Abstract
Sliced inverse regression (SIR) was developed to find effective linear dimension-reduction directions for exploring the intrinsic structure of the high-dimensional data. In this study, we present isometric SIR for nonlinear dimension reduction, which is a hybrid of the SIR method using the geodesic distance approximation. First, the proposed method computes the isometric distance between data points; the resulting distance matrix is then sliced according to K-means clustering results, and the classical SIR algorithm is applied. We show that the isometric SIR (ISOSIR) can reveal the geometric structure of a nonlinear manifold dataset (e.g., the Swiss roll). We report and discuss this novel method in comparison to several existing dimension-reduction techniques for data visualization and classification problems. The results show that ISOSIR is a promising nonlinear feature extractor for classification applications.
Similar content being viewed by others
References
Aizerman, M., Braverman, E., Rozonoer, L.: Theoretical foundations of the potential function method in pattern recognition learning. Autom. Remote Control 25, 821–837 (1964)
Alizadeh, A.A., et al.: Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature 403(6769), 503–511 (2000)
Alon, U., et al.: Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc. Natl. Acad. Sci. USA 96(12), 6745–6750 (1999)
Balasubramanian, M., Schwartz, E.L.: The isomap algorithm and topological stability. Science 295(5552), 7 (2002)
Belkin, M., Niyogi, P.: Laplacian eigenmaps for dimensionality reduction and data representation. Neural Comput. 15(6), 1373–1396 (2003)
Bengio, Y., Paiement, J., Vincent, P., Delalleau, O., Roux, N.L., Ouimet, M.: Out-of-sample extensions for LLE, isomap, MDS, eigenmaps, and spectral clustering. In: Neural Information Processing Systems, pp. 177–184. MIT Press, Cambridge (2003)
Bian, W., Tao, D.: Manifold regularization for SIR with rate root-n convergence. Adv. Neural Inf. Process. Syst. 22, 117–125 (2009)
Bura, E., Pfeiffer, R.M.: Graphical methods for class prediction using dimension reduction techniques on DNA microarray data. Bioinformatics 19(10), 1252–1258 (2003)
Chen, C.H.: Generalized association plots: information visualization via iteratively generated correlation matrices. Stat. Sin. 12, 7–29 (2002)
Chen, C.H., Li, K.C.: Can SIR be as popular as multiple linear regression? Stat. Sin. 8, 289–316 (1998)
Chen, C.H., Li, K.C.: Generalization of Fisher’s linear discriminant analysis via the approach of sliced inverse regression. J. Korean Stat. Soc. 30, 193–217 (2001)
Coifman, R.R., Lafon, S., Lee, A.B., Maggioni, M., Nadler, B., Warner, F., Zucker, S.W.: Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps. Proc. Natl. Acad. Sci. USA 102, 7426–7431 (2005)
Cook, R.D.: On the interpretation of regression plots. J. Am. Stat. Assoc. 89, 177–190 (1994)
Cook, R.D.: Graphics for regressions with a binary response. J. Am. Stat. Assoc. 91, 983–992 (1996)
Cook, R.D.: SAVE: a method for dimension reduction and graphics in regression. Commun. Stat., Theory Methods 29, 2109–2121 (2000)
Cook, R.D., Critchley, F.: Identifying regression outliers and mixtures graphically. J. Am. Stat. Assoc. 95, 781–794 (2000)
Cook, R.D., Ni, L.: Sufficient dimension reduction via inverse regression: a minimum discrepancy approach. J. Am. Stat. Assoc. 100(470), 410–428 (2005)
Cook, R.D., Ni, L.: Using intraslice covariances for improved estimation of the central subspace in regression. Biometrika 93(1), 65–74 (2006)
