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bioRxiv · 10.1101/2023.07.26.550749

Time-Informed Dimensionality Reduction for Longitudinal Microbiome Studies

Shi, P.·Martino, C.·Han, R.·Janssen, S.·Buck, G.·Serrano, M.·Owzar, K.·Knight, R.·Shenhav, L.·Zhang, A. R.
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Abstract

Longitudinal studies are crucial for understanding complex microbiome dynamics and their link to health. We introduce TEMPoral TEnsor Decomposition (TEMPTED), a time-informed dimensionality reduction method for high-dimensional longitudinal data that treats time as a continuous variable, effectively characterizing temporal information and handling varying temporal sampling. TEMPTED captures key microbial dynamics, facilitates beta-diversity analysis, and enhances reproducibility by transferring learned representations to new data. In simulations, it achieves 90% accuracy in phenotype classification, significantly outperforming existing methods. In real data, TEMPTED identifies vaginal microbial markers linked to term and preterm births, demonstrating robust performance across datasets and sequencing platforms.

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Shi, P., Martino, C., Han, R., Janssen, S., Buck, G., Serrano, M., Owzar, K., Knight, R., Shenhav, L., Zhang, A. R.. 2023-07-29. Time-Informed Dimensionality Reduction for Longitudinal Microbiome Studies. https://doi.org/10.1101/2023.07.26.550749

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