Swap-seq Benchmark Finds AlphaGenome-Class Models Miss Distal Silencers
anshulkundaje · x · 2026-10-10
Researchers used Swap-seq to benchmark three DNA sequence models, including AlphaGenome, and found they interpret deletions near promoters well but almost entirely fail to recognize distal regulatory elements, including silencers.
The work highlights that while DNA sequence models could be transformative, they remain hard to evaluate and have significant blind spots in long-range gene regulation.
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