Article

PathoLM: Identifying pathogenicity from the DNA sequence through the Genome Foundation Model

2024-06-22

Abstract excerpt

Pathogen identification is pivotal in diagnosing, treating, and preventing diseases, crucial for controlling infections and safeguarding public health. Traditional alignment-based methods, though widely used, are computationally intense and reliant on extensive reference databases, often failing to detect novel pathogens due to their low sensitivity and specificity. Similarly, conventional machine learning techniq...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 2e11ea7d-a230-52f9-b161-bc8fa85a69f0
DOI: 10.1101/2024.06.18.599629

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

PathoLM: Identifying pathogenicity from the DNA sequence through the Genome Foundation ModelDOI 10.1101/2024.06.18.599629Read

DeePaC: Predicting pathogenic potential of novel DNA with a universal framework for reverse-complement neural networksSemantic proximity Read

Detecting DNA of novel fungal pathogens using ResNets and a curated fungi-hosts data collectionSemantic proximity Read

Deep learning-based real-time detection of novel pathogens during sequencingSemantic proximity Read

Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models, with PathogenFinder2Semantic proximity Read

HViLM: A Foundation Model for Viral Genomics Enables Multi-Task Prediction of Pathogenicity, Transmissibility, and Host TropismSemantic proximity Read

Illuminating the Virosphere’s Dark Matter using Hierarchical Deep LearningSemantic proximity Read

GPAS: an online AI system for rapid and accurate pathogen identification and LLM-based interpretationSemantic proximity Read

LAMBDA: A Prophage Detection Benchmark for Genomic Language ModelsSemantic proximity Read

PaPrBaG: A random forest approach for the detection of novel pathogens from NGS dataSemantic proximity Read

HAVEN: Hierarchical Attention for Viral protEin-based host iNferenceSemantic proximity Read

ProkBERT PhaStyle: Accurate Phage Lifestyle Prediction with Pretrained Genomic Language ModelsSemantic proximity Read

Euktect: Enhanced Eukaryotic Sequence Detection and Classification in Metagenomes via the DNA Language ModelSemantic proximity Read