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[ENH] PCA: Remove SVD & add normalization for sparse #3581

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merged 2 commits into from
Feb 15, 2019

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pavlin-policar
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Based on #3573, needed so zero-centering can be skipped.

Until recently, PCA didn't support sparse data, so SVD was used instead in the PCA widget. However, PCA now fully supports sparse data, so SVD is no longer necessary.

Description of changes
  • Remove SVD from the PCA widget
  • Add option to normalize sparse data
Includes
  • Code changes
  • Tests
  • Documentation

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codecov bot commented Feb 4, 2019

Codecov Report

Merging #3581 into master will increase coverage by 0.02%.
The diff coverage is 98.6%.

@@            Coverage Diff            @@
##           master   #3581      +/-   ##
=========================================
+ Coverage   83.97%     84%   +0.02%     
=========================================
  Files         370     370              
  Lines       66976   67042      +66     
=========================================
+ Hits        56246   56318      +72     
+ Misses      10730   10724       -6

@codecov
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codecov bot commented Feb 4, 2019

Codecov Report

Merging #3581 into master will increase coverage by 0.01%.
The diff coverage is 100%.

@@            Coverage Diff            @@
##           master   #3581      +/-   ##
=========================================
+ Coverage   83.98%     84%   +0.01%     
=========================================
  Files         370     370              
  Lines       67139   67157      +18     
=========================================
+ Hits        56386   56412      +26     
+ Misses      10753   10745       -8

@pavlin-policar pavlin-policar force-pushed the pca-improvements branch 3 times, most recently from 2db6d91 to 177855c Compare February 11, 2019 12:23
@pavlin-policar pavlin-policar force-pushed the pca-improvements branch 3 times, most recently from a273118 to cf1746e Compare February 15, 2019 10:48
@janezd janezd merged commit 4bd1fba into biolab:master Feb 15, 2019
@pavlin-policar pavlin-policar deleted the pca-improvements branch February 15, 2019 14:06
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2 participants