Bioinformatics. 2026 Sep 4:btag658. doi: 10.1093/bioinformatics/btag658. Online ahead of print.
ABSTRACT
MOTIVATION: Temporal multivariate data is ubiquitous in many domains, for instance, being collected over time at planned visits (every few months/years) in longitudinal cohorts, or every few minutes/hours in challenge tests. The analysis of such data often focuses on revealing the underlying temporal patterns common across subjects. However, there are subject-specific differences in temporal patterns, which hold the promise to enhance our understanding of underlying mechanisms and facilitate personalized approaches. Nevertheless, extracting subject-specific temporal patterns from longitudinal multivariate data reliably is an open challenge.
RESULTS: We introduce coupled matrix factorizations (CMF) as effective tools to capture subject-specific temporal patterns focusing on two novel applications: analysis of longitudinal metabolomics data and sensitization data. Our analysis shows that CMF models reliably capture subject-specific (shape) differences in temporal patterns with the promise to reveal further insights compared to the state of the art. In metabolomics, CMF models reveal differences in metabolic responses of individuals (in a postprandial meal challenge) according to anthropometric and insulin sensitivity measures. In sensitization data analysis, CMF-based methods capture differences in temporal trajectories of children according to delivery/birth mode and atopic disease diagnosis. We demonstrate the reliability of extracted patterns using reproducibility and replicability.
AVAILABILITY: The code is available on github.com/cchatzis/Revealing-Subject-specific-Temporal-Patterns-from-Longitudinal-Data and doi.org/10.5281/zenodo.22084338. Clinical data is not publicly available due to privacy reasons. Data can be made available under a joint research collaboration by contacting COPSAC ([email protected]).
PMID:42693933 | DOI:10.1093/bioinformatics/btag658
