BPNet and Cherimoya excel at correcting open-chromatin confounds, says Kundaje
anshulkundaje · x · 2026-10-31
Responding to a question about whether BATv1 uses GC-matched non-peak negatives, Anshul Kundaje notes that BPNet and Cherimoya models are particularly effective at correcting confounding open-chromatin features that affect many multitask models (Enformer often confounds TF motifs with open-chromatin GC bias). He points to an example in the tangermeme paper comparing BPNet with DeepSEA on MYC.
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