CSHL Benchmark Shows Genome Models Still Struggle with Distal Enhancer Prediction

Cold Spring Harbor Laboratory researchers updated their Genomics×AI benchmark using CRISPRi perturbation data in K562 cells, finding AlphaGenome 2 leads only within 100kb of TSS while both it and Cerberus still fail to reliably predict distal enhancers.

2026-11-13 ~ 2026-11-13 · 2 related posts

• Enformer, Borzoi, NTv3, Cerberus & AlphaGenome 2 benchmarked: distal enhancer effects remain unsolved — anshulkundaje · 2026-11-13
• CSHL benchmark: AlphaGenome 2 leads only within ~100kb of TSS on distal enhancer effects — anshulkundaje · 2026-11-13