbergen-van de Kaa C, Bult P, van Ginneken B, van der Laak J. Deep learning as a tool for increased accuracy and efficiency of histopathological diagnosis. Sci Rep. 2016;6","DOI":"10.1038\/srep26286"},{"issue":"1","key":"2095_CR27","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1016\/j.patcog.2009.05.010","volume":"43","author":"G Martinez-Munoz","year":"2010","unstructured":"Martinez-Munoz G, Suarez A. Out-of-bag estimation of the optimal sample size in bagging. Pattern Recogn. 2010;43(1):143\u201352.","journal-title":"Pattern Recogn"},{"issue":"1\u20133","key":"2095_CR28","doi-asserted-by":"publisher","first-page":"287","DOI":"10.1023\/A:1013964023376","volume":"48","author":"T Bylander","year":"2002","unstructured":"Bylander T. Estimating generalization error on two-class datasets using out-of-bag estimates. Mach Learn. 2002;48(1\u20133):287\u201397.","journal-title":"Mach Learn"},{"key":"2095_CR29","doi-asserted-by":"crossref","unstructured":"Akbani R, Ng KS, Werner HM, Zhang F, Ju ZL, Liu WB, Yang JY, Lu YL, Weinstein JN, Mills GB. a pan-cancer proteomic analysis of the cancer genome atlas (TCGA) project. Cancer Res. 2014;74(19)","DOI":"10.1158\/1538-7445.AM2014-4262"},{"issue":"10","key":"2095_CR30","doi-asserted-by":"publisher","first-page":"1113","DOI":"10.1038\/ng.2764","volume":"45","author":"JN Weinstein","year":"2013","unstructured":"Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, Ellrott K, Shmulevich I, Sander C, Stuart JM, Network CGAR. The cancer genome atlas pan-cancer analysis project. Nat Genet. 2013;45(10):1113\u201320.","journal-title":"Nat Genet"},{"key":"2095_CR31","doi-asserted-by":"crossref","unstructured":"Diaz-Uriarte R, de Andres SA. Gene selection and classification of microarray data using random forest. Bmc Bioinformatics. 2006;7","DOI":"10.1186\/1471-2105-7-3"},{"key":"2095_CR32","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/j.ins.2013.07.007","volume":"250","author":"V Lopez","year":"2013","unstructured":"Lopez V, Fernandez A, Garcia S, Palade V, Herrera F. An insight into classification with imbalanced data: empirical results and current trends on using data intrinsic characteristics. Inf Sci. 2013;250:113\u201341.","journal-title":"Inf Sci"},{"issue":"2","key":"2095_CR33","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1016\/j.gene.2014.11.053","volume":"556","author":"M Bhattacharyya","year":"2015","unstructured":"Bhattacharyya M, Nath J, Bandyopadhyay S. MicroRNA signatures highlight new breast cancer subtypes. Gene. 2015;556(2):192\u20138.","journal-title":"Gene"},{"key":"2095_CR34","doi-asserted-by":"crossref","unstructured":"Bediaga NG, Acha-Sagredo A, Guerra I, Viguri A, Albaina C, Diaz IR, Rezola R, Alberdi MJ, Dopazo J, Montaner D, et al. DNA methylation epigenotypes in breast cancer molecular subtypes. Breast Cancer Res. 2010;12(5)","DOI":"10.1186\/bcr2721"},{"key":"2095_CR35","doi-asserted-by":"crossref","unstructured":"Cantini L, Isella C, Petti C, Picco G, Chiola S, Ficarra E, Caselle M, Medico E. MicroRNA-mRNA interactions underlying colorectal cancer molecular subtypes. Nat Commun. 2015;6","DOI":"10.1038\/ncomms9878"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2095-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2095-4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2095-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,14]],"date-time":"2019-10-14T22:48:47Z","timestamp":1571093327000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2095-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,4]]},"references-count":35,"journal-issue":{"issue":"S5","published-print":{"date-parts":[[2018,4]]}},"alternative-id":["2095"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2095-4","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,4]]},"assertion":[{"value":"11 April 2018","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"118"}}