【論】Furey,2000,Support vector machine～

Terrence S.Furey, Nello Cristianini, Nigel Duffy, David W.Bednarski, Michel Schummer and David Haussler
Support vector machine classification and validation of cancer tissue using microarray expression data
BIOINFORMATICS Vol.16 no.10 p.906-914, 2000
[PDFダウンロード][Webサイト]

・目的：SVMのDNAマイクロアレイ解析に対する有効性を実証する
・識別率(クラス分け)の評価法：Hold-one-out cross-validation
・実験1 手持ちのデータ(非公開)をクラス分け
　　データ：卵巣がん(ovarian cancer)、正常(卵巣+その他の組織)　合計31サンプル。97802遺伝子
・実験2　公開されているデータをクラス分けして、SVMの汎用性を実証する
　　データ1：AML/ALL [Golub]
　　データ2：Colon tumor [Alon]
・SVMのkernelによる識別率の差ははっきりと出なかった→サンプル数が少ないため

・将来の展望「If one can identify particular genes that are diagnostic for the classification one is trying to make, e.g. the presence of cancer, then there is also hope that some of these genes may be found to be of value in further investigations of the disease and in future therapies.」
・結果「Here we find that this dimensionality reduction does not significantly improve classification performance.」
・問題点「Most learning techniques do not perform well on datasets where the number of features is large comapred to the number of examples.」
・問題点「In the SVM tests reported here, only the simple dot-product kernel is used. A more complex kernel is not required.」
・将来の展望「we conclude that additional effort is needed to develop ways identifying meaningful features in these types of datasets.」
・予測「The SVM performs well using a simple kernel, and we believe that as datasets containing more examples become available, the use of mroe complex kernels may become necessary and will allow the SVM to continue its good performance.」

《チェック論文》
・Amir Ben-Dor, Laurakay Bruhn, Nir Friedman, Iftach Nachman, Michèl Schummer, Zohar Yakhini: Tissue classification with gene expression profiles. RECOMB 2000: 54-64 [ダウンロード]
・DeRisi J, Penland L, Brown PO, Bittner ML, Meltzer PS, Ray M, Chen Y, Su YA, Trent JM., Use of a cDNA microarray to analyse gene expression patterns in human cancer., Nat Genet. 1996 Dec;14(4):367-70.[ダウンロード]
・T.R.Golub,D.K.Slonim,P.Tamayo, C.Huard,M.Gaasenbeek, J.P.Mesirov, H.Coller, M.L.Loh, J.R.Downing, M.A.Caligiuri, C.D.Bloomfield, E.S.Lander, Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring, Science 15 October 1999:Vol.286.no.5439,pp.531-537.[ダウンロード]
・Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B., Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization., Mol Biol Cell. 1998 Dec;9(12):3273-97.[ダウンロード]
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