Spike and slab Bayesian sparse principal component analysis

DOI10.48550/ARXIV.2102.00305arXiv2102.00305MaRDI QIDQ130279

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Publication date: 30 January 2021

Abstract: Sparse principal component analysis (PCA) is a popular tool for dimensional reduction of high-dimensional data. Despite its massive popularity, there is still a lack of theoretically justifiable Bayesian sparse PCA that is computationally scalable. A major challenge is choosing a suitable prior for the loadings matrix, as principal components are mutually orthogonal. We propose a spike and slab prior that meets this orthogonality constraint and show that the posterior enjoys both theoretical and computational advantages. Two computational algorithms, the PX-CAVI and the PX-EM algorithms, are developed. Both algorithms use parameter expansion to deal with the orthogonality constraint and to accelerate their convergence speeds. We found that the PX-CAVI algorithm has superior empirical performance than the PX-EM algorithm and two other penalty methods for sparse PCA. The PX-CAVI algorithm is then applied to study a lung cancer gene expression dataset. $mathsfR$ package $mathsfVBsparsePCA$ with an implementation of the algorithm is available on The Comprehensive R Archive Network.

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