Semi-supervised Omics Factor Analysis (SOFA) disentangles known and latent sources of variation in multi-omic data.
T, C., H, V., KSA, K.S., RO, R.F., J, S.R., & W, H. (2026). Semi-supervised Omics Factor Analysis (SOFA) disentangles known and latent sources of variation in multi-omic data.. Nature communications. https://doi.org/10.1038/s41467-026-74694-6
T C, H V, KSA KS, RO RF, J SR, W H. Semi-supervised Omics Factor Analysis (SOFA) disentangles known and latent sources of variation in multi-omic data.. Nature communications. 2026; doi: 10.1038/s41467-026-74694-6
T C, H V, KSA KS, et al. Semi-supervised Omics Factor Analysis (SOFA) disentangles known and latent sources of variation in multi-omic data.[J]. Nature communications. 2026. DOI: 10.1038/s41467-026-74694-6.
@article{t2026,
author = {Capraz T and Vöhringer H and Kruger Serrano KSA and Ramirez Flores RO and Saez-Rodriguez J and Huber W},
title = {Semi-supervised Omics Factor Analysis (SOFA) disentangles known and latent sources of variation in multi-omic data.},
journal = {Nature communications},
year = {2026},
doi = {10.1038/s41467-026-74694-6},
note = {PMID: 42624833},
}
TY - JOUR AU - Capraz T AU - Vöhringer H AU - Kruger Serrano KSA AU - Ramirez Flores RO AU - Saez-Rodriguez J AU - Huber W TI - Semi-supervised Omics Factor Analysis (SOFA) disentangles known and latent sources of variation in multi-omic data. T2 - Nature communications PY - 2026 DO - 10.1038/s41467-026-74694-6 AN - PMID:42624833 ER -
A fundamental design pattern in biomolecular studies is to assay the same set of samples (organisms, tissue biopsies, or individual cells) by multiple different 'omics assays. Group Factor Analysis (GFA) and its adaptation to high-dimensional settings, Multi-Omics Factor Analysis (MOFA), are widely used as a first-line approach to analyze such data and are effective in detecting patterns of correlation, organize them into so-called latent factors, and identify common and assay-specific factors. However, in many applications, a subset of the found factors just rediscovers already known covariates (e.g., disease subtypes, environmental covariates) while others may represent genuine novelty.Here, we present Semi-supervised Omics Factor Analysis (SOFA), a method that incorporates known covariates into the model upfront and focuses the factor discovery on novel sources of variation. We show SOFA's effectiveness for discovering novel patterns by applying it to cancer, brain development and heart failure multi-omic data sets.