The Annals of Statistics

Influential features PCA for high dimensional clustering

Jiashun Jin and Wanjie Wang

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We consider a clustering problem where we observe feature vectors $X_{i}\in R^{p}$, $i=1,2,\ldots,n$, from $K$ possible classes. The class labels are unknown and the main interest is to estimate them. We are primarily interested in the modern regime of $p\gg n$, where classical clustering methods face challenges.

We propose Influential Features PCA (IF-PCA) as a new clustering procedure. In IF-PCA, we select a small fraction of features with the largest Kolmogorov–Smirnov (KS) scores, obtain the first $(K-1)$ left singular vectors of the post-selection normalized data matrix, and then estimate the labels by applying the classical $k$-means procedure to these singular vectors. In this procedure, the only tuning parameter is the threshold in the feature selection step. We set the threshold in a data-driven fashion by adapting the recent notion of Higher Criticism. As a result, IF-PCA is a tuning-free clustering method.

We apply IF-PCA to $10$ gene microarray data sets. The method has competitive performance in clustering. Especially, in three of the data sets, the error rates of IF-PCA are only $29\%$ or less of the error rates by other methods. We have also rediscovered a phenomenon on empirical null by Efron [J. Amer. Statist. Assoc. 99 (2004) 96–104] on microarray data.

With delicate analysis, especially post-selection eigen-analysis, we derive tight probability bounds on the Kolmogorov–Smirnov statistics and show that IF-PCA yields clustering consistency in a broad context. The clustering problem is connected to the problems of sparse PCA and low-rank matrix recovery, but it is different in important ways. We reveal an interesting phase transition phenomenon associated with these problems and identify the range of interest for each.

Article information

Ann. Statist. Volume 44, Number 6 (2016), 2323-2359.

Received: July 2014
Revised: December 2015
First available in Project Euclid: 23 November 2016

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Mathematical Reviews number (MathSciNet)

Primary: 62H30: Classification and discrimination; cluster analysis [See also 68T10, 91C20] 62G32: Statistics of extreme values; tail inference
Secondary: 62E20: Asymptotic distribution theory

Empirical null feature selection gene microarray Hamming distance phase transition post-selection spectral clustering sparsity


Jin, Jiashun; Wang, Wanjie. Influential features PCA for high dimensional clustering. Ann. Statist. 44 (2016), no. 6, 2323--2359. doi:10.1214/15-AOS1423.

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See also

  • Discussion of "Influential features PCA for high dimensional clustering".
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Supplemental materials

  • Supplement to “Influential Features PCA for high dimensional clustering”. Owing to space constraints, the technical proofs are relegated a supplementary document Jin and Wang (2016). It contains three sections: Appendices A–C.