The common factor analytic model is related to Helmholtz and Boltzmann machines, can be conceived as a linear autoencoder, or can be thought of as a single-hidden-layer generative neural network. We thus consider it a basal generative representation learner that can be used as a minimal model for studying the foundational characteristics of (deep) generative model architectures. We focus on the fundamental problem of indeterminacy in latent factor projections. This indeterminacy implies that, even when the intrinsic dimension of the latent vector is known, regularity conditions are met, and rotational indeterminacy is resolved, an inherent indefiniteness in the retrieval of causative latent sources remains: they will be uncertain, distributionally deviant, and non-unique. This can have major implications for data representation but remains an elusive issue, even to practitioners and theorists well-versed in the factor model. Moreover, this classic psychometric problem is intricately related to the modern issue of latent variable collapse in the variational autoencoder framework for deep generative modeling. Here, we assess this indeterminacy from various perspectives and show how these are mathematically and conceptually related and we discuss subsequent implications for the Psychometrics, Statistics, and Artificial Intelligence communities. We show that one has latent factor determinacy across all its facets when the feature-dimension grows to infinity. This feeds into an essentially distribution-free estimation approach in the sample case when the number of features grows very large. We conclude, as these are emergent properties at scale, that the factor model is suited for representation learning of very-high-dimensional data.

This paper presents OLinear, a linear-based multivariate time series forecasting model that operates in an orthogonally transformed domain. Recent forecasting models typically adopt the temporal forecast (TF) paradigm, which directly encode and decode time series in the time domain. However, the entangled step-wise dependencies in series data can hinder the performance of TF. To address this, some forecasters conduct encoding and decoding in the transformed domain using fixed, dataset-independent bases (e.g., sine and cosine signals in the Fourier transform). In contrast, we utilize OrthoTrans, a data-adaptive transformation based on an orthogonal matrix that diagonalizes the series' temporal Pearson correlation matrix.

Generating realistic brain connectivity matrices is key to analyzing population heterogeneity in brain organization, understanding disease, and augmenting data in challenging classification problems. Functional connectivity matrices lie in constrained spaces--such as the set of symmetric positive definite or correlation matrices--that can be modeled as Riemannian manifolds. However, using Riemannian tools typically requires redefining core operations (geodesics, norms, integration), making generative modeling computationally inefficient. In this work, we propose DIFFEOCFM, an approach that enables conditional flow matching (CFM) on matrix manifolds by exploiting pullback metrics induced by global diffeomorphisms on Euclidean spaces. We show that Riemannian CFM with such metrics is equivalent to applying standard CFM after data transformation. This equivalence allows efficient vector field learning, and fast sampling with standard ODE solvers.

Mean-field variational inference (VI), despite its scalability, is limited by the independence assumption, making it unsuitable for scenarios with correlated data instances. Existing structured VI methods either focus on correlations among latent dimensions which lack scalability for modeling instance-level correlations, or are restricted to simple first-order dependencies, limiting their expressiveness. In this paper, we propose High-order Tree-structured Variational Inference (HoT-VI)2, that explicitly models k-order instance-level correlations among latent variables. By expressing the global posterior through overlapping k-dimensional local marginals, our method enables efficient parameterized sampling via a sequential procedure. To ensure the validity of these marginals, we introduce a conditional correlation parameterization method that guarantees positive definiteness of their correlation matrices. We further extend our method with a tree-structured backbone to capture more flexible dependency patterns. Extensive experiments on time-series and graphstructured datasets demonstrate that modeling higher-order correlations leads to significantly improved posterior approximations and better performance across various downstream tasks.

Interpreting machine-learning models has attracted increasing attention, particularly in the physical sciences, where one often seeks to understand the underlying mechanisms rather than merely make predictions. Multiple linear regression is often regarded as an interpretable alternative to more complex models, such as deep neural networks, because its predictions are expressed as explicit weighted sums of input features. However, when input features are strongly correlated, namely in the presence of multicollinearity, the learned weights can exhibit large dataset-to-dataset fluctuations and oscillatory behavior across physically similar features, making their interpretation difficult or even impossible. Although the instability of the weights under multicollinearity is well known in statistics, its consequences for physical interpretation, in particular its connection to oscillatory weights across physically similar features, have not been systematically clarified. Here, we theoretically discuss the mechanism behind this loss of interpretability by analyzing the eigenmodes of the feature correlation matrix. We show that small-eigenvalue modes associated with multicollinearity amplify fluctuations in the weights and generate oscillatory patterns that do not necessarily reflect meaningful contributions. We test this theoretical picture numerically on physics datasets and show that Ridge regularization suppresses these unstable modes, although the resulting weights must still be interpreted with caution. We further confirm the generality of our findings beyond physics by analyzing a diverse collection of publicly available datasets. Our results clarify why, in the presence of multicollinearity, physical interpretation can remain difficult even for linear regression models.

