Paper Review - DeepSEA

In which I record my thoughts on DeepSEA.

Terminology #

What is this paper about? #

This paper trains a CNN to predict the presence of 919 “chromatin features”–different TF binding sites, DHSs, and histone marks–from 1000bp DNA sequences. It then tests this model by using a functional significance score based on its output to train a logistic regression classifier to predict whether SNPs will be present in a few different catalog of SNPs known to impact different biological functions, e.g. a GWAS catalog of disease-related SNPs.

Technical Methods #

Why is this important? #

Meta #

This is the clearest of the three papers I’ve read so far, but that may be because I’m slowly internalizing the language of the domain.

Questions #