Skip to content

Add SCOT to multimodal data integration - #357

Closed
scottgigante-immunai wants to merge 4 commits into
openproblems-bio:mainfrom
scottgigante-immunai:scottgigante/bugfix/scot_unbalanced
Closed

Add SCOT to multimodal data integration#357
scottgigante-immunai wants to merge 4 commits into
openproblems-bio:mainfrom
scottgigante-immunai:scottgigante/bugfix/scot_unbalanced

Conversation

@scottgigante-immunai

@scottgigante-immunai scottgigante-immunai commented Apr 14, 2022

Copy link
Copy Markdown
Collaborator

Submission type

  • 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

Testing

  • 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: )
  • If this pull request is not ready for review (including passing the "Run Benchmark" tests), I will open this PR as a draft (click on the down arrow next to the "Create Pull Request" button)

Submission guidelines

  • This submission follows the guidelines in our Contributing document
  • I have checked to ensure there aren't other open Pull Requests for the same update/change

PR review checklist

This PR will be evaluated on the basis of the following checks:

  • The task addresses a valid open problem in single-cell analysis
  • The latest version of master is merged and tested
  • The methods/metrics are imported to __init__.py and were tested in the pipeline
  • Method and metric decorators are annotated with paper title, year, author, code version, and date
  • The README gives an outline of the methods, metrics and datasets in the folder
  • The README provides a satisfactory task explanation (for new tasks)
  • The sample test data is appropriate to test implementation of all methods and metrics (for new tasks)

@scottgigante-immunai

Copy link
Copy Markdown
Collaborator Author

@atong01 the unbalanced SCOT method you merged a while back was never imported and therefore never tested. When we import it, it fails tests due to an overflow error returning the aligned space as all NaN. Would you prefer to a) figure out how to fix it or b) remove it?

@atong01

atong01 commented Apr 14, 2022

Copy link
Copy Markdown
Contributor

I'm probably not going to fix it in the near future. I'd recommend removing it until someone has time. The original repo seems to be updated with some "v2.0" since I last looked. Not sure what is changed in this version. I had to fork and make it installable at some point which is what we are currently using.

Thanks for your help Scott!

@scottgigante-immunai scottgigante-immunai changed the title Import unbalanced SCOT Add SCOT to multimodal data integration Apr 19, 2022
@github-actions

github-actions Bot commented Sep 4, 2024

Copy link
Copy Markdown
Contributor

This pull request has been automatically closed because it has not had recent activity.

@github-actions github-actions Bot added the Stale label Sep 4, 2024
@github-actions github-actions Bot closed this Sep 4, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

help wanted Extra attention is needed Stale

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants