Bayesian automatic relevance determination algorithms for classifying gene expression data

被引:119
作者
Li, Y
Campbell, C [1 ]
Tipping, M
机构
[1] Univ Bristol, Dept Engn Math, Bristol BS8 1TR, Avon, England
[2] Microsoft Res, Cambridge CB3 0FD, England
关键词
D O I
10.1093/bioinformatics/18.10.1332
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: We investigate two new Bayesian classification algorithms incorporating feature selection. These algorithms are applied to the classification of gene expression data derived from cDNA microarrays. Results: We demonstrate the effectiveness of the algorithms on three gene expression datasets for cancer, showing they compare well with alternative kernel-based techniques. By automatically incorporating feature selection, accurate classifiers can be constructed utilizing very few features and with minimal hand-tuning. We argue that the feature selection is meaningful and some of the highlighted genes appear to be medically important.
引用
收藏
页码:1332 / 1339
页数:8
相关论文
共 20 条
[1]   Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling [J].
Alizadeh, AA ;
Eisen, MB ;
Davis, RE ;
Ma, C ;
Lossos, IS ;
Rosenwald, A ;
Boldrick, JG ;
Sabet, H ;
Tran, T ;
Yu, X ;
Powell, JI ;
Yang, LM ;
Marti, GE ;
Moore, T ;
Hudson, J ;
Lu, LS ;
Lewis, DB ;
Tibshirani, R ;
Sherlock, G ;
Chan, WC ;
Greiner, TC ;
Weisenburger, DD ;
Armitage, JO ;
Warnke, R ;
Levy, R ;
Wilson, W ;
Grever, MR ;
Byrd, JC ;
Botstein, D ;
Brown, PO ;
Staudt, LM .
NATURE, 2000, 403 (6769) :503-511
[2]   Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays [J].
Alon, U ;
Barkai, N ;
Notterman, DA ;
Gish, K ;
Ybarra, S ;
Mack, D ;
Levine, AJ .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (12) :6745-6750
[3]  
Bishop C. M., 1995, NEURAL NETWORKS PATT
[4]   Knowledge-based analysis of microarray gene expression data by using support vector machines [J].
Brown, MPS ;
Grundy, WN ;
Lin, D ;
Cristianini, N ;
Sugnet, CW ;
Furey, TS ;
Ares, M ;
Haussler, D .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (01) :262-267
[5]  
*DUK U, 2000, P CAMDA DEC CRIT ASS
[6]  
FAUL A, 2001, IN PRESS ADV NEURAL, V15
[7]   Support vector machine classification and validation of cancer tissue samples using microarray expression data [J].
Furey, TS ;
Cristianini, N ;
Duffy, N ;
Bednarski, DW ;
Schummer, M ;
Haussler, D .
BIOINFORMATICS, 2000, 16 (10) :906-914
[8]   Molecular classification of cancer: Class discovery and class prediction by gene expression monitoring [J].
Golub, TR ;
Slonim, DK ;
Tamayo, P ;
Huard, C ;
Gaasenbeek, M ;
Mesirov, JP ;
Coller, H ;
Loh, ML ;
Downing, JR ;
Caligiuri, MA ;
Bloomfield, CD ;
Lander, ES .
SCIENCE, 1999, 286 (5439) :531-537
[9]   Gene selection for cancer classification using support vector machines [J].
Guyon, I ;
Weston, J ;
Barnhill, S ;
Vapnik, V .
MACHINE LEARNING, 2002, 46 (1-3) :389-422
[10]  
Hough CD, 2000, CANCER RES, V60, P6281