We study training-free fixed-length descriptors for multivariate time series and ask not merely whether such a descriptor performs well, but when it can be expected to work at all. Our object of study is $D(τ)$, built from a time-lagged correlation matrix truncated at the Marchenko-Pastur edge so that only signal-bearing eigenvalues survive and classified by cosine similarity to class centroids with zero learned parameters. The central contribution is not the descriptor but a falsifiable applicability criterion for it. Working from a stationary Gaussian VAR(1) model, we argue that $D(τ)$ separates two classes when the signals are approximately stationary and the class information lives in their cross-channel temporal coupling rather than in marginal per-channel power. We derive, semi-formally, three consequences: a distinguishability condition, why the static ($τ=0$) covariance collapses to chance, and why a stationary but power-discriminated paradigm defeats the descriptor. The criterion is operational: a two-part pre-flight test -- an augmented Dickey-Fuller stationarity check and a power-baseline saturation check -- predicts applicability before any training. We validate both halves on a mixed assortment. On four paradigms that satisfy the criterion (Sleep-EDF, BCI-IV-2a, MIT-BIH, ESC-50) the descriptor is competitive with strong baselines at a fraction of their cost, reaching $88.5\pm4.5\%$ under 20-subject leave-one-subject-out on Sleep-EDF on a single CPU thread. On three that violate it -- non-stationary ERPs, and financial-volatility and wearable-stress regimes that are power-discriminated -- it fails exactly as the pre-flight predicts, and these negatives are the more informative half. We are explicit that $D(τ)$ is not the most accurate representation; its value is a compact, training-free embedding whose domain of validity is known in advance.

Traditional correlation measures, such as Pearson's and Spearman's coefficients, are limited in their ability to capture complex relationships, particularly nonlinear and multivariate dependencies. The Hirschfeld-Gebelein-Rényi (HGR) maximal correlation offers a powerful alternative by measuring the highest Pearson correlation achievable through nonlinear transformations of two random variables. However, estimating the HGR coefficient remains challenging due to the complexity of optimizing arbitrary nonlinear functions. We introduce a new coefficient, satisfying Rényi's axioms, based on the extension of HGR with Spearman's rank correlation: the Spearman HGR (SHGR). We propose a neural network-based estimator tailored to estimate (i) the bivariate correlation matrix, (ii) the multivariate correlations between a set of variables and another one, and (iii) the full correlation between two sets of variables. This estimate effectively detects nonlinear dependencies and demonstrates robustness to noise, outliers, and spurious correlations (hallucinations). Additionally, it achieves competitive computational efficiency through designed neural architectures. Comprehensive numerical experiments and feature selection tasks confirm that SHGRoutperforms existing state-of-the-art methods.

Generating realistic brain connectivity matrices is key to analyzing population heterogeneity in brain organization, understanding disease, and augmenting data in challenging classification problems. Functional connectivity matrices lie in constrained spaces--such as the set of symmetric positive definite or correlation matrices--that can be modeled as Riemannian manifolds. However, using Riemannian tools typically requires redefining core operations (geodesics, norms, integration), making generative modeling computationally inefficient. In this work, we propose DiffeoCFM, an approach that enables conditional flow matching (CFM) on matrix manifolds by exploiting pullback metrics induced by global diffeomorphisms on Euclidean spaces. We show that Riemannian CFM with such metrics is equivalent to applying standard CFM after data transformation. This equivalence allows efficient vector field learning, and fast sampling with standard ODE solvers.

Despite its importance to applications in protein design, predicting protein properties like binding affinity and thermostability from sparse experimental data remains a significant challenge. Accordingly, we introduce a class of sequence kernels that exploit evolutionary substitution matrices as well as local linearity and demonstrate that the resulting Gaussian processes provide data-efficient models of protein property landscapes, frequently outperforming alternatives that rely on foundation model embeddings. Furthermore--by learning what are in effect structure-aware substitution matrices--we show that our kernels can readily incorporate structural information from foundation models. We demonstrate that these structure-conditioned kernels are well suited to multi-task learning across multiple protein property landscapes and can decisively outperform local supervised learning methods.

Many nonlinear iterative procedures generate high-dimensional trajectories whose early behavior is informative but difficult to compare directly. This paper studies a soft-computing representation problem: how to convert a short early trajectory segment into compact, interpretable, fixed-dimensional fuzzy coordinates that preserve information about subsequent convergence and trajectory geometry. The problem is investigated for iterated Pearson correlation matrices, a nonlinear matrix iteration historically connected with CONCOR-type blockmodeling and repeated-correlation methods. The proposed descriptor uses two logarithmic signals from the early post-transient regime: a step-size signal, measuring contraction magnitude, and a contraction-ratio signal, measuring local contraction evolution. Each signal is projected onto a three-node triangular fuzzy partition using zero-degree F-transform coefficients and one centered first-degree coefficient. This yields an eight-dimensional two-channel representation separating local level from local trend and contraction magnitude from contraction evolution. Across 22 matrix dimensions with 1000 trajectories per dimension, the descriptor is compared with raw trajectory samples, statistical summaries, and PCA-compressed raw features using Random Forest regression for convergence-length approximation. It achieves mean R^2 = 0.6480, close to raw trajectories (0.6518) and statistical summaries (0.6528), while improving over the step-size-only F-transform descriptor (0.5001). Repeated random-split and shifted-window experiments confirm stability. PCA and clustering further show reproducible low-dimensional organization, with the first two principal components explaining 84.26% of variance and k = 3 favored by the mean silhouette criterion.