Many applications, such as photon-limited imaging and genomics, involve large datasets with noisy entries from exponential family distributions. It is of interest to estimate the covariance structure and principal components of the noiseless distribution. Principal Component Analysis (PCA), the standard method for this setting, can be inefficient when the noise is non-Gaussian. We develop @math PCA (exponential family PCA), a new methodology for PCA on exponential family distributions. @math PCA can be used for dimensionality reduction and denoising of large data matrices. @math PCA involves the eigendecomposition of a new covariance matrix estimator, constructed in a simple and deterministic way using moment calculations, shrinkage, and random matrix theory. We provide several theoretical justifications for our estimator, including the finite-sample convergence rate, and the Marchenko-Pastur law in high dimensions. @math PCA compares favorably to PCA and various PCA alternatives for exponential families, in simulations as well as in XFEL and SNP data analysis. An open-source implementation is available.
To give context for our method, we review related work. The reader intersted in the methodology can skip directly to Section . We refer to @cite_5 for a detailed overview of PCA methodology, to @cite_12 for a more general overview of multivariate statistical analysis including PCA, and to @cite_0 for discussions of high-dimensional statistics, random matrix theory and PCA.
@cite_0 @cite_5 @cite_12
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1. Introduction 2. Limiting spectral distributions 3. CLT for linear spectral statistics 4. The generalised variance and multiple correlation coefficient 5. The T2-statistic 6. Classification of data 7. Testing the general linear hypothesis 8. Testing independence of sets of variates 9. Testing hypotheses of equality of covariance matrices 10. Estimation of the population spectral distribution 11. Large-dimensional spiked population models 12. Efficient optimisation of a large financial portfolio. Introduction * Properties of Population Principal Components * Properties of Sample Principal Components * Interpreting Principal Components: Examples * Graphical Representation of Data Using Principal Components * Choosing a Subset of Principal Components or Variables * Principal Component Analysis and Factor Analysis * Principal Components in Regression Analysis * Principal Components Used with Other Multivariate Techniques * Outlier Detection, Influential Observations and Robust Estimation * Rotation and Interpretation of Principal Components * Principal Component Analysis for Time Series and Other Non-Independent Data * Principal Component Analysis for Special Types of Data * Generalizations and Adaptations of Principal Component Analysis Preface to the Third Edition.Preface to the Second Edition.Preface to the First Edition.1. Introduction.2. The Multivariate Normal Distribution.3. Estimation of the Mean Vector and the Covariance Matrix.4. The Distributions and Uses of Sample Correlation Coefficients.5. The Generalized T2-Statistic.6. Classification of Observations.7. The Distribution of the Sample Covariance Matrix and the Sample Generalized Variance.8. Testing the General Linear Hypothesis: Multivariate Analysis of Variance9. Testing Independence of Sets of Variates.10. Testing Hypotheses of Equality of Covariance Matrices and Equality of Mean Vectors and Covariance Matrices.11. Principal Components.12. Cononical Correlations and Cononical Variables.13. The Distributions of Characteristic Roots and Vectors.14. Factor Analysis.15. Pattern of Dependence Graphical Models.Appendix A: Matrix Theory.Appendix B: Tables.References.Index.