Article

1 CodonBERT and ESM-2 Embedding Spaces Share an Evolutionarily Con-served Paired Geometry Encoding Synonymous Codon Information

2026-07-03

Abstract excerpt

1.1 Synonymous codons encode the same amino acid yet are used non-randomly across genomes, a phenomenon with well-documented functional consequences for translation efficiency and mRNA stability. Whether the information embedded in synonymous codon choice is recoverable from the internal representations of in-dependently trained deep learning models—one operating on coding DNA sequences (CDS) and the other on prot...

Topics

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

Identifiers and source

Literature Corpus work: bb84f39d-b690-5989-b981-224da9970caa
DOI: 10.64898/2026.06.30.735115

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

1 CodonBERT and ESM-2 Embedding Spaces Share an Evolutionarily Con-served Paired Geometry Encoding Synonymous Codon InformationDOI 10.64898/2026.06.30.735115Read

A Suite of Foundation Models Captures the Contextual Interplay Between CodonsSemantic proximity Read

Embeddings from protein language models predict conservation and variant effectsSemantic proximity Read

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

Third-nucleotide codon bias and synonymous codon bias define functional translational programs that shape human tissue and cancer proteomesSemantic proximity Read

MINA: linear probes reveal coding-sequence family signal in frozen DNA encoders up to protein compositionSemantic proximity Read

Covary: A translation-aware framework for alignment-free phylogenetics using machine learningSemantic proximity Read

BioGraphX-RNA: A Universal Physicochemical Graph Encoding for Interpretable RNA Subcellular Localization PredictionSemantic proximity Read

Findings from Sparse Autoencoders for DNA Sequence Models: Motif Detectors, Reading-Frame Features, and the Scarcity of Regulatory LogicSemantic proximity Read

vir2vec: A Viral Genome-Wide Viral EmbeddingSemantic proximity Read

Geometric Representations of Knowledge Inside Biological Large Language Models: an Empirical AnalysisSemantic proximity Read

Quantifying uncertainty in Protein Representations Across Models and TaskSemantic proximity Read

Position-dependent Codon Usage Bias in the Human TranscriptomeSemantic proximity Read