Umap vs tsne single-cell

1. Is UMAP better than t-SNE?
2. Why is UMAP superior over t-SNE?
3. What is better than UMAP?
4. Is UMAP better than PCA?

Is UMAP better than t-SNE?

Thanks to the solution in building the high dimensional graph, UMAP theoretically saves more time and computation cost than t-SNE. It is reported that dimensionality reduction of a dataset from 784-D to 3-D took UMAP only 3 minutes, while it took t-SNE 45!

Why is UMAP superior over t-SNE?

However, the math behind those two is very different. While tSNE is purely for visualization purposes, UMAP is much more than that. For the scRNAseq community, the most important probably is that it is fine to cluster on UMAP components while this is not the case for tSNE.

What is better than UMAP?

Ivis outperforms UMAP at preserving global structure and should be considered for many applications of dimensionality reduction.

Is UMAP better than PCA?

UMAP outperformed t-SNE and PCA, if we look at the 2d and 3d plot, we can see mini-clusters that are being separated well. It is very effective for visualizing clusters or groups of data points and their relative proximities.