Boosting for tumor classification with gene expression data

Bioinformatics

Volumn 19, Issue 9, 2003, Pages 1061-1069

  Dettling, Marcel ^a   Bühlmann, Peter ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTICAL ERROR; ARTICLE; CLASSIFICATION; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; CONTROLLED STUDY; DATA ANALYSIS; DECISION THEORY; DIAGNOSTIC ACCURACY; DNA MICROARRAY; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; HUMAN; METHODOLOGY; NEOPLASM; PATTERN RECOGNITION; PERFORMANCE; PRIORITY JOURNAL; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; TUMOR CLASSIFICATION;

EID: 0038391397     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btf867     Document Type: Article

References (24)

1. Alizadeh,A., Eisen,M., Davis,R., Ma,C., Lossos,I., Rosenwald,A., Boldrick,J., Sabet,H., Tran,T., Yu,X. et al., (2000) Distinct types of diffuse large B-cell-lymphoma identified by gene expression profiling. Nature, 403, 503-511.
2. Alon,U., Barkai,N., Notterman,D., Gish,K., Mack,S. and Levine,J. (1999) Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. PNAS, 96, 6745-6750.
3. Allwein,E., Schapire,R. and Singer,Y. (2000) Reducing multiclass to binary: a unifying approach for margin classifiers. J. Machine Learning Res., 1, 113-141.
4. Ben-Dor,A., Bruhn,L., Friedman,N., Nachman,I., Schummer,M. and Yakhini,Z. (2000) Tissue classification with gene expression profiles. J. Comput. Biol., 7, 559-583.
5. Breiman,L., Friedman,J., Olshen,R. and Stone,C. (1984) Classification and Regression Trees. Wadsworth, Belmont, CA.
6. Breiman,L. (1999) Prediction games & arcing algorithms. Neural Computation, 11, 1493-1517.
7. Dudoit,S., Fridlyand,J. and Speed,T. (2002) Comparison of discrimination methods for the classification of tumors using gene expression data. JASA, 97, 77-87.
8. Fix,E. and Hodges,J. (1951) Discriminatory Analysis-Nonparametric Discrimination: Consistency Properties. US Air Force School of Aviation Medicine, Random Field, Texas. Published in Agrawala, A., (1977), Machine Recognition of Patterns, Report No. 4, IEEE Press, New York.
9. Freund,Y. and Schapire,R. (1996) Experiments with a New boosting algorithm. Machine Learning: Proceedings to the Thirteenth International Conference. Morgan Kaufmann, San Francisco, pp. 148-156.
10. Freund,Y. and Schapire,R. (1997) A decision-theoretic generalization of online learning and an application to boosting. J. Comput. System Sci., 55, 119-139.
11. Friedman,J., Hastie,T. and Tibshirani,R. (2000) Additive logistic regression: a statistical view of boosting. Ann. Stat., 28, 337-407 (with discussion).
12. Furey,T., Cristianini,N., Duffy,N., Bednarski,D., Schummer,M. and Haussler,D. (2000) Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics, 16, 906-914.
13. Golub,T., Slonim,D., Tamayo,P., Huard,C., Gaasenbeek,M., Mesirov,J., Coller,H., Loh,M., Downing,J.et al., (1999) Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science, 286, 531-537.
14. Hampel,F., Ronchetti,E., Rousseeuw,P. and Stahel,W. (1986) Robust Statistics: The Approach Based on Influence Functions. Wiley, New York.
15. Hastie,T. and Tibshirani,R. (1998) Classification by pairwise coupling. Ann. Stat., 26, 451-471.
16. Hastie,T., Tibshirani,R. and Friedman,J. (2001) The Elements of Statistical Learning. Springer, New York.
17. Quinlan, (1993) C4.5: Programs for Machine Learning. Morgan Kaufmann, San Francisco.
18. Park,P., Pagano,M. and Bonetti,M. (2001) A nonparametric scoring algorithm for identifying informative genes from microarray data. Pac. Symp. Biocomput., 6, 52-63.
19. Ripley,B. (1996) Pattern Recognition and Neural Networks. Cambridge University Press, Cambridge.
20. Ross,D., Scherf,U., Eisen,M., Perou,C., Rees,C., Spellman,P., Iyer,V., Jeffrey,S., Van de Rijn,M.et al., (2000) Systematic variation in gene expression patterns in human cancer cell lines. Nat. Genet., 24, 227-235.
21. Slonim,D., Tamayo,P., Mesirov,J., Golub,T. and Lander,E. (2000) Class prediction and discovery using gene expression data. In Proceedings of the 4th International Confererence on Computational Molecular Biology. Universal Academy Press, Tokyo, Japan, pp. 263-272.
22. Spang,R., Blanchette,C., Zuzan,H., Marks,J., Nevins,J. and West,M. (2001) Prediction and uncertainty in the analysis of gene expression profiles. In Wingender,E., Hofestädt,R. and Liebich,I. (eds), Proceedings of the German Conference on Bioinformatics GCB 2001. Braunschweig.
23. West,M., Blanchette,C., Dressman,H., Huang,E., Ishida,S., Spang,R., Zuzan,H., Olson,J., Marks,J. and Nevins,J. (2001) Predicting the clinical status of human breast cancer by using gene expression profiles. PNAS, 98, 11462-11467.
24. Zhang,H., Yu,C., Singer,B. and Xiong,M. (2001) Recursive partitioning for tumor classification with gene expression microarray data. PNAS, 98, 6730-6735.