Disentangled methylation dimension reduction
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Description
PCA generates a dense, ~Gaussian feature matrix, which may not play nicely with elastic net. We want to see if we can do better with a less "entangled" or sparser dimension reduction method.
VAEs have been used successfully for methylation data:
* https://www.biorxiv.org/content/10.1101/433763v5.full.pdf
* https://pdfs.semanticscholar.org/64a5/c234078f2facb3916a475c4af63a2ef90b70.pdf
* https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3443-8
Maybe this would work better?
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