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kymata-atlas / kymata-core

Core Kymata codebase, including statistical analysis and plotting tools
https://kymata.org
MIT License
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Doing expression plot is slow for 1000+ functions #354

Open young-x-skyee opened 1 month ago

young-x-skyee commented 1 month ago

When I tried to do expression plot using expression_plot for the activation of whisper large model, I noticed that it is very slow with a large memory use (increased slowly) at the beginning and then high CPU use but low memory use. That was where it got stuck.

young-x-skyee commented 1 month ago

I think the problem is inside the for loop of plotting all the show_only functions at around line 465 in plot.py. The loop is actually pretty quick when I plot ~1280 functions (~200 iterations/sec on average) but when there are ~80000 functions the loop is much much slower (~3 iterations/sec).