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@scottgigante-immunai
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@scottgigante-immunai scottgigante-immunai commented Jan 5, 2023

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@lazappi lazappi left a comment

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Looks pretty good to me. Comments are mostly about documentation except for the one about resetting the normalisation.

openproblems/tasks/dimensionality_reduction/README.md Outdated Show resolved Hide resolved
openproblems/tasks/dimensionality_reduction/README.md Outdated Show resolved Hide resolved
@lazappi lazappi mentioned this pull request Jan 9, 2023
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@lazappi can you please re-review to unblock? Thanks!

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codecov bot commented Jan 10, 2023

Codecov Report

Base: 94.78% // Head: 94.86% // Increases project coverage by +0.07% 🎉

Coverage data is based on head (8570c56) compared to base (3d8964a).
Patch coverage: 98.85% of modified lines in pull request are covered.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #768      +/-   ##
==========================================
+ Coverage   94.78%   94.86%   +0.07%     
==========================================
  Files         155      154       -1     
  Lines        4163     4226      +63     
  Branches      215      220       +5     
==========================================
+ Hits         3946     4009      +63     
  Misses        142      142              
  Partials       75       75              
Flag Coverage Δ
unittests 94.86% <98.85%> (+0.07%) ⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files Coverage Δ
...oblems/data/Wagner_2018_zebrafish_embryo_CRISPR.py 0.00% <ø> (ø)
openproblems/data/multimodal/citeseq.py 100.00% <ø> (ø)
openproblems/data/tabula_muris_senis.py 83.11% <ø> (ø)
...ration/batch_integration_embed/metrics/cc_score.py 100.00% <ø> (ø)
...n/batch_integration_embed/metrics/iso_label_sil.py 100.00% <ø> (ø)
...ntegration/batch_integration_embed/metrics/kBET.py 100.00% <ø> (ø)
...integration/batch_integration_embed/metrics/pcr.py 100.00% <ø> (ø)
...ation/batch_integration_embed/metrics/sil_batch.py 100.00% <ø> (ø)
...tion/batch_integration_embed/metrics/silhouette.py 100.00% <ø> (ø)
...tion/batch_integration_feature/methods/baseline.py 100.00% <ø> (ø)
... and 83 more

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@scottgigante-immunai scottgigante-immunai merged commit 14d70b3 into openproblems-bio:main Jan 10, 2023
@scottgigante-immunai scottgigante-immunai deleted the dimensionality_reduction/prenormalize branch January 10, 2023 09:00
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[Dimensionality reduction] Metrics implicitly prefer specific normalizations

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