Cox, T.F., Cox, M.A.A.: Multidimensional Scaling. Chapman and Hall, London (1994)
Dettling, M., Bühlmann, P.: Supervised clustering of genes. Genome Biol. 3(12), 0069 (2002)
Donoho, D.L., Grimes, C.: Hessian eigenmaps: locally linear embedding techniques for high-dimensional data. Proc. Natl. Acad. Sci. USA 100(10), 5591–5596 (2003)
Frank, A., Asuncion, A.: UCI machine learning repository. Irvine, CA: University of California, School of Information and Computer Science (2010). http://archive.ics.uci.edu/ml
Fukumizu, K., Bach, F.R., Jordan, M.I.: Kernel dimension reduction in regression. Ann. Stat. 37(4), 1871–1905 (2009)
Gaoa, X., Liang, J.: The dynamical neighborhood selection based on the sampling density and manifold curvature for isometric data embedding. Pattern Recognit. Lett. 32(2), 202–209 (2011)
Garber, M., et al.: Diversity of gene expression in adenocarcinoma of the lung. Proc. Natl. Acad. Sci. USA 98(24), 13784–13789 (2001)
Gather, U., Hilker, T., Becker, C.: A note on outlier sensitivity of sliced inverse regression. Statistics 36(4), 271–281 (2002)
Geng, X., Zhan, D.C., Zhou, Z.H.: Supervised nonlinear dimensionality reduction for visualization and classification. IEEE Trans. Syst. Man Cybern., Part B, Cybern. 35(6), 1098–1107 (2005)
Golub, T.R., et al.: Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science 286(5439), 531–537 (1999)
Ham, J., Lee, D.D., Mika, S., Scholkopf, B.: A kernel view of the dimensionality reduction of manifolds. In: Proceedings of the Twenty-First International Conference on Machine Learning. ACM International Conference Proceeding Series, vol. 69 (2004)
Hartigan, J.A., Wong, M.A.: A k-means clustering algorithm. Appl. Stat. 28, 100–108 (1979)
Hastie, T., Tibshirani, R.: Discriminant analysis by Gaussian mixtures. J. R. Stat. Soc. B 58, 155–176 (1996)
Hastie, T., Tibshirani, R., Friedman, J.: The Elements of Statistical Learning: Data Mining, Inference, and Prediction, 2nd edn. Springer, Berlin (2009)
Hsing, T.: Nearest neighbor inverse regression. Ann. Stat. 27(2), 697–731 (1999)
Khan, J., et al.: Classification and diagnostic prediction of cancers using gene expression profiling and artificial neural networks. Nat. Med. 7, 673–679 (2001)
Kuss, M.: Nonlinear multivariate analysis with geodesic kernels. Technische Universitat Berlin, Diploma Theses (2002)
Lee, Y.J., Huang, S.Y.: Reduced support vector machines: a statistical theory. IEEE Trans. Neural Netw. 18, 1–13 (2007)
Li, K.C.: Sliced inverse regression for dimension reduction. J. Am. Stat. Assoc. 86, 316–342 (1991)
Li, L.: Sparse sufficient dimension reduction. Biometrika 94(3), 603–613 (2007)
Li, C.G., Guo, J.: Supervised isomap with explicit mapping. In: Proceedings of the First International Conference on Innovative Computing, Information and Control, vol. 3, pp. 345–348 (2006)
Li, L., Yin, X.: Sliced inverse regression with regularizations. Biometrics 64(1), 124–131 (2007)
Ni, L., Cook, R.D.: A robust inverse regression estimator. Stat. Probab. Lett. 77(3), 343–349 (2007)
Nilsson, J., Fioretos, T., Höglund, M., Fontes, M.: Approximate geodesic distances reveal biologically relevant structures in microarray data. Bioinformatics 20(6), 874–880 (2004)
Pomeroy, S.L., et al.: Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature 415(24), 436–442 (2002)
Roweis, S., Saul, L.: Nonlinear dimensionality reduction by locally linear embedding. Science 290, 2323–2326 (2000)
