Small performance improvement to process_item#395
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…improvements to process
jstjohn
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malcolmgreaves
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Nov 4, 2024
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LGTM but needs changes because of imports. bionemo-testing isn't a main, run-time dependency for bionemo-geneformer. It's a test-time only. To unblock this PR, the load function needs to be moved into bionemo-core and bionemo-testing needs to be refactored to import this so that we don't break backwards compatability.
sub-packages/bionemo-geneformer/src/bionemo/geneformer/data/singlecell/dataset.py
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sub-packages/bionemo-geneformer/src/bionemo/geneformer/data/singlecell/dataset.py
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sichu2023
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LGTM. Can eventually move this profiling to unittest.
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sub-packages/bionemo-geneformer/src/bionemo/geneformer/data/singlecell/dataset.py
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…nglecell/dataset.py Co-authored-by: Malcolm Greaves <malcolmgreaves@users.noreply.github.com> Signed-off-by: John St. John <jstjohn@users.noreply.github.com>
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Summary
Run
python -m bionemo.geneformer.data.singlecell.datasetBaseline:
Processed 31208 rows in 47.10491418838501 seconds
Processed 31208 rows in 47.388004779815674 seconds
After vectorization:
Processed 31208 rows in 44.2215359210968 seconds
Processed 31208 rows in 44.54389500617981 seconds