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Abstract We study a class of Approximate Message Passing (AMP) algorithms for symmetric and rectangular spiked random matrix models with orthogonally invariant noise. The AMP iterates have fixed dimension $$K \geq 1$$, a multivariate non-linearity is applied in each AMP iteration, and the algorithm is spectrally initialized with $$K$$ super-critical sample eigenvectors. We derive the forms of the Onsager debiasing coefficients and corresponding AMP state evolution, which depend on the free cumulants of the noise spectral distribution. This extends previous results for such models with $K=1$ and an independent initialization. Applying this approach to Bayesian principal components analysis, we introduce a Bayes-OAMP algorithm that uses as its non-linearity the posterior mean conditional on all preceding AMP iterates. We describe a practical implementation of this algorithm, where all debiasing and state evolution parameters are estimated from the observed data, and we illustrate the accuracy and stability of this approach in simulations. 

Abstract 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.