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Savitha/new profiling experiments#500

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savitha-eng wants to merge 30 commits intomainNVIDIA/bionemo-framework:mainfrom savitha/new-profiling-experimentsNVIDIA/bionemo-framework:savitha/new-profiling-experimentsCopy head branch name to clipboard

+2,100-709

Commits

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

  committed
  08ef851

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

  

  Savitha Srinivasan

  committed
  c9ff683

• Modify Single Cell Memmap Dataset unit tests to reflect changes

  

  Savitha Srinivasan

  committed
  5f86da4

• remove conversion to np.array in get_row for now

  

  Savitha Srinivasan

  committed
  896bad0

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

  committed
  eb17845

Commits on Nov 22, 2024

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

  

  Savitha Srinivasan

  committed
  1663903

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

  savitha-eng

  authored
  0497c98

Commits on Nov 25, 2024

• Made changes requested in review.

  

  Savitha Srinivasan

  committed
  7a43706

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

  

  Savitha Srinivasan

  committed
  da395b4

Commits on Nov 26, 2024

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

  

  Savitha Srinivasan

  committed
  9e11ab8

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

  savitha-eng

  authored
  37de5d1

• Tests for Geneformer SingleCellDataset

  

  Savitha Srinivasan

  committed
  546f84e

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

  

  Savitha Srinivasan

  committed
  0dcc56b

• Data directory fixtures needed for pytest

  

  Savitha Srinivasan

  committed
  9d4c6a4

• Add bypass_tokenize_vocab to the arguments for this script

  

  Savitha Srinivasan

  committed
  eea6b42

Commits on Dec 2, 2024

• Changes to Inference tutorial notebook to support SCDL integrated Geneformer

  

  Savitha Srinivasan

  committed
  e642bc9

• modify dataset dir creation

  

  Savitha Srinivasan

  committed
  d755901

• all scdl integration changes

  

  Savitha Srinivasan

  committed
  507e31b

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

  savitha-eng

  authored
  f6d9380

Commits on Dec 4, 2024

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

  

  Savitha Srinivasan

  committed
  9846894

• Files for profiling

  

  Savitha Srinivasan

  committed
  e36446e

• added function for iterating with dataloader

  

  Savitha Srinivasan

  committed
  e5298bf

Commits on Dec 5, 2024

• Docstrings

  

  Savitha Srinivasan

  committed
  d65de39

• change lengths to 2048

  

  Savitha Srinivasan

  committed
  dc16c71

Commits on Dec 6, 2024

• Add MultiEpochResampler

  

  Savitha Srinivasan

  committed
  b9d188e

Commits on Dec 8, 2024

• profile_explore

  polinabinder1

  committed
  99bf84e

Commits on Dec 10, 2024

• profiling file changes

  

  Savitha Srinivasan

  committed
  2ad8307

• Merge branch 'savitha/new-profiling-experiments' of github.com:NVIDIA/bionemo-fw-ea into savitha/new-profiling-experiments

  

  Savitha Srinivasan

  committed
  9fe9104

• Revert "profile_explore"

  Show description for 6b6394c
  

  Savitha Srinivasan

  committed
  6b6394c

• profiling file

  

  Savitha Srinivasan

  committed
  e9cc2e7