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Added metrics for BraTS Path challenge #885

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@sarthakpati sarthakpati commented Jun 20, 2024

Fixes #817

Proposed Changes

  • auroc has been fixed
  • added matthews correlation coefficient (mcc) from torchmetrics
  • changed output format to json (YAML was giving issues with mcc)
  • updated output dict of metrics to ensure that the averaging types are not overwritten
  • TODO: add tests using binary classification so that auroc gets tested

Checklist

  • CONTRIBUTING guide has been followed.
  • PR is based on the current GaNDLF master .
  • Non-breaking change (does not break existing functionality): provide as many details as possible for any breaking change.
  • Function/class source code documentation added/updated (ensure typing is used to provide type hints, including and not limited to using Optional if a variable has a pre-defined value).
  • Code has been blacked for style consistency and linting.
  • If applicable, version information has been updated in GANDLF/version.py.
  • If adding a git submodule, add to list of exceptions for black styling in pyproject.toml file.
  • Usage documentation has been updated, if appropriate.
  • Tests added or modified to cover the changes; if coverage is reduced, please give explanation.
  • If customized dependency installation is required (i.e., a separate pip install step is needed for PR to be functional), please ensure it is reflected in all the files that control the CI, namely: python-test.yml, and all docker files [1,2,3].

@sarthakpati sarthakpati requested a review from a team as a code owner June 20, 2024 14:16
@sarthakpati sarthakpati marked this pull request as draft June 20, 2024 14:16
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github-actions bot commented Jun 20, 2024

MLCommons CLA bot All contributors have signed the MLCommons CLA ✍️ ✅

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@szmazurek szmazurek left a comment

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I believe it is fine now, good idea with adding average type to the metric name. LGTM

@sarthakpati sarthakpati added the enhancement New feature or request label Jun 28, 2024
@szmazurek szmazurek marked this pull request as ready for review June 28, 2024 16:02
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Thanks for the review, @szmazurek!

I will wait for @Geeks-Sid and @vpchung to test this before merging.

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The test failure is related to #889.

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