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Add BERNN batch integration method - #117

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spell00 wants to merge 1 commit into
openproblems-bio:mainfrom
spell00:method/bernn-clean-main
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spell00 wants to merge 1 commit into
openproblems-bio:mainfrom
spell00:method/bernn-clean-main

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@spell00

@spell00 spell00 commented Oct 14, 2026 •

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Describe your changes

This PR adds BERNN (Batch Effect Removal Neural Network) as a new method for the OpenProblems batch integration benchmark.

BERNN is a neural network-based approach designed to reduce technical batch effects while preserving biological information.

Changes include:

  • Add the BERNN method implementation and Viash configuration.
  • Register BERNN in the benchmark workflow.
  • Update CHANGELOG.md.

Reference: https://doi.org/10.1038/s41467-024-48177-5

Checklist before requesting a review

  • I have performed a self-review of my code

  • Check the correct box. Does this PR contain:

    • Breaking changes
    • New functionality
    • Major changes
    • Minor changes
    • Bug fixes
  • Proposed changes are described in the CHANGELOG.md

  • CI Tests succeed and look good!

@spell00
spell00 marked this pull request as ready for review October 14, 2026 16:04
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