The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling

Andre Cornman, Jacob West-Roberts, Antonio Pedro Camargo, Simon Roux, Martin Beracochea, Milot Mirdita, Sergey Ovchinnikov, Yunha Hwang

Keywords: metagenomics, pretraining dataset, genomic language model

TL;DR: We introduce the OMG dataset and gLM2. OMG is a massive Open MetaGenomic corpus totaling 3.1T base-pairs, and we train gLM2, the first mixed-modality genomic language model which learns zero-shot protein-protein interfaces.

Abstract: Biological language model performance depends heavily on pretraining data quality, diversity, and size. While metagenomic datasets feature enormous biological diversity, their utilization as pretraining data has been limited due to challenges in data accessibility, quality filtering and deduplication. Here, we present the Open MetaGenomic (OMG) corpus, a genomic pretraining dataset totalling 3.1T base pairs and 3.3B protein coding sequences, obtained by combining two largest metagenomic dataset repositories (JGI's IMG and EMBL's MGnify). We first document the composition of the dataset and describe the quality filtering steps taken to remove poor quality data. We make the OMG corpus available as a mixed-modality genomic sequence dataset that represents multi-gene encoding genomic sequences with translated amino acids for protein coding sequences, and nucleic acids for intergenic sequences. We train the first mixed-modality genomic language model (gLM2) that leverages genomic context information to learn robust functional representations, as well as coevolutionary signals in protein-protein interfaces and genomic regulatory syntax. Furthermore, we show that deduplication in embedding space can be used to balance the corpus, demonstrating improved performance on downstream tasks. The OMG dataset is publicly hosted on the Hugging Face Hub at https://huggingface.co/datasets/tattabio/OMG and gLM2 is available at https://huggingface.co/tattabio/gLM2_650M.

Primary Area: applications to physical sciences (physics, chemistry, biology, etc.)

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Submission Number: 10586