multiprocessing and faster matrix operations#17
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anders-w-rasmussen wants to merge 3 commits intopinellolab:mainfrom
Open
multiprocessing and faster matrix operations#17anders-w-rasmussen wants to merge 3 commits intopinellolab:mainfrom
anders-w-rasmussen wants to merge 3 commits intopinellolab:mainfrom
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Re-implemented the compute_deviations function with multiprocessing with X (fragment counts) in shared memory. Also changed some of the matrix operations.
I looked at the original chromVAR paper so math might be slightly different.
Correlation with original implementation seems good (~0.99 on example data). I time with n_jobs=1 it is 2-3X faster and with n_jobs=5 it is 9X faster.
(this version doesn't use compute_expectation which fails existing test)