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single Numpy array option#503

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polinabinder1 wants to merge 36 commits intomainNVIDIA/bionemo-framework:mainfrom polinabinder/geneformer_modsNVIDIA/bionemo-framework:polinabinder/geneformer_modsCopy head branch name to clipboard

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Commits on Nov 20, 2024

• Change RowFeatureIndex and RowFeatureIndex tests to use a list of dictionaries instead of Pandas dataframes in the feature array

  

  Savitha Srinivasan

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• Update load_h5ad to append features in dict format to to the row feature index

  

  Savitha Srinivasan

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• Modify Single Cell Memmap Dataset unit tests to reflect changes

  

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• remove conversion to np.array in get_row for now

  

  Savitha Srinivasan

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Commits on Nov 21, 2024

• Convert values and col indices to np array so that we're not returning a np memmap array to users

  

  Savitha Srinivasan

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Commits on Nov 22, 2024

• Revert conversion to np array, and refactor num_vars_at_row to use internal state

  

  Savitha Srinivasan

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• Merge branch 'main' into savitha/scdl-performance-improvements

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Commits on Nov 25, 2024

• Made changes requested in review.

  

  Savitha Srinivasan

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• Merge branch 'savitha/scdl-performance-improvements' of github.com:NVIDIA/bionemo-fw-ea into savitha/scdl-performance-improvements

  

  Savitha Srinivasan

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Commits on Nov 26, 2024

• Integrate SCDL into Geneformer, rebased on the latest changes in main

  

  Savitha Srinivasan

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• Merge branch 'main' into savitha/integrate-scdl-geneformer-rebased

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• Tests for Geneformer SingleCellDataset

  

  Savitha Srinivasan

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• Merge branch 'savitha/integrate-scdl-geneformer-rebased' of github.com:NVIDIA/bionemo-fw-ea into savitha/integrate-scdl-geneformer-rebased

  

  Savitha Srinivasan

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• Data directory fixtures needed for pytest

  

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• Add bypass_tokenize_vocab to the arguments for this script

  

  Savitha Srinivasan

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Commits on Dec 2, 2024

• Changes to Inference tutorial notebook to support SCDL integrated Geneformer

  

  Savitha Srinivasan

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• modify dataset dir creation

  

  Savitha Srinivasan

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• all scdl integration changes

  

  Savitha Srinivasan

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• Merge branch 'main' into savitha/integrate-scdl-geneformer-rebased

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Commits on Dec 4, 2024

• Updated documentation, removed refs to sc_memmap, & made changes requested in review

  

  Savitha Srinivasan

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• Merge branch 'main' into savitha/integrate-scdl-geneformer-rebased

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Commits on Dec 5, 2024

• single array

  polinabinder1

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• better fix

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• remove notebook for tests

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• more correct

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• string formatting

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• Merge branch 'main' into savitha/integrate-scdl-geneformer-rebased

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• wandb version

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• Merge branch 'savitha/integrate-scdl-geneformer-rebased' into polinabinder/geneformer_mods

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• not using row feature index

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• subclasses

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Commits on Dec 6, 2024

• adding the length caching more

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• cast as int

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Commits on Dec 9, 2024

• profiling

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Commits on Dec 10, 2024

• full loading

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• whole dataset

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