Nothing Special   »   [go: up one dir, main page]

skip to main content
article

Sample-space-based feature extraction and class preserving projection for gene expression data

Published: 01 July 2013 Publication History

Abstract

In order to overcome the problems of high computational complexity and serious matrix singularity for feature extraction using Principal Component Analysis PCA and Fisher's Linear Discrinimant Analysis LDA in high-dimensional data, sample-space-based feature extraction is presented, which transforms the computation procedure of feature extraction from gene space to sample space by representing the optimal transformation vector with the weighted sum of samples. The technique is used in the implementation of PCA, LDA, Class Preserving Projection CPP which is a new method for discriminant feature extraction proposed, and the experimental results on gene expression data demonstrate the effectiveness of the method.

References

[1]
Alizadeh, A.A., Eisen, M.B., Davis, R.E., Ma, C., Lossos, I.S., Rosenwald, A., Boldrick, J.C., Sabet, H., Tran, T., Yu, X., Powell, J.I., Yang, L., Marti, G.E., Moore Jr, J.H., Lu, L., Lewis, D.B., Tibshirani, R., Sherlock, G., Chan, W.C., Greiner, T.C., Weisenburger, D.D., Armitage, J.O., Warnke, R., Levy, R., Wilson, W., Grever, M.R., Byrd, J.C., Botstein, D., Brown, P.O. and Staudt, L.M. (2000) 'Distinct types of diffuse large b-cell lymphoma identified by gene expression profiling', Nature, Vol. 403, No. 6769, pp.503-511.
[2]
Alon, U., Barkai, N., Notterman, D.A., Gish, K., Ybarra, S., Mack, D. and Levine, A.J. (1999) 'Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays', Proc. Nat'l Academy of Science, Vol. 96, No. 12, pp.6745-6750.
[3]
Belhumeur, P.N., Hespanha, J.P. and Kriegman, D.J. (1997) 'Eigenfaces vs. Fisherfaces: recognition using class specific linear projection', IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 19, No. 7, pp.711-720.
[4]
Cheng, Z.D., Zhang, Y.J., Fan X. and Zhu, B. (2010) 'Study on discriminant matrices of commonly-used Fisher discriminant functions', Acta Automatica Sinica, Vol. 36, No. 10, pp.1361-1370.
[5]
Gao, H. and Davis, J.W. (2006) 'Why direct LDA is not equivalent to LDA', Pattern Recognition, Vol. 39, No. 5, pp.1002-1006.
[6]
Golub, T.R., Slonim, D.K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J.P., Coller, H., Loh, M.L., Downing, J.R., Caligiuri, M.A., Bloomfield, C.D. and Lander, E.S. (1999) 'Molecular classification of cancer: class discovery and class prediction by gene expression monitoring', Science, Vol. 286, No. 5439, pp.531-537.
[7]
Gordon, G.J., Jensen, R.V., Hsiao, L.L., Gullans, S.R., Blumenstock, J.E., Ramaswamy, S., Richards, W.G., Sugarbaker, D.J. and Bueno, R. (2002) 'Translation of microarray data into clinically relevant cancer diagnostic tests using gene expression ratios in lung cancer and mesothelioma', Cancer Research, Vol. 62, No. 17, pp.4963-4967.
[8]
Kazmi, S.A., Kim, Y.A. and Shin, D.G. (2010) 'Meta analysis algorithms for microarray gene expression data using Gene Regulatory Networks', Int. J. Data Mining and Bioinformatics, Vol. 4, No. 5, pp.487-504.
[9]
Khan, J., Wei, J.S., Ringnér, M., Saal, L.H., Ladanyi, M., Westermann, F., Berthold, F., Schwab, M., Antonescu, C.R., Peterson, C. and Meltzer, P.S. (2001) 'Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks', Nature Medicine, Vol. 7, No. 6, pp.673-679.
[10]
Kirby, M. and Sirovich, L. (1990) 'Application of the Karhunen-Loeve procedure for the characterization of human faces', IEEE Trans. Pattern Analysis and Machine Intelligence, Vol. 12, No. 1, pp.103-108.
[11]
Kossenkov, A.V. and Ochs, M.F. (2010) 'Matrix factorisation methods applied in microarray data analysis', Int. J. Data Mining and Bioinformatics, Vol. 4, No. 1, pp.72-90.
[12]
Lockhart, D.J., Dong, H., Byrne, M.C., Follettie, M.T., Gallo, M.V., Chee, M.S., Mittmann, M., Wang, C., Kobayashi, M., Horton, H. and Brown, E.L. (1996) 'Expression monitoring by hybridization to high-density oligonucleotide arrays', Nat. Biotechnol., Vol. 14, No. 13, pp.1675-1680.
[13]
Nayar, S.K., Nene, N.A. and Murase, H. (1996) 'Subspace Methods for Robot Vision', IEEE Trans. Robotics and Automation, Vol. 12, No. 5, pp.750-758.
[14]
Pomeroy, S.L., Tamayo, P., Gaasenbeek, M., Sturla, L.M., Angelo, M., McLaughlin, M.E., Kim, J.Y.H., Goumnerova, L.C., Black, P.M., Lau, C., Allen, J.C., Zagzag, D., Olson, J.M., Curran, T., Wetmore, C., Biegel, J.A., Poggio, T., Mukherjee, S., Rifkin, R., Califano, A., Stolovitzky, G., Louis, D.N., Mesirov, J.P., Lander, E.S. and Golub, T.R. (2002) 'Prediction of central nervous system embryonal tumour outcome based on gene expression', Nature, Vol. 415, No. 6870, pp.436-442.
[15]
Qu, Y. and Xu, S. (2004) 'Supervised cluster analysis for microarray data based on multivariate Gaussian mixture', Bioinformatics, Vol. 20, No. 12, pp.1905-1913.
[16]
Ramaswamy, S., Tamayo, P., Rifkin, R., Mukherjee, S., Yeang, C.H., Angelo, M., Ladd, C., Reich, M., Latulippe, E., Mesirov, J.P., Poggio, T., Gerald, W., Loda, M., Lander, E.S. and Golub, R.T. (2001) 'Multiclass cancer diagnosis using tumor gene expression signatures', Acad. Sci. Proc. Natl., Vol. 98, No. 26, pp.15149-15154.
[17]
Schena, M., Shalon, D., Davis, R.W. and Brown, P.O. (1995) 'Quantitative monitoring of gene expression patterns with a complementary dna microarray', Science, Vol. 270, No. 5235, pp.467-470.
[18]
Singh, D., Febbo, P.G., Ross, K., Jackson, D.G., Manola, J., Ladd, C., Tamayo, P., Renshaw, A.A., D'Amico, A.V., Richie, J.P., Lander, E.S., Loda, M., Kantoff, P.W., Golub, T.R. and Sellers, W.R. (2002) 'Gene expression correlates of clinical prostate cancer behavior', Cancer Cell, Vol. 1, No. 2, pp. 203-209.
[19]
Swets, D.L. and Weng, J.J. (1996) 'Using discriminant eigenfeatures for image retrieval', IEEE Trans. Pattern Analysis and Machine Intelligence, Vol. 18, No. 8, pp.831-836.
[20]
Tian, Q., Barbero, M., Gu, Z.H. and Lee, S.H. (1986) 'Image classification by the Foley-Sammon transform', Opt. Eng., Vol. 25, No. 7, pp.834-840.
[21]
Turk, M. and Pentland A. (1991) 'Eigenfaces for recognition', J. Cognitive Neuroscience, Vol. 3, No. 1, pp.71-86.
[22]
Wang, H., Yan, S.C., Xu, D., Tang, X.O. and Huang, T. (2007) 'Trace ratio vs. ratio trace for dimensionality reduction', Proceedings of the 2007 IEEE Conference on Computer Vision and Pattern Recognition, pp.108-115.
[23]
Yu, H. and Yang, J. (2001) 'A direct LDA algorithm for high-dimensional data - with application to face recognition', Pattern Recognition, Vol. 34, No. 10, pp.2067-2070.
[24]
Zheng, C. and Jian T. (2010) 'Using gene ontology to enhance effectiveness of similarity measures for microarray data', Int. J. Data Mining and Bioinformatics, Vol. 4, No. 5, pp.520-534.

