t-SNE(t-distributed stochastic neighbor embedding)

MIA PrimerJoseph Nasser, Yinqing Li

April 13 2016

What is t-SNE?Dimensionality reduction technique specialized for visualization

Example: MNIST

6,000 images28 x 28 = 784 pixels per image

t-SNE

tSNE Sammon Mapping

Isomap Locally Linear Embedding

Dimensionality Reduction in Biology - Gene Expression

Gen

es

Samples

DimensionalityReduction

Samples

PCA

tSNESamples

TCGA (4 cohorts)~1000 samples~20,000 genes

t-SNE: t-Distributed Stochastic Neighbor Embedding

PCA t-SNE

Cancer Cell Line EncyclopediaCCLE (~20 lineages)~1000 Samples~12000 genes

PCA t-SNE

tSNE1

tSN

E2

Biclustering on tSNEidentification of neuronal subtypes

A novel algorithmto score genesby expr pattern