The Map Is Not the Territory: PCA, t-SNE, UMAP, Autoencoders and Misleading Embedding Plots

Deep End Era. Engineering with Sankalp · Oct 28, 2026 · 51m

PhD student Mateo finds a perfectly round island of six hundred cells in his single-cell UMAP and thinks it is a new cell type. His supervisor Yuki asks three questions, and within a week the island has turned out to be a pile of stressed, dying cells. Part six of The Deep End's Machine Learning series is about turning many measurements into a few. We find the best shadow of a teapot, compress a photograph twenty-five to one, watch Europe's map emerge from genomes, unroll a Swiss roll, and meet the theorem that says a random projection preserves distances almost for free. Then we sit down…