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YuLab-SMU / GOSemSim

:golf: GO-terms Semantic Similarity Measures
https://yulab-smu.top/biomedical-knowledge-mining-book/
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Running calculations in parallel #31

Open y1zhou opened 4 years ago

y1zhou commented 4 years ago

Is it possible to replace the sapply and apply's in the code with BiocParallel::bplapply? For example mclusterSim becomes really slow when the number of clusters / the size of the clusters gets large. Thanks for the good work!

dkainer commented 3 years ago

i had the same issue with mgeneSim for a large number of genes. I modified it with a parallelised outer for-loop using foreach and found that for thousands of genes it kept the run-time down considerably.

I think there are a lot of points in the GOSemSim code that could benefit from simple parallelising.

estayless commented 3 years ago

@dkainer Could you share your solution for mgeneSim please? I am trying to improve the same function.