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Add Method SCOT to Multi-modal data Integration Task #298

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merged 7 commits into from
Apr 5, 2021

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atong01
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@atong01 atong01 commented Mar 31, 2021

This PR adds the Single-cell Optimal Transport method to the multimodal integration task.

Some potential questions:

  • I have a long URL link that fails our flake8 test, this is useful for documenting where these parameters came from.
  • There are a number of options on exactly what to compare existing methods use two normalization schemes, for SCOT I included both of these as well as the balanced option, which is quite important (as it represents separate but important variants of the Gromov-Wasserstein distance).
  • SCOT is not well packaged, therefore I had to do my own packaging and so we currently install SCOT via my forked repository. I have submitted a PR on the SCOT GitHub, if this is merged up there it should be a quick fix. Not sure how we want to support these not quite fully packaged methods in the future.

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  • This submission adds a new dataset
  • This submission adds a new method
  • This submission adds a new metric
  • This submission adds a new task
  • This submission adds a new Docker image
  • This submission fixes a bug (link to related issue: )
  • This submission adds a new feature not listed above

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  • This submission was written on a forked copy of SingleCellOpenProblems
  • GitHub Actions "Run Benchmark" tests are passing on this base branch of this pull request (include link to passed test: Link to Passing Test )
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Looks good to me. Matches the API and is fully metadata annotated.

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atong01 commented Mar 31, 2021

I broke some strings into multiline strings and added a #noqa tag so flake will ignore this long url, so pre-commit should pass now.

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LuckyMD commented Mar 31, 2021

let's wait for tests and then merge.

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Codecov Report

Merging #298 (fa51089) into master (e4c009f) will decrease coverage by 2.43%.
The diff coverage is 0.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #298      +/-   ##
==========================================
- Coverage   91.67%   89.23%   -2.44%     
==========================================
  Files          70       71       +1     
  Lines        1465     1505      +40     
  Branches       89       89              
==========================================
  Hits         1343     1343              
- Misses         94      134      +40     
  Partials       28       28              
Flag Coverage Δ
unittests 89.23% <0.00%> (-2.44%) ⬇️

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Impacted Files Coverage Δ
.../tasks/multimodal_data_integration/methods/scot.py 0.00% <0.00%> (ø)

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@dburkhardt dburkhardt merged commit 0068ba0 into openproblems-bio:master Apr 5, 2021
lazappi added a commit to lazappi/openproblems that referenced this pull request Apr 16, 2021
* master:
  fix region
  fix nf wkdir
  use env.BRANCH
  rm echo
  BRANCH -> WKDIR for s3
  set branch variable in S3 setup job
  Fix s3 bucket clash
  Dimred methods preprocessing (openproblems-bio#301)
  Add trustworthiness score for dimred task (openproblems-bio#258)
  Add Method SCOT to Multi-modal data Integration Task (openproblems-bio#298)
  Update README.md
  Update README.md
  Update README.md
lazappi added a commit to lazappi/openproblems that referenced this pull request Apr 16, 2021
* master:
  fix region
  fix nf wkdir
  use env.BRANCH
  rm echo
  BRANCH -> WKDIR for s3
  set branch variable in S3 setup job
  Fix s3 bucket clash
  Dimred methods preprocessing (openproblems-bio#301)
  Add trustworthiness score for dimred task (openproblems-bio#258)
  Add Method SCOT to Multi-modal data Integration Task (openproblems-bio#298)
  Update README.md
  Update README.md
  Update README.md
lazappi added a commit to lazappi/openproblems that referenced this pull request Apr 16, 2021
* master:
  fix region
  fix nf wkdir
  use env.BRANCH
  rm echo
  BRANCH -> WKDIR for s3
  set branch variable in S3 setup job
  Fix s3 bucket clash
  Dimred methods preprocessing (openproblems-bio#301)
  Add trustworthiness score for dimred task (openproblems-bio#258)
  Add Method SCOT to Multi-modal data Integration Task (openproblems-bio#298)
  Update README.md
  Update README.md
  Update README.md
lazappi added a commit to lazappi/openproblems that referenced this pull request May 12, 2021
…ction

* dimred-methods: (34 commits)
  Update alra.py (openproblems-bio#304)
  updated template for PR with PR evaluation checks (openproblems-bio#314)
  pre-commit
  Fix preprocessing
  Fix preprocessing
  Add new preprocessing
  Add new preprocessing
  fix region
  fix nf wkdir
  use env.BRANCH
  rm echo
  BRANCH -> WKDIR for s3
  set branch variable in S3 setup job
  Fix s3 bucket clash
  Dimred methods preprocessing (openproblems-bio#301)
  Add trustworthiness score for dimred task (openproblems-bio#258)
  Add Method SCOT to Multi-modal data Integration Task (openproblems-bio#298)
  Change batch size to 1k cells for aff. matrix
  Add preprocessing
  Fix some small bugs
  ...
rcannood pushed a commit that referenced this pull request Sep 4, 2024
* Add nf-tower cli for dataset loader

* add mising directive labels for dataset loader

* add missing directive labels process datasets

* remove space in file name
rcannood pushed a commit that referenced this pull request Sep 4, 2024
* Add nf-tower cli for dataset loader

* add mising directive labels for dataset loader

* add missing directive labels process datasets

* remove space in file name

Former-commit-id: 6ed72c7
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4 participants