Abstract
Isometric feature mapping (Isomap) has proven high potential for nonlinear dimensionality reduction in a wide range of application domains. Isomap finds low-dimensional data projections by preserving global geometrical properties, which are expressed in terms of the Euclidean distances among points. In this paper we investigate the use of a recent variant of Isomap, called double-bounded tree-connected Isomap (dbt-Isomap), for dimensionality reduction in the context of time series gene expression classification. In order to deal with the projection of temporal sequences dbt-Isomap is combined with different lock-step and elastic measures which have been extensively proposed to evaluate time series similarity. These are represented by three \(\mathcal L_p\)-norms, dynamic time warping and the distance based on the longest common subsequence model. Computational experiments concerning the classification of two time series gene expression data sets showed the usefulness of dbt-Isomap for dimensionality reduction. Moreover, they highlighted the effectiveness of \(\mathcal L_1\)-norm which appeared as the best alternative to the Euclidean metric for time series gene expression embedding.
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References
Peddada, S., Lobenhofer, E., Li, L., Afshari, C., Weinberg, C., Umbach, D.: Gene selection and clustering for time-course and dose-response microarray experiments using order-restricted inference. Bioinformatics 19, 834–841 (2003)
Hamadeh, H., Bushel, P., Paules, R., Afshari, C.: Discovery in toxicology: mediation by gene expression array technology. Journal of Biochemical and Molecular Toxicology 15, 231–242 (2001)
Baranzini, S., Mousavi, P., Rio, J., Caillier, S., Stillman, A., Villoslada, P., Wyatt, M., Comabella, M., Greller, L., Somogyi, R., Montalban, X., Oksenberg, J.: Transcription-based prediction of response to IFNβ using supervised computational methods. PLoS Biology 3, 166–176 (2005)
Jolliffe, I.T.: Principal component analysis. Springer, New York (1986)
Cox, T.F., Cox, M.A.A.: Multidimensional Scaling. Chapman and Hall, London (1994)
Tenenbaum, J.B., de Silva, V., Langford, J.C.: A global geometric framework for nonlinear dimensionality reduction. Science 290, 2319–2323 (2000)
Roweis, S.T., Saul, L.K.: Nonlinear dimensionality reduction by locally linear embedding. Science 290, 2323–2326 (2000)
Belkin, M., Niyogi, P.: Laplacian eigenmaps for dimensionality reduction and data representation. Neural Computation 15, 1373–1396 (2003)
Orsenigo, C., Vercellis, C.: A comparative study of nonlinear manifold learning methods for cancer microarray data classification. Expert Systems with Applications 40, 2189–2197 (2013)
Mizuhara, Y., Hayashi, A., Suematsu, N.: Embedding of Time Series Data by Using Dynamic Time Warping Distances. Systems and Computers in Japan 37, 241–249 (2006)
Balasubramanian, M., Schwartz, E.L., Tenenbaum, J.B., de Silva, V., Langford, J.C.: The Isomap algorithm and topological stability. Science 295, 7 (2002)
Orsenigo, C., Vercellis, C.: An effective double-bounded tree-connected Isomap algorithm for microarray data classification. Pattern Recognition Letters 33, 9–16 (2012)
Dawson, K., Rodriguez, R.L., Malyj, W.: Sample phenotype clusters in high-density oligonucleotide microarray data sets are revealed using Isomap, a nonlinear algorithm. BMC Bioinformatics 6, 195 (2005)
Park, H.: ISOMAP induced manifold embedding and its application to Alzheimer’s disease and mild cognitive impairment. Neuroscience Letters 513, 141–145 (2012)
Geng, X., Zhan, D.C., Zhou, Z.H.: Supervised nonlinear dimensionality reduction for visualization and classification. IEEE Transactions on Systems, Man and Cybernetics - Part B: Cybernetics 35, 1098–1107 (2005)
Orsenigo, C., Vercellis, C.: Kernel ridge regression for out-of-sample mapping in supervised manifold learning. Expert Systems with Applications 39, 7757–7762 (2012)
Wang, X., Mueen, A., Ding, H., Trajcevski, G., Scheuermann, P., Keogh, E.: Experimental comparison of representation methods and distance measures for time series data. Data Mining and Knowledge Discovery (2012), doi:10.1007/s10618-012-0250-5
Yi, B.-K., Faloutsos, C.: Fast time sequence indexing for arbitrary Lp norms. In: Proc. of the 26th International Conference on Very Large Data Bases, pp. 385–394. Morgan Kaufmann, San Francisco (2000)
Sakoe, H., Chiba, C.: Dynamic programming algorithm optimization for spoken word recognition. IEEE Transactions on Acoustics, Speech and Signal Processing 26, 43–49 (1978)
Keogh, E., Ratanamahatana, C.A.: Exact indexing of dynamic time warping. Knowledge and Information Systems 7, 358–386 (2004)
Vlachos, M., Hadjieleftheriou, M., Gunopulos, D., Keogh, E.: Indexing multidimensional time-series. The VLDB Journal 15, 1–20 (2006)
Orsenigo, C., Vercellis, C.: Combining discrete SVM and fixed cardinality warping distances for multivariate time series classification. Pattern Recognition 43, 3787–3794 (2010)
Keogh, E.J., Ratanamahatana, C.A.: Exact indexing of dynamic time warping. Knowledge and Information Systems 7, 358–386 (2005)
Vlachos, M., Gunopulos, D., Kollios, G.: Discovering similar multidimensional trajectories. In: Proc. of the 18th International Conference on Data Engineering, pp. 673–684. IEEE Computer Society, Washington (2002)
Cho, R.J., Campbell, M.J., Winzeler, E.A., Steinmetz, L., Conway, A., Wodicka, L., Wolfsberg, T.G., Gabrielian, A.E., Landsman, D., Lockhart, D.J., Davis, R.W.: A genome-wide transcriptional analysis of the mitotic cell cycle. Molecular Cell 2, 65–73 (1998)
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Orsenigo, C., Vercellis, C. (2013). Dimensionality Reduction via Isomap with Lock-Step and Elastic Measures for Time Series Gene Expression Classification. In: Vanneschi, L., Bush, W.S., Giacobini, M. (eds) Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics. EvoBIO 2013. Lecture Notes in Computer Science, vol 7833. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37189-9_9
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DOI: https://doi.org/10.1007/978-3-642-37189-9_9
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