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arXiv · 2605.12286

Set-Aggregated Genome Embeddings for Microbiome Abundance Prediction

Younhun Kim·Georg K. Gerber·Travis E. Gibson
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Abstract

Microbiome functions are encoded within the genes of the community-wide metagenome. A natural question is whether properties of a microbial community can be predicted just from knowing the raw DNA sequences of its members. In this work, we employ set-aggregated genome embeddings (SAGE) to predict community-level abundance profiles, exploiting the few-shot learning capabilities of genomic language models (GLMs). We benchmark this approach to show improved generalization on novel genomes compared to classical bioinformatics approaches. Model ablation shows that community-level latent representations directly result in improved performance. Lastly, we demonstrate the benefits of intermediate transformations between latent representations and demonstrate the differences between GLM embedding choices.

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Younhun Kim, Georg K. Gerber, Travis E. Gibson. 2026-05-12. Set-Aggregated Genome Embeddings for Microbiome Abundance Prediction. https://arxiv.org/abs/2605.12286

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