Samko, O., Marshall, A.D., Rosin, P.L.: Selection of the optimal parameter value for the ISOMAP algorithm. Pattern Recognit. Lett. 27(9), 968–979 (2006)
Saul, L.K., Roweis, S.T.: Think globally, fit locally: unsupervised learning of low dimensional manifolds. J. Mach. Learn. Res. 4, 119–155 (2003)
Setodji, C.M., Cook, R.D.: K-means inverse regression. Technometrics 46(4), 421–429 (2004)
Singh, D., et al.: Gene expression correlates of clinical prostate cancer behavior. Cancer Cell 1(2), 203–209 (2002)
Smola, A.J., Schölkopf, B.: Sparse greedy matrix approximation for machine learning. In: Proceedings of the 17th International Conference on Machine Learning, Stanford University, CA, pp. 911–918. Morgan Kaufmann, San Mateo (2000)
Schölkopf, B., Smola, A.J.: Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond. MIT Press, Cambridge (2002)
Tenenbaum, J.B., de Silva, V., Langford, J.C.: A global geometric framework for nonlinear dimensionality reduction. Science 290, 2319–2323 (2000)
Tien, Y.J., Lee, Y.S, Wu, H.M., Chen, C.H.: Methods for simultaneously identifying coherent local clusters with smooth global patterns in gene expression profiles. BMC Bioinform. 9, 155 (2008)
Vlachos, M., Domeniconi, C., Gunopulos, D., Kollios, G., Koudas, N.: Nonlinear dimensionality reduction techniques for classification and visualization. In: Proceedings of the 8th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 645–651 (2002)
Weinberger, K.Q., Sha, F., Saul, L.K.: Learning a kernel matrix for nonlinear dimensionality reduction. In: Proceedings of the Twenty First International Conference on Machine Learning (ICML 2004), Banff, Canada, pp. 839–846 (2004)
Williams, C., Seeger, M.: Using the Nystrom method to speed up kernel machines. In: Leen, T.K., Dietterich, T.G., Tresp, V. (eds.) Advances in Neural Information Processing System, vol. 13, pp. 682–688. MIT Press, Cambridge (2001)
Wu, H.M.: Kernel sliced inverse regression with applications on classification. J. Comput. Graph. Stat. 17(3), 590–610 (2008)
Wu, H.M., Lu, H.H.-S.: Supervised motion segmentation by spatial-frequential analysis and dynamic sliced inverse regression. Stat. Sin. 14, 413–430 (2004)
Wu, H.M., Lu, H.H.-S.: Iterative sliced inverse regression for segmentation of ultrasound and MR images. Pattern Recognit. 40(12), 3492–3502 (2007)
Wu, H.M., Tien, Y.J., Chen, C.H.: GAP: a graphical environment for matrix visualization and cluster analysis. Comput. Stat. Data Anal. 54, 767–778 (2010)
Wu, Q., Mukherjee, S., Liang, F.: Localized Sliced Inverse Regression. Advances in Neural Information Processing Systems, vol. 20. MIT Press, Cambridge (2008)
Yeh, Y.R., Huang, S.Y., Lee, Y.J.: Nonlinear dimension reduction with kernel sliced inverse regression. IEEE Trans. Knowl. Data Eng. 21(11), 1590–1603 (2009)
Zhong, W., Zeng, P., Ma, P., Liu, J.S., Zhu, Y.: RSIR: regularized sliced inverse regression for motif discovery. Bioinformatics 21(22), 4169–4175 (2005)
Acknowledgements
The author thanks the associate editor and the referees for their valuable comments and suggestions. This research was supported by the grants from National Science Council at Taiwan, R.O.C. (NSC 99-2118-M-032-006-).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Yao, WT., Wu, HM. Isometric sliced inverse regression for nonlinear manifold learning. Stat Comput 23, 563–576 (2013). https://doi.org/10.1007/s11222-012-9330-z
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11222-012-9330-z