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Batch correction #37

Closed
wants to merge 12 commits into from
Closed

Batch correction #37

wants to merge 12 commits into from

Commits on Jun 21, 2024

  1. First draft of pushing results to notion via API endpoint

    @bputzeys
    bputzeys committed Jun 21, 2024
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Commits on Jun 22, 2024

  1. Fully automation to populate leaderboard 

    Probably need some refactoring as currently it
is close to unmaintainable.
    @bputzeys
    bputzeys committed Jun 22, 2024
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Commits on Jun 24, 2024

  1. Merge branch 'include-notion-endpoint' into develop

    @bputzeys
    bputzeys committed Jun 24, 2024
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Commits on Jun 25, 2024

  1. changed License for scGPT

    @maxiallard
    maxiallard committed Jun 25, 2024
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  2. Merge branch 'develop' of https://github.com/helicalAI/helical into d… 

    …evelop
    @bputzeys
    bputzeys committed Jun 25, 2024
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  3. Fix bug where validation data is not encoded

    @bputzeys
    bputzeys committed Jun 25, 2024
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  4. Save model and encoder in one function directly.

    @bputzeys
    bputzeys committed Jun 25, 2024
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  5. Move classifier into models folder. 

    Rename helical.py to base_models.py
Move BaseTaskModel to base_models.py
Move BaseModelProtocol to base_models.py
    @bputzeys
    bputzeys committed Jun 25, 2024
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Commits on Jun 28, 2024

  1. Add silhouette metric to compute batch effect 

    correction performance.
Taken and adapted from scIB
https://github.com/theislab/scib/tree/main
    @bputzeys
    bputzeys committed Jun 28, 2024
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  2. Add processed pbmc3k_concat_68k.h5ad file as LFS

    @bputzeys
    bputzeys committed Jun 28, 2024
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  3. Add git lfs to pull for GitHub pipeline to run 

    unit tests.
    @bputzeys
    bputzeys committed Jun 28, 2024
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  4. Merge branch 'main' into batch-correction

    @bputzeys
    bputzeys committed Jun 28, 2024
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