AUTHOR=Ding Ke , Dixit Gunjan , Parker Brian J. , Wen Jiayu TITLE=CRMnet: A deep learning model for predicting gene expression from large regulatory sequence datasets JOURNAL=Frontiers in Big Data VOLUME=6 YEAR=2023 URL=https://www.frontiersin.org/journals/big-data/articles/10.3389/fdata.2023.1113402 DOI=10.3389/fdata.2023.1113402 ISSN=2624-909X ABSTRACT=

Recent large datasets measuring the gene expression of millions of possible gene promoter sequences provide a resource to design and train optimized deep neural network architectures to predict expression from sequences. High predictive performance due to the modeling of dependencies within and between regulatory sequences is an enabler for biological discoveries in gene regulation through model interpretation techniques. To understand the regulatory code that delineates gene expression, we have designed a novel deep-learning model (CRMnet) to predict gene expression in Saccharomyces cerevisiae. Our model outperforms the current benchmark models and achieves a Pearson correlation coefficient of 0.971 and a mean squared error of 3.200. Interpretation of informative genomic regions determined from model saliency maps, and overlapping the saliency maps with known yeast motifs, supports that our model can successfully locate the binding sites of transcription factors that actively modulate gene expression. We compare our model's training times on a large compute cluster with GPUs and Google TPUs to indicate practical training times on similar datasets.