English

Improving Genomic Models via Task-Specific Self-Pretraining

Genomics 2025-06-24 v1

Abstract

Pretraining DNA language models (DNALMs) on the full human genome is resource-intensive, yet often considered necessary for strong downstream performance. Inspired by recent findings in NLP and long-context modeling, we explore an alternative: self-pretraining on task-specific, unlabeled data. Using the BEND benchmark, we show that DNALMs trained with self-pretraining match or exceed the performance of models trained from scratch under identical compute. While genome-scale pretraining may still offer higher absolute performance, task-specific self-pretraining provides a practical and compute-efficient strategy for building stronger supervised baselines.

Keywords

Cite

@article{arxiv.2506.17766,
  title  = {Improving Genomic Models via Task-Specific Self-Pretraining},
  author = {Sohan Mupparapu and Parameswari Krishnamurthy and Ratish Puduppully},
  journal= {arXiv preprint arXiv:2506.17766},
  year   = {2025}
}

Comments

4 pages

R2 v1 2026-07-01T03:27:56.445Z