LOCO-EPI: Leave-one-chromosome-out (LOCO) as a benchmarking paradigm for deep learning based prediction of enhancer-promoter interactions

In mammalian and vertebrate genomes, the promoter regions of the gene and their distal enhancers may be located millions of base-pairs from each other, while a promoter may not interact with the closest enhancer. Since base-pair proximity is not a good indicator of these interactions, there is considerable work toward developing methods for predicting Enhancer-Promoter Interactions (EPI). Several machine learning methods have reported increasingly higher accuracies for predicting EPI. Typically, these approaches randomly split the dataset of Enhancer-Promoter (EP) pairs into training and testing subsets followed by model training. However, the aforementioned random splitting causes information leakage by assigning EP pairs from the same genomic region to both testing and training sets, leading to performance overestimation. In this paper we propose to use a more thorough training and testing paradigm i.e., Leave-one-chromosome-out (LOCO) cross-validation for EPI-prediction. We demonstrate that a deep learning algorithm, which gives higher accuracies when trained and tested on random-splitting setting, drops drastically in performance under LOCO setting, confirming overestimation of performance. We further propose a novel hybrid deep neural network for EPI-prediction that fuses k-mer features of the nucleotide sequence. We show that the hybrid architecture performs significantly better in the LOCO setting, demonstrating it can learn more generalizable aspects of EP interactions. With this paper we are also releasing the LOCO splitting-based EPI dataset. Research data is available in this public repository:this https URL

@article{tahir2025_2504.00306,
  title={ LOCO-EPI: Leave-one-chromosome-out (LOCO) as a benchmarking paradigm for deep learning based prediction of enhancer-promoter interactions },
  author={ Muhammad Tahir and Shehroz S. Khan and James Davie and Soichiro Yamanaka and Ahmed Ashraf },
  journal={arXiv preprint arXiv:2504.00306},
  year={ 2025 }
}