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Jacob West-Roberts

dblp:404/6533 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2025
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 2 heaviest of 3, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › sequence analysis
DNA language model
0.912025
The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling · ICLR 2025
Bioinformatics and computational biology › protein analysis › protein bioinformatics
protein representation learning
0.312025
The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling · ICLR 2025

Methods — techniques the papers use, named apart from their topics

genomic language model · 0.9embedding-space deduplication · 0.9
YearPublicationVenuePosition
2025 The OMG dataset: An Open MetaGenomic corpus for mixed-modality genomic language modeling
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.
Andre Cornman, Jacob West-Roberts, Antonio Pedro Camargo, Simon Roux, Martin Beracochea, Milot Mirdita, Yunha Hwang
ICLR2