Frozen but Not Always Accessible: A Representation Analysis of Genomic Language Models

Genomic foundation models are increasingly reused as frozen feature extractors for downstream sequence prediction, offering a compute-efficient alternative to full fine-tuning. However, it remains unclear when biological information encoded by these models is accessible without task-specific adaptation. We present a representation-accessibility analysis of frozen genomic language models across regulatory, epigenetic, promoter, splice-site, and variant-effect prediction tasks. We evaluate DNABERT-2, Nucleotide Transformer, HyenaDNA, GENERATOR-v2, and Omni-DNA under unified frozen-probing protocols, while separating diagnostic readout analyses from validation-selected checks. Our results reveal a consistent task-dependent pattern: frozen probes recover 95-100 % of fine-tuned performance on promoter tasks, but average splice-site recovery drops to 60-88 %. Frozen embeddings are also competitive on broad Genomic Benchmark tasks such as coding-region and species-discrimination classification, but show larger gaps on some regulatory and OCR tasks. Layer-wise probing, in-silico mutagenesis, variant-effect prediction, and embedding geometry show that local biological signal is partially present in frozen representations, but is not always accessible through final pooled embeddings.

Source: arXiv:2608.05329v1 - http://arxiv.org/abs/2608.05329v1 PDF: https://arxiv.org/pdf/2608.05329v1 Original Link: http://arxiv.org/abs/2608.05329v1