WIP: Add distance metrics #45
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ctb
reviewed
Sep 23, 2024
ctb
reviewed
Sep 23, 2024
|
see #48 - I added a bit to the tests. Overall this looks great, thank you!! |
…f paranoia thrown in (#48) * test symmetric * Style fixes by Ruff --------- Co-authored-by: ctb <[email protected]>
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This PR will add simple distance metrics for comparing count tables. Starting with Jaccard and Cosine Similarity.
Closes #39
This initial commit adds
cosine()method to calculate cosine similarity between twoKmerCountTables.Have attempted to use Rayon to make hash lookup multithreaded.
@ctb can you check the logic on this + look over the tests?
I've benchmarked against the scipy cosine function (allowing for a 0.001% margin - not sure where the diff is coming from)
In the test
test_cosine_similarity_identical_tables()my function is giving 0.999999999 instead of 1. No idea why this is happening.