Sparse Functional Singular Value Decomposition for Biclustering and Triclustering Longitudinal Data
Authors: Yue Zhao, Thierry Chekouo, Sandra Safo
Organizations: Division of Biostatistics and Health Data Science University of Minnesota 2221 University Avenue SE2026 Minneapolis, MN 55414, United States
Abstract
Identifying subtypes of complex conditions, such as Inflammatory Bowel Disease (IBD), often requires capturing latent patterns in longitudinal omics data. However, these data are typically high-dimensional, sparsely sampled, and irregularly observed over time, posing substantial challenges for conventional (bi)clustering and functional data analysis methods. We propose Tri-SfSVD, a unified sparse functional Singular Value Decomposition framework for discovering biclusters and triclusters in longitudinal data. Unlike existing functional biclustering methods that rely on ad hoc imputation or enforce restrictive shape-homogeneity assumptions, Tri-SfSVD integrates continuous trajectory estimation with simultaneous subject, feature, and temporal selection within a single optimization framework. By imposing sparse penalties across subjects, variables, and temporal subregions, the proposed method works directly on observed data to uncover localized structures at the subject, subject-feature, and subject-feature-time levels. Extensive simulations demonstrate that Tri-SfSVD outperforms existing approaches in high-dimensional settings. Applied to IBD multi-omics data, the method identified three biclusters linking sample clusters with distinct IBD-related clinical characteristics to microbial pathway groups associated with specific bacterial taxa, providing interpretable subject-pathway associations for characterizing disease heterogeneity. Applied to multi-channel EEG data, the method identified three triclusters linking sample clusters with distinct alcohol-related phenotypes to localized brain activity patterns, including subgroup differences separated by temporal subregions within the same spatial region.
Functional data present unique challenges for clustering due to their infinite-dimensional nature and potential sensitivity to outliers. An extension of the OCLUST algorithm to the functional setting is proposed to address these issues. The approach leverages the OCLUST framework, creating a robust method to cluster curves and trim outliers. The methodology is evaluated on both simulated and real-world functional datasets, demonstrating strong performance in clustering and outlier identification.
This paper introduces a novel framework for Regularized Multivariate Functional Principal Component Analysis (ReMFPCA) via Functional Singular Value Decomposition (SVD). The proposed method extends existing MFPCA approaches by incorporating a generalized functional SVD within a Hilbert space framework, enabling simultaneous regularization of both functional principal components (PCs) and their associated PC scores. A key innovation of this framework is the inclusion of a sparsity penalty on the PC scores, which enhances interpretability by filtering out irrelevant subject-specific variations. This dual-penalization strategy represents a significant advancement beyond existing covariance-based eigen decomposition methods, which penalize only the functional PCs. Two power algorithm implementations, sequential and joint, are proposed, together with a cross-validation approach based on iterative regression for optimal smoothing parameter selection. Comprehensive simulation studies and real data applications demonstrate that the proposed framework substantially improves the extraction of informative and interpretable components, offering methodological and practical benefits for analyzing multivariate functional data across diverse domains.
Modeling shared and subject-specific structure in multisubject spatiotemporal data remains challenging, particularly in neuroimaging, where both spatial and temporal patterns exhibit rich variability across subjects. Existing matrix and tensor decompositions provide interpretable factorizations, but rely on fixed multilinear structures or coupling schemes that may limit their flexibility in capturing complex variability. In this work, we introduce a spatiotemporal variational tensor decomposition (ST-VTD) framework that combines a tensor factorization generative model with structured priors to jointly represent spatial maps and temporal dynamics. Spatial factors are regularized to promote a low-rank structure inspired by the LL1 decomposition, while temporal factors are modeled using a learned Long short-term memory (LSTM)-based prior, enabling flexible and adaptive dynamics. Posterior inference is performed using an amortized variational formulation by unrolling iterations of an optimization algorithm, leading to an interpretable and parameter-efficient architecture. The proposed inference framework employs a warm-start strategy based on group independent component analysis, which we found to improve optimization performance. Experiments on a realistic synthetic functional MRI (fMRI) dataset demonstrate that the proposed approach significantly improves latent factor recovery compared with representative classical and probabilistic decomposition benchmarks.
Laura M. Montaldo, Ricardo A. Borsoi, Sebastian Miron +1