Genome Sequence Models Need 500bp Jitter to Remove Center Bias

Stanford's Anshul Kundaje shared that 2K-input genome sequence models need around 500bp of jitter to eliminate center-position bias, which otherwise causes variant effect predictions to drift with position, though too much jitter dilutes peak signal strength and reduces negative samples.

2026-10-31 ~ 2026-10-31 · 4 related posts

• Jitter trade-off in sequence models: too large dilutes peak signal — anshulkundaje · 2026-10-31
• 500bp jitter needed to kill center bias in genomic sequence models, says Kundaje — anshulkundaje · 2026-10-31
• Center-biased models shift variant effect predictions by position — anshulkundaje · 2026-10-31
• Genomics ML vet warns center-biased models skew variant effect predictions — anshulkundaje · 2026-10-31