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Published November 11, 2023 | Version 0.0.17
Software Open

GaNDLF: the generally nuanced deep learning framework for scalable end-to-end clinical workflows

Authors/Creators

Description

What's Changed

  • Version update for development by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/648
  • Added citation file by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/654
  • Added new optimizers by @AdiSir05 in https://github.com/mlcommons/GaNDLF/pull/646
  • Allow histology patches to be extracted without ground truth labels by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/657
  • Added metric calculation from CLI by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/663
  • Added a few segmentation metrics by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/661
  • Repository badges have been updated by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/667
  • Added instructions on creating new tutorials by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/664
  • Ensure parameters are built into the model dictionary by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/673
  • Calculating penalty after all compute objects are initialized by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/675
  • Add image similarity metrics by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/669
  • Allow the penalty and class weights in the config to be used by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/677
  • Added documentation related to OpenFL by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/683
  • Add MLCube wrapper for metrics API by @hasan7n in https://github.com/mlcommons/GaNDLF/pull/681
  • Adding mechanism to curate each extracted patch by @shubhaminnani in https://github.com/mlcommons/GaNDLF/pull/653
  • Added mask to SSIM function call by @FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/685
  • Removed history file by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/690
  • Updated the metrics output by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/687
  • Update docker image name in workflow by @hasan7n in https://github.com/mlcommons/GaNDLF/pull/692
  • Fixed plotting function for final stats by @Geeks-Sid in https://github.com/mlcommons/GaNDLF/pull/691
  • Fixed import for collect stats by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/694
  • HED augmentations for digital pathology image by @Geeks-Sid in https://github.com/mlcommons/GaNDLF/pull/649
  • Added focal loss by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/696
  • Added a temporary fix for protobuf by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/702
  • Use torchmetric PSNR implementation and argument ordering by @FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/693
  • Introduced percentile normalization for synthesis challenge metrics by @FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/700
  • Upgrade openvino version to latest by @Geeks-Sid in https://github.com/mlcommons/GaNDLF/pull/699
  • Additional PSNR evaluations for the normalized synthesis case by @FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/703
  • Improved formatting by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/707
  • Updated checkout version and test names for clarity by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/708
  • Updated default options for sgd by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/709
  • Added matthews correlation coefficient loss by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/706
  • Using tuples for PSNR datarange by @FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/712
  • Deploy model entrypoint by @hasan7n in https://github.com/mlcommons/GaNDLF/pull/711
  • Added parameter to toggle NCC computation by @FelixSteinbauer in https://github.com/mlcommons/GaNDLF/pull/717
  • Adding second classification tutorial by @vavali08 in https://github.com/mlcommons/GaNDLF/pull/698
  • Minor code refactoring by @tosemml in https://github.com/mlcommons/GaNDLF/pull/719
  • Combined writing and temp file creation in a single step by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/720
  • Update usage information for anonymizer by @sanashah007 in https://github.com/mlcommons/GaNDLF/pull/716
  • Move unit testing data to the mlcommons storage by @sarthakpati in https://github.com/mlcommons/GaNDLF/pull/722
  • Fixed model saving when git repo not found by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/729
  • Removing dev from version for tagging by @scap3yvt in https://github.com/mlcommons/GaNDLF/pull/731

New Contributors

  • @AdiSir05 made their first contribution in https://github.com/mlcommons/GaNDLF/pull/646
  • @shubhaminnani made their first contribution in https://github.com/mlcommons/GaNDLF/pull/653
  • @FelixSteinbauer made their first contribution in https://github.com/mlcommons/GaNDLF/pull/685
  • @vavali08 made their first contribution in https://github.com/mlcommons/GaNDLF/pull/698
  • @tosemml made their first contribution in https://github.com/mlcommons/GaNDLF/pull/719
  • @sanashah007 made their first contribution in https://github.com/mlcommons/GaNDLF/pull/716
  • @scap3yvt made their first contribution in https://github.com/mlcommons/GaNDLF/pull/729

Full Changelog: https://github.com/mlcommons/GaNDLF/compare/0.0.16...0.0.17

Other

If you use this software, please cite it using this manuscript.

Files

mlcommons/GaNDLF-0.0.17.zip

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Additional details

Related works

Is supplement to
Software: https://github.com/mlcommons/GaNDLF/tree/0.0.17 (URL)