# Set-Aggregated Genome Embeddings for Microbiome Abundance Prediction

arXiv: https://arxiv.org/abs/2605.12286 · HTML: https://mlsanity.com/paper/2605.12286/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 4 of its 28 references that are in the map.
- First posted on arXiv 12 May 2026.

## Builds on (most cited first, 4 of 4)

- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [Training Compute-Optimal Large Language Models](https://mlsanity.com/paper/2203.15556/) (2022)
- [UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction](https://mlsanity.com/paper/1802.03426/) (2018)
- [Abundance-Aware Set Transformer for Microbiome Sample Embedding](https://mlsanity.com/paper/2508.11075/) (2025)

## Abstract (arXiv)

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.