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edward130603 / BayesSpace

Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.
http://edward130603.github.io/BayesSpace
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enhance gene expression of enhanced clusters taking too long to run #109

Open joachimsiaw opened 1 year ago

joachimsiaw commented 1 year ago

Hi. Thank you for the wonderful tool you have developed. I was trying to generate enhanced gene expression profile for my enhanced spatial clusters. I wanted to run the enhanced gene expression algorithm on about 14000 genes. This process was running for almost 2 weeks until i stopped it. I ran this with slurm using 100 cores. Do you have any suggestion on how i can speed up this process?? Or is this expected for the number of genes i wanted to analyze?

Thank you

edward130603 commented 1 year ago

Hi there. A couple of solutions.

  1. Try using a smaller number of genes that you are interested in.
  2. Use the lm method instead of xgboost.
  3. Set the nrounds parameter for xgboost.

FYI @senbaikang, if you have time in the future, this is another function that can be parallelized for great performance increases.

senbaikang commented 1 year ago

Sure, I will have a look when I get free.