Heteroskedastic PCA: Algorithm, Optimality, and Applications

Principal component analysis (PCA) and singular value decomposition (SVD) are widely used in statistics, machine learning, and applied mathematics. It has been well studied in the case of homoskedastic noise, where the noise levels of the contamination are homogeneous. In this paper, we consider PCA and SVD in the presence of heteroskedastic noise, which arises naturally in a range of applications. We introduce a general framework for heteroskedastic PCA and propose an algorithm called HeteroPCA, which involves iteratively imputing the diagonal entries to remove the bias due to heteroskedasticity. This procedure is computationally efficient and provably optimal under the generalized spiked covariance model. A key technical step is a deterministic robust perturbation analysis on the singular subspace, which can be of independent interest. The effectiveness of the proposed algorithm is demonstrated in a suite of applications, including heteroskedastic low-rank matrix denoising, Poisson PCA, and SVD based on heteroskedastic and incomplete data.