ProkBERT family: genomic language models for microbiome applications

Ligeti Balázs; Szepesi-Nagy István; Bodnár Babett; Ligeti-Nagy Noémi; Juhász János: ProkBERT family: genomic language models for microbiome applications.
FRONTIERS IN MICROBIOLOGY, 14. ISSN 1664-302X (2024)

Szöveg
fmicb-14-1331233.pdf - Megjelent verzió
Download (2MB)

Mű típusa:

Folyóiratcikk

Szerző azonosítók:

Név	ORCID	MTMT szerző azonosító
Ligeti Balázs		10034554
Szepesi-Nagy István		10095542
Bodnár Babett
Ligeti-Nagy Noémi		10062392
Juhász János		10049994

Absztrakt (kivonat):

In the evolving landscape of microbiology and microbiome analysis, the integration of machine learning is crucial for understanding complex microbial interactions, and predicting and recognizing novel functionalities within extensive datasets. However, the effectiveness of these methods in microbiology faces challenges due to the complex and heterogeneous nature of microbial data, further complicated by low signal-to-noise ratios, context-dependency, and a significant shortage of appropriately labeled datasets. This study introduces the ProkBERT model family, a collection of large language models, designed for genomic tasks. It provides a generalizable sequence representation for nucleotide sequences, learned from unlabeled genome data. This approach helps overcome the above-mentioned limitations in the field, thereby improving our understanding of microbial ecosystems and their impact on health and disease.MethodsProkBERT models are based on transfer learning and self-supervised methodologies, enabling them to use the abundant yet complex microbial data effectively. The introduction of the novel Local Context-Aware (LCA) tokenization technique marks a significant advancement, allowing ProkBERT to overcome the contextual limitations of traditional transformer models. This methodology not only retains rich local context but also demonstrates remarkable adaptability across various bioinformatics tasks.ResultsIn practical applications such as promoter prediction and phage identification, the ProkBERT models show superior performance. For promoter prediction tasks, the top-performing model achieved a Matthews Correlation Coefficient (MCC) of 0.74 for E. coli and 0.62 in mixed-species contexts. In phage identification, ProkBERT models consistently outperformed established tools like VirSorter2 and DeepVirFinder, achieving an MCC of 0.85. These results underscore the models' exceptional accuracy and generalizability in both supervised and unsupervised tasks.ConclusionsThe ProkBERT model family is a compact yet powerful tool in the field of microbiology and bioinformatics. Its capacity for rapid, accurate analyses and its adaptability across a spectrum of tasks marks a significant advancement in machine learning applications in microbiology. The models are available on GitHub (https://github.com/nbrg-ppcu/prokbert) and HuggingFace (https://huggingface.co/nerualbioinfo) providing an accessible tool for the community.

Folyóirat címe:

FRONTIERS IN MICROBIOLOGY

Megjelenés éve:

2024

Kötet:

ISSN:

1664-302X

Intézmény:

Pázmány Péter Katolikus Egyetem

Kar:

Információs Technológiai és Bionikai Kar (2013.07.-)

Nyelv: