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[ENH] Faster normalization #6202
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pavlin-policar
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biolab:master
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markotoplak:normalize-basic-stats
Nov 21, 2022
Merged
[ENH] Faster normalization #6202
pavlin-policar
merged 6 commits into
biolab:master
from
markotoplak:normalize-basic-stats
Nov 21, 2022
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markotoplak
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Nov 14, 2022
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Related (discovered in or needed) to the Dask adaptation
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Nov 14, 2022
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## master #6202 +/- ##
==========================================
- Coverage 86.66% 86.66% -0.01%
==========================================
Files 316 316
Lines 68021 68027 +6
==========================================
+ Hits 58951 58955 +4
- Misses 9070 9072 +2 |
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[ENH] Faster normalization
[NOMERGE][ENH] Faster normalization
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This one works for dask tables
Use the same argument names as in Table. Fixes a test that started failing after using basic stats for normalization.
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[NOMERGE][ENH] Faster normalization
[ENH] Faster normalization
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Looks good to me. |
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Issue
Fixes #5219
Description of changes
The computation of distributions is slow (it works through contingencies and requires sorting).
This slowdown was especially problematic for dask tables.
The new code does not currently support weights! Supporting them would require making a weighted variance computation. Should we go there?Done in #6205.Requires #6204 and #6205.
Testing performance on 1000x1000 tables.
Before:
After:
The mean/variance estimation part is 3x faster. Of course, this PR has no influence on the actual transformation (the domain contains the same variables).
Includes