In many longitudinal studies, a large number of variables are measured repeatedly over time, with substantial missing data. Existing methods, such as probabilistic principal component analysis (PPCA), are ill-equipped to handle such incomplete, high-dimensional longitudinal data, as they fail to account for the nested sources of variation and temporal dependency inherent in repeated measures. We introduce hierarchical probabilistic principal component analysis (HPPCA), a two-level probabilistic factor model that explicitly separates between-subject variance from time-varying within-subject dynamics. The within-subject latent factors are modeled by a Gaussian process. We develop an EM algorithm to handle missing data and flexible covariance kernels, accelerated by computationally efficient initializers. Simulation studies demonstrated that HPPCA robustly recovers model parameters subspaces and substantially outperforms both standard PPCA and multivariate functional PCA in imputation accuracy, even under heavy missingness and model misspecification. An application to the long COVID symptoms in the Researching COVID to Enhance Recovery adult cohort revealed that HPPCA effectively captured the data's hierarchical structure and its learned features significantly improved the prediction of clinical outcomes and the recovery of masked clinical records compared to exisiting methods.

A.1 Does our neural regression method work? To ensure our neural regression method works, we verify its efficacy on a known benchmark: the activity of 256 cells in the V4 and IT regions of two Rhesus macaque monkeys, a core component of BrainScore [4]. BrainScore's in-house method involves a combination of principal components analysis (for dimensionality reduction) and k-fold cross-validated partial least squares regression (for the linear mapping of model to brain activity). Here, we exchange principal components analysis for sparse random projection and partial least squares regression for ridge regression with generalized cross-validation. We compute the scores for each benchmark in the same fashion as BrainScore: as the Pearson correlation coefficient between the actual and predicted (cross-validated) activity of the biological neurons in the V4 and IT samples.

We study efficient distributed algorithms for the fundamental problem of principal component analysis and leading eigenvector computation on the sphere, when the data are randomly distributed among a set of computational nodes. We propose a new quantized variant of Riemannian gradient descent to solve this problem, and prove that the algorithm converges with high probability under a set of necessary spherical-convexity properties. We give bounds on the number of bits transmitted by the algorithm under common initialization schemes, and investigate the dependency on the problem dimension in each case.

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We introduce Metric-Aware Principal Component Analysis (MAPCA), a unified framework for scale-invariant representation learning based on the generalised eigenproblem max Tr(W^T Sigma W) subject to W^T M W = I, where M is a symmetric positive definite metric matrix. The choice of M determines the representation geometry. The canonical beta-family M(beta) = Sigma^beta, beta in [0,1], provides continuous spectral bias control between standard PCA (beta=0) and output whitening (beta=1), with condition number kappa(beta) = (lambda_1/lambda_p)^(1-beta) decreasing monotonically to isotropy. The diagonal metric M = D = diag(Sigma) recovers Invariant PCA (IPCA), a method rooted in Frisch (1928) diagonal regression, as a distinct member of the broader framework. We prove that scale invariance holds if and only if the metric transforms as M_tilde = CMC under rescaling C, a condition satisfied exactly by IPCA but not by the general beta-family at intermediate values. Beyond its classical interpretation, MAPCA provides a geometric language that unifies several self-supervised learning objectives. Barlow Twins and ZCA whitening correspond to beta=1 (output whitening); VICReg's variance term corresponds to the diagonal metric. A key finding is that W-MSE, despite being described as a whitening-based method, corresponds to M = Sigma^{-1} (beta = -1), outside the spectral compression range entirely and in the opposite spectral direction to Barlow Twins. This distinction between input and output whitening is invisible at the level of loss functions and becomes precise only within the MAPCA framework.

We decompose the Kullback--Leibler generalization error (GE) -- the expected KL divergence from the data distribution to the trained model -- of unsupervised learning into three non-negative components: model error, data bias, and variance. The decomposition is exact for any e-flat model class and follows from two identities of information geometry: the generalized Pythagorean theorem and a dual e-mixture variance identity. As an analytically tractable demonstration, we apply the framework to $ε$-PCA, a regularized principal component analysis in which the empirical covariance is truncated at rank $N_K$ and discarded directions are pinned at a fixed noise floor $ε$. Although rank-constrained $ε$-PCA is not itself e-flat, it admits a technical reformulation with the same total GE on isotropic Gaussian data, under which each component of the decomposition takes closed form. The optimal rank emerges as the cutoff $λ_{\mathrm{cut}}^{*} = ε$ -- the model retains exactly those empirical eigenvalues exceeding the noise floor -- with the cutoff reflecting a marginal-rate balance between model-error gain and data-bias cost. A boundary comparison further yields a three-regime phase diagram -- retain-all, interior, and collapse -- separated by the lower Marchenko--Pastur edge and an analytically computable collapse threshold $ε_{*}(α)$, where $α$ is the dimension-to-sample-size ratio. All claims are verified numerically.

Quantum principal component analysis (qPCA) is commonly formulated as the extraction of eigenvalues and eigenvectors of a covariance-encoded density operator. Yet in many qPCA settings, the practical objective is simpler: projecting data onto the dominant spectral subspace. In this work, we introduce a projection-first framework, the Filtered Spectral Projection Algorithm (FSPA), which bypasses explicit eigenvalue estimation while preserving the essential spectral structure. FSPA amplifies any nonzero warm-start overlap with the leading principal subspace and remains robust in small-gap and near-degenerate regimes without inducing artificial symmetry breaking in the absence of bias. To connect this approach to classical datasets, we show that for amplitude-encoded centered data, the ensemble density matrix $ρ=\sum_i p_i|ψ_i\rangle\langleψ_i|$ coincides with the covariance matrix. For uncentered data, $ρ$ corresponds to PCA without centering, and we derive eigenvalue interlacing bounds quantifying the deviation from standard PCA. We further show that ensembles of quantum states admit an equivalent centered covariance interpretation. Numerical demonstrations on benchmark datasets, including Breast Cancer Wisconsin and handwritten Digits, show that downstream performance remains stable whenever projection quality is preserved. These results suggest that, in a broad class of qPCA settings, spectral projection is the essential primitive, and explicit eigenvalue estimation is often unnecessary.

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