Article

Nucleotide dependency analysis of DNA language models reveals genomic functional elements

2024-07-27

Abstract excerpt

Deciphering how nucleotides in genomes encode regulatory instructions and molecular machines is a long-standing goal in biology. DNA language models (LMs) implicitly capture functional elements and their organization from genomic sequences alone by modeling probabilities of each nucleotide given its sequence context. However, using DNA LMs for discovering functional genomic elements has been challenging due to the...

Topics

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

Identifiers and source

Literature Corpus work: afad8f25-3631-54ce-9b5a-1012e07de46e
DOI: 10.1101/2024.07.27.605418

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Nucleotide dependency analysis of DNA language models reveals genomic functional elementsDOI 10.1101/2024.07.27.605418Read

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genomeSemantic proximity Read

The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human GenomicsSemantic proximity Read

The Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human GenomicsSemantic proximity Read

GENA-Web - GENomic Annotations Web Inference using DNA language modelsSemantic proximity Read

Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappingsSemantic proximity Read

Context dependency of nucleotide probabilities and variants in human DNASemantic proximity Read

Genomic Touchstone: Benchmarking Genomic Language Models in the Context of the Central DogmaSemantic proximity Read

Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappings.Semantic proximity Read

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

The human genome’s vocabulary as proposed by the DNA language model GROVERSemantic proximity Read

GPN-MSA: an alignment-based DNA language model for genome-wide variant effect predictionSemantic proximity Read

NucEL: Single-Nucleotide ELECTRA-Style Genomic Pre-training for Efficient and Interpretable RepresentationsSemantic proximity Read