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Neurips2021/joint embedding migration#61

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KaiWaldrant wants to merge 46 commits intomainopenproblems-bio/openproblems-v2:mainfrom neurips2021/joint_embeddingopenproblems-bio/openproblems-v2:neurips2021/joint_embeddingCopy head branch name to clipboard

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Commits

Commits on Dec 14, 2022

• add mask_dataset

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  committed
  0db12b5

• debug mask_dataset test

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  bc99112

• add masked anddata api

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  262a1ed

• add random_embed negative control

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  3f367e1

• update control_method api

  KaiWaldrant

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  861072e

Commits on Dec 15, 2022

• add zeros_embed control

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  8749e2a

• add lmds method

  KaiWaldrant

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  7c89329

• add mnn method

  KaiWaldrant

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  0d29dd0

• add newwave method

  KaiWaldrant

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  3c46c4d

• add pca method

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  4ddb315

Commits on Dec 16, 2022

• Add totalVI method

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  3ae1855

• add umap method

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  87f84cb

• add metric ari

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  7cc07bf

• update comp_metric

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  caff25d

• update ari metric

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  f7e0e0b

• add asw_batch metric

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  22c7f46

• add asw_label metric

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  d7e03de

• add cc_cons metric

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  1b47472

Commits on Jan 4, 2023

• remove DI docker because of old anndata package

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  ea82ca5

• add check_format metric

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  16ce776

• add graph connectivity metric

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  4bce62c

• add latent mixing metric

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  bdbdbfd

• add nmi metric

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  5457a6c

• add rfoob metric

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  6d50fc4

• add ti_cons metric

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  82ae20e

• add ti_cons_batch metric

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  acfb631

Commits on Jan 5, 2023

• add metric unit test

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  71ae0e9

• add task_info.yaml

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  ed38c11

Commits on Jan 6, 2023

• Merge remote-tracking branch 'origin/main' into neurips2021/joint_embedding

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  88419ae

• create NF workflow

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  b6d5bbd

• update changelog

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  99b0524

• update changelog

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  c8ae601

• fix typo in changelog

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  10f75d4

• fix typo in changelog

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  e0aef20

Commits on Jan 9, 2023

• convert sparse matrix to array

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  8327637

• use denormalized counts data

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  1b2dd90

Commits on Jan 13, 2023

• fix directive labels

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  a8895dc

• update configs to align with v1 metadata

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  a849f0b

• add readme

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  399a316

• update readme

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  be3e175

Commits on Jan 16, 2023

• Merge remote-tracking branch 'origin/main' into neurips2021/joint_embedding

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  4d749cd

Commits on Jan 24, 2023

• Merge remote-tracking branch 'origin/main' into neurips2021/joint_embedding

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  78c0db7

• update task info and readme

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  0bce137

• update comp_metric

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  e7abed3

Commits on Jan 25, 2023

• resolve personal comments

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  f781da5

• Merge remote-tracking branch 'origin/main' into neurips2021/joint_embedding

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  committed
  9381228