Chronological age estimation from human microbiomes with transformer-based Robust Principal Component Analysis
: Myers, Tyler; Song, Se Jin; Chen, Yang; De Pessemier, Britta; Khatib, Lora; Mcdonald, Daniel; Huang, Shi; Gallo, Richard; Callewaert, Chris; Havulinna, Aki S.; Lahti, Leo; Roeselers, Guus; Laiola, Manolo; Shetty, Sudarshan A.; Kelley, Scott T.; Knight, Rob; Bartko, Andrew
Publisher: NATURE PORTFOLIO
: 2025
: Communications Biology
: 1159
: 8
: 2399-3642
DOI: https://doi.org/10.1038/s42003-025-08590-y
: https://www.nature.com/articles/s42003-025-08590-y
: https://research.utu.fi/converis/portal/detail/Publication/500029572
Deep learning for microbiome analysis has shown potential for understanding microbial communities and human phenotypes. Here, we propose an approach, Transformer-based Robust Principal Component Analysis(TRPCA), which leverages the strengths of transformer architectures and interpretability of Robust Principal Component Analysis. To investigate benefits of TRPCA over conventional machine learning models, we benchmarked performance on age prediction from three body sites(skin, oral, gut), with 16S rRNA gene amplicon(16S) and whole-genome sequencing(WGS) data. We demonstrated prediction of age from longitudinal samples and combined classification and regression tasks via multi-task learning(MTL). TRPCA improves age prediction accuracy from human microbiome samples, achieving the largest reduction in Mean Absolute Error for WGS skin (MAE: 8.03, 28% reduction) and 16S skin (MAE: 5.09, 14% reduction) samples, compared to conventional approaches. Additionally, TRPCA's MTL approach achieves an accuracy of 89% for birth country prediction across 5 countries, while improving age prediction from WGS stool samples. Notably, TRPCA uncovers a link between subject and error prediction through residual analysis for paired samples across sequencing method (16S/WGS) and body site(oral/gut). These findings highlight TRPCA's utility in improving age prediction while maintaining feature-level interpretability, and elucidating connections between individuals and microbiomes.
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This work was funded by Danone Nutricia Research and the Center for Microbiome Innovation and supported by the Microsetta initiative. B.D.P. was supported by the Research Foundation Flanders (grant numbers 1S04122N and V477223N).
