lmcinnes / lmcinnes/umap

UMAP shuffle samples leads to quit different result

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Description

Dear authors,
Thanks for presenting quite usefule UMAP and the nice documention.
I have some samples from cell single and processed them into binary matrix (M,N), where M is the number of cells and N is the number of features. There are different kinds (3) cells in the groups, originally sorted by labels like A_1,A_2,A_3,...B_1,B_2,B_3,...,C_1,C_2,C_3...
I first tried feed the matrix to UMAP with parameters as umap.UMAP(n_neighbors=30,n_components=2,metric="manhattan",random_state=123,n_epochs=500).fit_transform(mat). UMAP indeed works very well, the cells are seperated by into observed 3 groups.
However, by chance, I shuffled the cell orders in the (M,N) matrix, the projection result is total a mess, with the same parameters. So I wonder if there's key parameters to control the UMAP behavior like this.
Thanks very much!
Yaqiang Cao

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Research direction

The report names no repository files or tests; start by reproducing umap.UMAP(...).fit_transform(mat) with the stated parameters on the original and shuffled matrices. Compare the projections and investigate whether row ordering changes the result; done means explaining the discrepancy and identifying whether a parameter or code change is required.

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Assessment

Tech stack
python
Domain
data-visualization, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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