How to run runNMF in parallel?
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p.joshi ▴ 40
@pjoshi-22718
Last seen 22 months ago
Germany

Hi,

I am trying to use the new runNFM() from scater. I have two questions.

First, I am trying to perform first reduce dimension using NMF rather than PCA, just to test it if it better represent the data, which I would obviously plot using UMAP. So, I am trying to get 50 NMF components rather than just. Do you think I am doing something conceptually wrong?

Because I am trying to get 50 NMF components, it is running for very long. So, I tried to use multiple cores. As it uses nmf function, where parallel computations can be specified using .opt = 'p6' or .pbackend= 8, which uses doParallel package, I am still not able to use multiple cores. How can I fix that? I did call registerDoParallel(cl=10). Still no speed up.

Thanks!

Piyush

scater single SingleCellExperiment • 2.5k views
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Aaron Lun ★ 28k
@alun
Last seen 2 hours ago
The city by the bay

I suspect the parallel mode only works when you are requesting multiple runs - each run seems to be assigned to a single core. If you only have one run, it doesn't appear to parallelize _within_ that run.

To illustrate:

library(Biobase)
data(esGolub)
out <- nmf(esGolub, 3, nrun=5, .opt='vp8')
## NMF algorithm: 'brunet'
## Multiple runs: 5
## # NOTE - CRAN check detected: limiting maximum number of cores [2/12]
## Mode: parallel (2/12 core(s))
## Runs: |==================================================| 100%
## System time:
##    user  system elapsed 
##   6.014   0.561   7.831

Running top at the same time indicates that, indeed, multiple R processes have been started up. But if we remove the nrun= argument:

out <- nmf(esGolub, 3, .opt='vp8')
## NMF algorithm: 'brunet'
## NMF seeding method: random
## Iterations:  600/2000 
## DONE (converged at 610/2000 iterations)

Note the lack of any commentary about parallelization in the latter.

Personally, I found NMF (or at least, the implementation in NMF) too slow to serve as a routine dimensionality reduction technique. The main appeal of NMF lies in the interpretability of the factors but that wasn't something I really cared about for my analyses, so I just stuck to PCA. I should mention that scater originally used the NNLM package, which was much faster; unfortunately, that got kicked off CRAN.

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Thanks once again Aaron. The reason I am trying to test NMF is because various papers suggesting using NMF for integrating multimodal data.

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Check out LIGER. It’s a great NMF-based method for integrating multimodal data. It’s also reasonably scalable. Expect a comparable and faster implementation of integrative NMF in the RcppML package in the next month or so.

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Thanks a lot for providing an NMF implementation in scater, Aaron! If you are still interested in a fast (and potentially more reproducible) NMF implementation, perhaps the RcppML R package is worth a look? The authors have a nice preprint illustrating the improvements they made. (Code to reproduce their figures is in the supplements.)

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Seems like it would be a good request/PR for the scater repo.

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Author/maintainer of RcppML here. Please share any feature requests/suggestions that would make RcppML NMF more useful for Bioconductor packages. I’m committed to making this the fastest, most painless, robust, and flexible NMF implementation out there.

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