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openproblems-bio / openproblems

Formalizing and benchmarking open problems in single-cell genomics
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[Dimensionality reduction] denSNE #250

Closed bendemeo closed 1 day ago

bendemeo commented 3 years ago

What is the method? denSNE (and the related densMAP, separate issue) address the issue of density preservation in two-dimensional visualization. While t-SNE assigns larger populations a greater area in the projection, denSNE aims to assign area based not on population size but on the amount of space it takes up in the input multi-dimensional space. denSNE is published here.

Where is the code located? https://github.com/hhcho/densvis

Which task(s) could it be used for? Dimensionality reduction, label projection

dkobak commented 3 years ago

+1 but this should go hand-in-hand with a metric that assesses how well the density is preserved in the embedding. This can be taken directly from the denSNE paper -- Eq (10) in https://www.nature.com/articles/s41587-020-00801-7.

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