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arXiv · 2501.02045

METAGENE-1: Metagenomic Foundation Model for Pandemic Monitoring

Ollie Liu·Sami Jaghouar·Johannes Hagemann·Shangshang Wang·Jason Wiemels·Jeff Kaufman·Willie Neiswanger
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Abstract

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

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Ollie Liu, Sami Jaghouar, Johannes Hagemann, Shangshang Wang, Jason Wiemels, Jeff Kaufman, Willie Neiswanger. 2025-01-03. METAGENE-1: Metagenomic Foundation Model for Pandemic Monitoring. https://arxiv.org/abs/2501.02045

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