Deep learning in epigenomics and the new Python tool MethylNet

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Deep learning in epigenomics and the new Python tool MethylNet

Deep learning applications in everyday life



The use of deep learning in analyses of DNA methylation data is beginning to emerge and distill non-linear relationships among high-dimensional data features. However, a generalized and user-friendly approach for execution, training, and interpreting models for methylation data is lacking.


We introduce and demonstrate the robust performance of MethylNet on downstream tasks of DNA methylation analysis, including cell-type deconvolution, pan-cancer classification, and subject age prediction. We interrogate the learned features from a pan-cancer classification to show high fidelity clustering of cancer subtypes, and compare the importance assigned to CpGs for the age and cell-type analyses to demonstrate concordance with expected biology.


Our findings demonstrate high accuracy of end-to-end deep learning methods on methylation prediction tasks. Together, our results highlight the promise of future steps to use transfer learning, hyperparameter optimization and feature interpretations on DNA methylation data.

Joshua J. Levy, Alexander J. Titus, Curtis L. Petersen, Youdinghuan Chen, Lucas A. Salas, Brock C. Christensen (2019) MethylNet: A Modular Deep Learning Approach to Methylation Prediction. bioRxiv. [DOI: 10.1101/692665] [PDF].

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