An excerpt from the Epilogue of my PhD thesis. These are the lessons I've learnt, the predictions I have, and the hopes I harbor.
t-SNE is one of the most commonly used methods for dimensionality reduction in RNA-seq analysis, yet few people know how it actually works. Here we'll walk through the original t-SNE paper by van der Maaten and Hinton; looking at the motivation behind it, the mathematics that fuel its power, and how to interpret its hyperparameters.
For this bi-weekly paper review, my choice fell upon a paper that I’ve skimmed through multiple times before, but never gave the proper read-through it deserves. It was a definite given when I started to curate a list of papers that I wanted to include in this series of reviews.
For quite some while now, I’ve carried a slight sensation of guilt within me. Guilt for being so caught up in my own projects and activities that I’ve come to neglect one of the most essential duties as a researcher: to survey, read, and contemplate upon new (and old) material that have been published.