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Use scikit-learn for LDAModel #607

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merged 20 commits into from
Jan 6, 2022
Merged

Use scikit-learn for LDAModel #607

merged 20 commits into from
Jan 6, 2022

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@tsalo tsalo commented Nov 13, 2021 •
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Closes #606.

Changes proposed in this pull request:

  • Create Python-only LDAModel using scikit-learn.
  • Add executable example showing how to use the new LDAModel.

@tsalo tsalo added documentation Improving documentation for the project annotate Issues related to the annotate module labels Nov 13, 2021
@tsalo tsalo marked this pull request as draft November 13, 2021 16:45
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codecov bot commented Nov 13, 2021 •
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Codecov Report

Merging #607 (1435bc6) into main (46e4e50) will increase coverage by 1.62%.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #607      +/-   ##
==========================================
+ Coverage   85.91%   87.54%   +1.62%     
==========================================
  Files          40       40              
  Lines        4402     4318      -84     
==========================================
- Hits         3782     3780       -2     
+ Misses        620      538      -82
Impacted Files Coverage Δ
nimare/extract/__init__.py 100.00% <ø> (ø)
nimare/extract/extract.py 55.42% <ø> (+3.94%) ⬆️
nimare/utils.py 95.49% <ø> (+0.09%) ⬆️
nimare/annotate/lda.py 100.00% <100.00%> (+76.25%) ⬆️

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@tsalo tsalo changed the title [ENH] Replace MALLET-based LDAModel with example using scikit-learn [ENH] Replace MALLET-based LDAModel with one using scikit-learn Dec 8, 2021
@tsalo tsalo changed the title [ENH] Replace MALLET-based LDAModel with one using scikit-learn [ENH] Use scikit-learn for LDAModel and add Annotator base class Dec 8, 2021
@tsalo tsalo marked this pull request as ready for review December 8, 2021 18:20
This was referenced Dec 10, 2021
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@tsalo tsalo changed the title [ENH] Use scikit-learn for LDAModel and add Annotator base class Use scikit-learn for LDAModel and add Annotator base class Dec 14, 2021
@tsalo tsalo mentioned this pull request Dec 14, 2021
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tsalo added 2 commits December 14, 2021 13:53
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Merge branch 'main' into python-lda
c1c3550
@tsalo
Remove Annotator class.
075a5f0 
The Annotator and Annotation classes will be developed in neurostuff#618.
@tsalo tsalo changed the title Use scikit-learn for LDAModel and add Annotator base class Use scikit-learn for LDAModel Dec 16, 2021
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tsalo commented Jan 6, 2022

I'm going to move forward with this and release 0.0.11 for the sake of the Jupyter Book, although we will definitely be overhauling annotations with #617, #488, and #218.

@tsalo tsalo mentioned this pull request Jan 6, 2022
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@tsalo tsalo merged commit 7e094f2 into neurostuff:main Jan 6, 2022
@tsalo tsalo deleted the python-lda branch January 6, 2022 21:31
@tsalo tsalo added the breaking-change PRs that change results or interfaces. label Jan 6, 2022
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Look into lda library or sklearn as alternative to MALLET
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