PEDLA: predicting enhancers with a deep learning-based algorithmic framework

Abstract Transcriptional enhancers are non-coding segments of DNA that play a central role in the spatiotemporal regulation of gene expression programs. However, systematically and precisely predicting enhancers on a genome-wide scale remain a major challenge. Although existing methods have achieved some success in enhancer prediction, they still suffer from a limited number of training samples, a simplicity of features, class-imbalanced data, and inconsistent performance across diverse cell types/tissues. Here, we developed a deep learning-based algorithmic framework named PEDLA (https://github.com/wenjiegroup/PEDLA), which can directly learn an enhancer predictor from massively heterogeneous data and generalize in ways that are mostly consistent across various cell types/tissues. We first trained PEDLA with 1,114-dimensional heterogeneous features in H1 cells, and we demonstrated that our PEDLA framework integrates diverse heterogeneous features and gives state-of-the-art performance relative to…


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