Enigma: An Efficient Model for Deciphering Regulatory Genomics

Andrew J Jung, ALICE J. GAO, Vivian Chu, Leo J Lee, Brendan Frey

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Track: long paper (4–8 pages excluding references)

Keywords: sequence-to-function modeling, genomics, regulatory genomics

Abstract: Genomic sequence-to-function models have emerged as powerful tools for deciphering cis-regulatory grammar to advance our understanding of disease biology and guide therapeutic development. Recent advances have been driven by multi-task training of large transformer-based models on thousands of genome tracks. However, these performance gains have come at significant computational cost for both training and inference, hindering large-scale applications and slowing future model development. Here, rather than continuing to scale model size and add more training tracks, we focus on architectural efficiency and train on a substantially smaller, curated set of genome tracks. Our model Enigma achieves competitive performance with current state-of-the-art models at single-base resolution while substantially reducing computational cost. On zero-shot variant effect prediction benchmarks, Enigma outperforms the leading open-source model, the Borzoi ensemble, while using 10.9% of its compute and improving resolution from 32 bases to a single base. Compared to AlphaGenome, Enigma achieves 90.4 - 97.3% of its performance using 7.5% of its estimated compute. These improvements in efficiency can facilitate further development of models for regulatory genomics. We demonstrate this by fine-tuning Enigma on predicting three new molecular phenotypes (ChIP-seq, RNA half-life, and translation efficiency) achieving or exceeding the performance of state-of-the-art task-specific models. We are providing Enigma for non-commercial use to benefit the broader research field.

Anonymization: This submission has been anonymized for double-blind review via the removal of identifying information such as names, affiliations, and identifying URLs.

Submission Number: 67