When the dimension of data is comparable to or larger than the number of data samples, principal components analysis (PCA) may exhibit problematic high-dimensional noise. In this work, we propose an empirical Bayes PCA method that reduces this noise by estimating a joint prior distribution for the principal components. EB-PCA is based on the classical Kiefer–Wolfowitz non-parametric maximum likelihood estimator for empirical Bayes estimation, distributional results derived from random matrix theory for the sample PCs and iterative refinement using an approximate message passing (AMP) algorithm. In theoretical ‘spiked’ models, EB-PCA achieves Bayes-optimal estimation accuracy in the same settings as an oracle Bayes AMP procedure that knows the true priors. Empirically, EB-PCA significantly improves over PCA when there is strong prior structure, both in simulation and on quantitative benchmarks constructed from the 1000 Genomes Project and the International HapMap Project. An illustration is presented for analysis of gene expression data obtained by single-cell RNA-seq.
This content will become publicly available on August 1, 2024
Approximate message passing from random initialization with applications to Z 2 synchronization
This paper is concerned with the problem of reconstructing an unknown rank-one matrix with prior structural information from noisy observations. While computing the Bayes optimal estimator is intractable in general due to the requirement of computing high-dimensional integrations/summations, Approximate Message Passing (AMP) emerges as an efficient first-order method to approximate the Bayes optimal estimator. However, the theoretical underpinnings of AMP remain largely unavailable when it starts from random initialization, a scheme of critical practical utility. Focusing on a prototypical model called Z 2 synchronization, we characterize the finite-sample dynamics of AMP from random initialization, uncovering its rapid global convergence. Our theory—which is nonasymptotic in nature—in this model unveils the non-necessity of a careful initialization for the success of AMP.
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- NSF-PAR ID:
- 10434808
- Date Published:
- Journal Name:
- Proceedings of the National Academy of Sciences
- Volume:
- 120
- Issue:
- 31
- ISSN:
- 0027-8424
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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