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Add support for WSI-level classification #542

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merged 31 commits into from
Jun 24, 2024

Commits on Apr 10, 2024

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Commits on Apr 16, 2024

  1. Add baseline panda workflow (#373)

    * add panda config
    
    * adjust batch size
    
    * addressed comments
    
    * addressed comments
    
    * addressed comments
    roman807 authored Apr 16, 2024
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Commits on Apr 23, 2024

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Commits on Apr 25, 2024

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Commits on Apr 26, 2024

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Commits on Apr 30, 2024

  1. Simple baseline sampler for foreground patches (#394)

    * add foreground kaggle
    
    * added random foreground sampler kaggle
    
    * refactored sampler
    
    * moved get_mask
    
    * typo
    
    * refactor sampler
    
    * refactor sampler
    
    * addressed comments
    
    * addressed comments
    roman807 authored Apr 30, 2024
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Commits on May 2, 2024

  1. Merge remote-tracking branch 'origin/main' into 360-aggregated-featur…

    …e-support-wsi-level-tasks
    nkaenzig committed May 2, 2024
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Commits on May 6, 2024

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Commits on May 7, 2024

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Commits on May 8, 2024

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Commits on May 10, 2024

  1. Retrieve MPP from WSIs (#432)

    * add mpp conversion
    
    * formatting
    
    * addressed comments
    
    * addressed comments
    
    * addressed comments
    
    * formatting
    
    * formatting
    
    * formatting
    roman807 authored May 10, 2024
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Commits on May 13, 2024

  1. updated panda config (#437)

    roman807 authored May 13, 2024
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Commits on May 21, 2024

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Commits on May 22, 2024

  1. Add PANDA dataset class (#430)

    nkaenzig authored May 22, 2024
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  2. fixed panda (#463)

    roman807 authored May 22, 2024
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Commits on May 23, 2024

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Commits on May 24, 2024

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Commits on May 27, 2024

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Commits on May 29, 2024

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Commits on Jun 6, 2024

  1. 459 add camelyon16 slide level task (#476)

    * added panda dataset class
    
    * clean up
    
    * remove samples with noisy labels
    
    * clean up table in dataset readme
    
    * added function for stratified splits
    
    * added unit tests
    
    * cleanup
    
    * addressed comments
    
    * fixed issue with resource download
    
    * validation fix
    
    * updated readme
    
    * added to mkdocs
    
    * added image_dir to exception print
    
    * updated root path in yaml config
    
    * added panda to datasets overview table in docs
    
    * added md5 hash for downloaded resources
    
    * update init
    
    * added camelyon16
    
    * added camelyon16
    
    * updated camelyon16 class
    
    * added tests and config
    
    * formatting
    
    * formatting
    
    * formatting
    
    * formatting
    
    * added test files
    
    * formatting
    
    * lint
    
    * added target transforms
    
    * formatting
    
    * fixed dataset
    
    * addressed comments
    
    * addressed comments
    
    * fix test
    
    * fix test
    
    * fixed test
    
    * addressed comments
    
    * updated loss
    
    * fix annotations
    
    * lint
    
    ---------
    
    Co-authored-by: Nicolas Kaenzig <nkaenzig@gmail.com>
    roman807 and nkaenzig authored Jun 6, 2024
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Commits on Jun 10, 2024

  1. 475 define slide level evaluation protocol (#511)

    * updated configs
    
    * adjust patience
    
    * addressed comments
    
    * fixed typo
    
    * remove prefetch factor
    roman807 authored Jun 10, 2024
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Commits on Jun 11, 2024

  1. update 360-aggregated-feature before PR to main (#527)

    * Updated developer guide (#418)
    
    * Update `TotalSegmentator2D` dataset to fetch all the slices (#416)
    
    * Move metrics to CPU when using single device (#446)
    
    * Remove total segmentator classification dataset (#450)
    
    * updated eva logo (#454)
    
    * updated eva logo
    
    * renamed files
    
    * Update actions/checkout digest to a5ac7e5 (#458)
    
    Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
    
    * Add configuration logger (#466)
    
    * Update `README` with paper citation (#474)
    
    * update docs (#482)
    
    * Update img shields of README (#480)
    
    * Fix `torch` and `jsonargparse` versions (#483)
    
    * update depedencies
    
    * update
    
    * bump micro version (#486)
    
    * update config links (#487)
    
    * Update paper citation format (#489)
    
    * Update the vision dataset return types to `tv_tensors` (#478)
    
    * Refactor embeddings writer (#461)
    
    * fixed phikon configs (#493)
    
    * Refactor embeddings datasets (#495)
    
    * Add doc tests and minor fixes (#492)
    
    * support setting download as env-variable (#514)
    
    * updated confis and doc
    
    * typo
    
    * update datasets
    
    * fixed types
    
    * src/eva/core/callbacks/writers/embeddings/base.py
    
    * formatting
    
    * types
    
    ---------
    
    Co-authored-by: Nicolas Känzig <36882833+nkaenzig@users.noreply.github.com>
    Co-authored-by: ioangatop <johngatop@gmail.com>
    Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
    4 people authored Jun 11, 2024
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Commits on Jun 12, 2024

  1. Updated documentation with new datasets and leaderboard (#531)

    * updated layout
    
    * updated layout
    
    * addressed comment
    roman807 authored Jun 12, 2024
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Commits on Jun 17, 2024

  1. 532 update leaderboard results with slide level tasks (#538)

    * updated docs
    
    * update leaderboard
    
    * update docs and links
    roman807 authored Jun 17, 2024
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Commits on Jun 18, 2024

  1. updated configs (#539)

    roman807 authored Jun 18, 2024
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Commits on Jun 21, 2024

  1. updated leaderboard (#543)

    roman807 authored Jun 21, 2024
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