Non-local modeling of enhancer-promoter interactions, a correspondence on “LOCO-EPI: Leave-one-chromosome-out (LOCO) as a benchmarking paradigm for deep learning based prediction of enhancer-promoter interactions”

Abstract

A recent paper by Tahir et al. (Appl Intell 55:71, 2024) in Applied Intelligence reported a computational model of enhancer promoter interactions without realizing that many of their conclusions were previously published in 2018. In addition to correcting this record, the authors appear to be unaware of an additional body of previous work on enhancer-promoter interactions, which can explain why their computational model performs poorly. We describe how the weak predictive power of their model is consistent with new insights gained from substantial recent progress in the area of detecting and modeling enhancer promoter interactions constrained by DNA looping, extrusion by cohesin, and CTCF.