aertslab/arboreto

network = grnboost2(.. takes too long. Something wrong?

franciscogrisanti opened this issue · 3 comments

franciscogrisanti commented

Hi!

I'm trying to run the GRNBoost2 - GRN algorithm on a matrix of shape (11744, 9031) in my cluster of 104GB RAM / Intel(R) Xeon(R) CPU @ 2.30GHz / 16 CPU (s). So far it's running for +20h.

I have a couple of questions:

  1. Should I use the raw expression matrix? Or should I use the log-transformed/normalized expression matrix?

  2. I don't have the list of TF? Can I put all the genes present in the dataset? Or leave it blank?

Thanks in advance for any help!

Best,

Francisco Grisanti

wangjiawen2013 commented

I have the same question. grnboost2 takes too long.

divyanshusrivastava commented

It's 2023 and I have the same question.

tfrudakis commented

I have this problem every time I do a run,. When I try a run on data 2835 cells by 26048 genes it will run for a week before I abandon it (Intel(R) Core(TM) i7-10610U CPU @ 1.80GHz 2.30GHz 64.0GB installed RAM). I always cut the data down with highly_variable genes to about 30M elements (eg. 7K genes if I have 4K cells) to get it to run within a reasonable time frame. I always wonder if I am losing important data when doing that ...