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Clustering by principal component analysis with Gaussian kernel in high-dimension, low-sample-size settings

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  • Nakayama, Yugo
  • Yata, Kazuyoshi
  • Aoshima, Makoto

Abstract

In this paper, we consider clustering based on the kernel principal component analysis (KPCA) for high-dimension, low-sample-size (HDLSS) data. We give theoretical reasons why the Gaussian kernel is effective for clustering high-dimensional data. In addition, we discuss a choice of the scale parameter yielding a high performance of the KPCA with the Gaussian kernel. Finally, we test the performance of the clustering by using microarray data sets.

Suggested Citation

  • Nakayama, Yugo & Yata, Kazuyoshi & Aoshima, Makoto, 2021. "Clustering by principal component analysis with Gaussian kernel in high-dimension, low-sample-size settings," Journal of Multivariate Analysis, Elsevier, vol. 185(C).
    • Handle: RePEc:eee:jmvana:v:185:y:2021:i:c:s0047259x21000579
    DOI: 10.1016/j.jmva.2021.104779
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    References listed on IDEAS

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    1. Peter Hall & J. S. Marron & Amnon Neeman, 2005. "Geometric representation of high dimension, low sample size data," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 67(3), pages 427-444, June.
    2. Yugo Nakayama & Kazuyoshi Yata & Makoto Aoshima, 2020. "Bias-corrected support vector machine with Gaussian kernel in high-dimension, low-sample-size settings," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 72(5), pages 1257-1286, October.
    3. Makoto Aoshima & Kazuyoshi Yata, 2019. "Distance-based classifier by data transformation for high-dimension, strongly spiked eigenvalue models," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 71(3), pages 473-503, June.
    4. Borysov, Petro & Hannig, Jan & Marron, J.S., 2014. "Asymptotics of hierarchical clustering for growing dimension," Journal of Multivariate Analysis, Elsevier, vol. 124(C), pages 465-479.
    5. Kazuyoshi Yata & Makoto Aoshima, 2020. "Geometric consistency of principal component scores for high‐dimensional mixture models and its application," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 47(3), pages 899-921, September.
    6. Liu, Yufeng & Hayes, David Neil & Nobel, Andrew & Marron, J. S, 2008. "Statistical Significance of Clustering for High-Dimension, Low–Sample Size Data," Journal of the American Statistical Association, American Statistical Association, vol. 103(483), pages 1281-1293.
    7. Patrick K. Kimes & Yufeng Liu & David Neil Hayes & James Stephen Marron, 2017. "Statistical significance for hierarchical clustering," Biometrics, The International Biometric Society, vol. 73(3), pages 811-821, September.
    8. Yata, Kazuyoshi & Aoshima, Makoto, 2012. "Effective PCA for high-dimension, low-sample-size data with noise reduction via geometric representations," Journal of Multivariate Analysis, Elsevier, vol. 105(1), pages 193-215.
    9. Makoto Aoshima & Kazuyoshi Yata, 2014. "A distance-based, misclassification rate adjusted classifier for multiclass, high-dimensional data," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 66(5), pages 983-1010, October.
    10. Kristoffer H. Hellton & Magne Thoresen, 2017. "When and Why are Principal Component Scores a Good Tool for Visualizing High-dimensional Data?," Scandinavian Journal of Statistics, Danish Society for Theoretical Statistics;Finnish Statistical Society;Norwegian Statistical Association;Swedish Statistical Association, vol. 44(3), pages 581-597, September.
    11. Jeongyoun Ahn & J. S. Marron & Keith M. Muller & Yueh-Yun Chi, 2007. "The high-dimension, low-sample-size geometric representation holds under mild conditions," Biometrika, Biometrika Trust, vol. 94(3), pages 760-766.
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    2. Jolliffe, Ian, 2022. "A 50-year personal journey through time with principal component analysis," Journal of Multivariate Analysis, Elsevier, vol. 188(C).

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