Function to compute Dice coefficients of bitarray pairs #567
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…pairs of bitarrays
cleanup PR
Codecov Report
Additional details and impacted files@@ Coverage Diff @@
## main #567 +/- ##
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+ Coverage 94.19% 94.28% +0.09%
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Files 16 16
Lines 792 805 +13
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+ Hits 746 759 +13
Misses 46 46 |
wilko77
approved these changes
Apr 30, 2023
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Anonlink's similarity functions currently compare every possible candidate pair via a cartesian product, and works really well with a fairly large number of encodings. With very fine grained blocking such as p-sig you may have many small blocks. Anonlink doesn't do to well with this as we optimized the comparison function for high throughput with large batches - not for low latency with tiny batches.
To get higher throughput it is tempting to merge together a bunch of these small blocks before calling anonlink - however this approach adds candidate pairs that were not explicitly in the blocking rules - skewing results and performing unnecessary work.
This PR adds a function in
anonlink.similaritiesto compute the Dice coefficient on pairs of bitarrays. If useful we could also implement an accelerated version.