arXiv:2606.04525v1 Announce Type: cross Abstract: Progress in genomic foundation models is difficult to assess due to fragmented benchmarks, incompatible evaluation protocols, and task-specific reporting. As a result, claims of superiority or generality across models are often not directly comparable. We introduce GENEB, a large-scale diagnostic benchmark that evaluates frozen representations from 40 genomic foundation models across 100 tasks spanning 13 functional categories under a unified probing-based protocol, including few-shot regimes. GENEB enables controlled comparison across model sc
The proliferation of genomic foundation models necessitates robust benchmarking to ensure valid comparisons and advancements, as current evaluation methods are fragmented.
A unified benchmark like GENEB will accelerate progress in synthetic biology by providing clear metrics for model performance, reducing wasted effort on incompatible evaluations.
The ability to accurately compare and assess genomic foundation models under standardized conditions will lead to more efficient development and deployment of these technologies.
- · Synthetic Biology Researchers
- · Pharmaceutical Companies
- · Biotech Startups
- · AI Model Developers
- · Researchers using fragmented benchmarks
- · Models with exaggerated claims
- · Incompatible evaluation protocols
GENEB establishes a standardized evaluation framework for genomic foundation models.
This standardization will accelerate model innovation and practical applications in drug discovery and personalized medicine.
Improved genomic models could lead to breakthroughs in disease prevention, gene editing, and bio-manufacturing, fundamentally altering healthcare and industrial processes.
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Read at arXiv cs.LG