Cited By

View all
  • (2015)Cuckoo search optimisation for feature selection in cancer classificationInternational Journal of Data Mining and Bioinformatics10.1504/IJDMB.2015.07209213:3(248-265)Online publication date: 1-Sep-2015

Recommendations

Comments

Please enable JavaScript to view thecomments powered by Disqus.

Information & Contributors

Information

Published In

cover image International Journal of Data Mining and Bioinformatics
International Journal of Data Mining and Bioinformatics  Volume 8, Issue 2
July 2013
124 pages
ISSN:1748-5673
EISSN:1748-5681
Issue’s Table of Contents

Publisher

Inderscience Publishers

Geneva 15, Switzerland

Publication History

Published: 01 July 2013

Qualifiers

  • Article

Contributors

Other Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

  • Downloads (Last 12 months)0
  • Downloads (Last 6 weeks)0
Reflects downloads up to 23 Nov 2024

Other Metrics

Citations

Cited By

View all
  • (2015)Cuckoo search optimisation for feature selection in cancer classificationInternational Journal of Data Mining and Bioinformatics10.1504/IJDMB.2015.07209213:3(248-265)Online publication date: 1-Sep-2015

View Options

View options

Login options

Media

Figures

Other

Tables

Share

Share

Share this Publication link

Share on social media