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It's already quite fast, but memory usage is excessive with more than ~200-300k sequences. @felixpetschko already mentioned that he has some ideas to improve on that.
I also believe that the way how this is parallelized could be optimized adapting the code from here (using joblib.parallel):
The "tcrdist" metric was added by @felixpetschko in #502.
It's already quite fast, but memory usage is excessive with more than ~200-300k sequences. @felixpetschko already mentioned that he has some ideas to improve on that.
I also believe that the way how this is parallelized could be optimized adapting the code from here (using
joblib.parallel
):scirpy/src/scirpy/ir_dist/metrics.py
Lines 225 to 235 in d1db848
There are two main advantages of using
joblib
over themultiprocessing
module:@ShihanL fyi
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