Abstract
Tumor clustering is becoming a powerful method in cancer class discovery. In this community, non-negative matrix factorization (NMF) has shown its advantages, such as the accuracy and robustness of the representation, over other conventional clustering techniques. Though NMF has shown its efficiency in tumor clustering, there is a considerable room for improvement in clustering accuracy and robustness. In this paper, gene selection and explicitly enforcing sparseness are introduced into clustering process. The independent component analysis (ICA) is employed to select a subset of genes. The unsupervised methods NMF and its extensions, sparse NMF (SNMF) and NMF with sparseness constraint (NMFSC), are then used for tumor clustering on the subset of genes selected by ICA. The experimental results demonstrate the efficiency of the proposed scheme.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
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., Lander, E.S.: Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring. Science 286, 531–537 (1999)
Brunet, J.-P., Tamayo, P., Golub, T.R., Mesirov, J.P.: Metagenes and Molecular Pattern Discovery Using Matrix Factorization. Proc. Natl. Acad. Sci. USA 101(12), 4164–4416 (2004)
Kong, X.Z., Zheng, C.H., Wu, Y.Q., Shang, L.: Molecular Cancer Class Discovery Using Non-negative Matrix Factorization with Sparseness Constraint. In: Huang, D.-S., Heutte, L., Loog, M. (eds.) ICIC 2007. LNCS, vol. 4681, pp. 792–802. Springer, Heidelberg (2007)
Gao, Y., George, C.: Improving Molecular Cancer Class Discovery Through Sparse Non-negative Matrix Factorization. Bioinformatics 21, 3970–3975 (2005)
Daniela, G., Calò., G.G., Marilena, P., Cinzia, V.: Variable Selection in Cell Classification Problems: A Strategy Based on Independent Component Analysis. Studies in Classification. Data Analysis, and Knowledge Organization, Part I, 21–29 (2006)
Pan, W.: A Comparative Review of Statistical Methods for Discovering Differently Expressed Genes in Replicated Microarray Experiments. Bioinformatics 18, 546–554 (2002)
Hyvärinen, A., Oja, E.: Independent Component Analysis: Algorithm and Applications. Neural Netw. 2000(13), 411–430 (2000)
Huang, D.S., Zheng, C.H.: Independent Component Analysis-based Penalized Discriminant Method for Tumor Classification Using Gene Expression Data. Bioinformatics 22, 1855–1862 (2006)
Hyvärinen, A.: Fast and Robust Fixed-point Algorithms for Independent Component Analysis. IEEE Trans. Neural Netw. 10, 626–634 (1999)
Chiappetta, P., Roubaud, M.C., Torresani, B.: Blind Source Separation and the Analysis of Microarray Data. J. Comput. Biol. 11, 1090–1109 (2004)
Hoyer, P.O.: Non-negative Sparse Coding Neural Networks for Signal Processing. In: Proceedings of IEEE Workshop on Neural Networks for Signal Processing, Martigny, Switzerland, pp. 557–565 (2002)
Hoyer, P.O.: Non-negative Matrix Factorization with Sparseness Constraints. J. Mach. Learn. Res. 5, 1457–1469 (2004)
Pomeroy, S.L., Tamayo, P., Gaasenbeek, M., Sturla, L.M., Angelo, M., McLaughlin, M.E., Kim, J.Y., Goumneroval, L.C., Clack, P.M., Lau, C., Allen, J.C.: Prediction of Central Nervous System Embryonal Tumour Outcome Based on Gene Expression. Nature 415, 436–442 (2002)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kong, X., Zheng, C., Wu, Y., Wang, Y. (2008). Improving Tumor Clustering Based on Gene Selection. In: Huang, DS., Wunsch, D.C., Levine, D.S., Jo, KH. (eds) Advanced Intelligent Computing Theories and Applications. With Aspects of Theoretical and Methodological Issues. ICIC 2008. Lecture Notes in Computer Science, vol 5226. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-87442-3_6
Download citation
DOI: https://doi.org/10.1007/978-3-540-87442-3_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-87440-9
Online ISBN: 978-3-540-87442-3
eBook Packages: Computer ScienceComputer Science (R0)