Refactor SCDL Row Feature Index for Performance Improvement (Rebased) #466
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added 4 commits
November 20, 2024 14:47
…tionaries instead of Pandas dataframes in the feature array
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savitha-eng
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Nov 20, 2024
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…g a np memmap array to users
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savitha-eng
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polinabinder1 and
skothenhill-nv
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…IDIA/bionemo-fw-ea into savitha/scdl-performance-improvements
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Nov 25, 2024
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Summary
We improve performance for looking up features in SCDL's row feature index via the .lookup function.
Details
We modify SCDL's RowFeatureIndex's feature_arr to store dictionaries (structured like: {"feat1_name": np.array(values1), "feat2_name": np.array(values2)} instead of Pandas dataframes. This significantly speeds up the feature lookup when return_features=True and feature_vars is specified in the call to scdl.get_row().
Usage
No changes for user interaction.
Testing
Added and modified unit tests for RowFeatureIndex and SingleCellMemmapDataset.
Tests for these changes can be run via: