McInnes et alia: UMAP and HDBSCAN - Githubissues

reconstrue / single_cell

Single cell analysis tools built to run on Jupyter, especially Colab

http://reconstrue.com

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McInnes et alia: UMAP and HDBSCAN #12

Open JohnTigue opened 4 years ago

JohnTigue commented 4 years ago

See also #28 (comparing clusters to Allen cell types)

Nature Biotech paper (2018): Dimensionality reduction for visualizing single-cell data using UMAP)
his tSNE juxt UMAP (2018) talk
Notice end of page: UMAP and HDBSCAN
HDBSCAN perf
Accelerated Hierarchical Density Clustering McInnes & Healy

JohnTigue commented 4 years ago

HDBSCAN

McInnes PCA(50) => HDBSCAN

JohnTigue commented 4 years ago

UMAP => hdbscan

UMAP for clustering

This sounds like it could scale rather well:Impact of cancer mutational signatures on transcription factor motifs in the human genome

We first used the UMAP dimensionality reduction method on the table of exposure values of the 2708 samples, and then defined clusters using the hdbscan method, as implemented in the largeVis R-package.

JohnTigue commented 4 years ago

How to filter outliers to train a model on cleaner data?

How about tune UMAP to accentuate outliers. The HDBSCAN cluster. The take only the clustered nodes and run them through UMAP.

https://youtu.be/DinhTHoDRjk?t=1038