Deciphering how DNA sequence encodes gene regulation remains a central challenge in biology. Advances in machine learning and functional genomics have enabled sequence-to-function (seq2func)...

The rise of large-scale, sequence-based deep neural networks (DNNs) for predicting gene expression has introduced challenges in their evaluation and interpretation. Current evaluations align DNN...

Deep convolutional neural networks (CNNs) trained on regulatory genomic sequences tend to learn distributed feature representations across many filters, making it challenging to decipher biologically...