Initial commit -- Adding calibration loss specific to segmentation #7819

Bala93 · 2024-06-02T02:12:49Z

Description

Model calibration has helped in developing reliable deep learning models. In this pull request, I have added a new loss function NACL (https://arxiv.org/abs/2303.06268, https://arxiv.org/abs/2401.14487) which has shown promising results for both discriminative and calibration in segmentation.

Future Plans: Currently, MONAI has some of the alternative loss functions (Label Smoothing, and Focal Loss), but it doesn't have the calibration specific loss functions (https://arxiv.org/abs/2111.15430, https://arxiv.org/abs/2209.09641). Besides, these methods are better evaluated with calibration metrics, Expected Calibration Error (https://lightning.ai/docs/torchmetrics/stable/classification/calibration_error.html).

Types of changes

Non-breaking change (fix or new feature that would not break existing functionality).
Breaking change (fix or new feature that would cause existing functionality to change).
New tests added to cover the changes.
Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.
In-line docstrings updated.
Documentation updated, tested make html command in the docs/ folder.

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Fix the order of loss function in import statement

Fixed the formatting and minor issues.

Reorder import statements

Reorder system imports.

isort inferred one

Updated class name according to standard

Fixed the inline comment

Add datatype in functions and classes

ericspod

Thanks for the contribution! I had a few comments, and the CICD errors are easy fixes I think. The test fail is from accuracy it seems which can be fixed by changing the error.

monai/losses/segcalib.py

Co-authored-by: Eric Kerfoot <[email protected]> Signed-off-by: Balamurali <[email protected]>

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Add model description.

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Fixed the initialization issues with return types

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Use Any instead of tensor

Import typing

Fix return type formatting

DCO Remediation Commit for bala93 <[email protected]> I, Balamurali <[email protected]>, hereby add my Signed-off-by to this commit: c4f8283 I, bala93 <[email protected]>, hereby add my Signed-off-by to this commit: 8fbec82 I, bala93 <[email protected]>, hereby add my Signed-off-by to this commit: 7c121a0 I, bala93 <[email protected]>, hereby add my Signed-off-by to this commit: dccde47 Signed-off-by: bala93 <[email protected]>

DCO Remediation Commit for bala93 <[email protected]> I, bala93 <[email protected]>, hereby add my Signed-off-by to this commit: 8fbec82 I, bala93 <[email protected]>, hereby add my Signed-off-by to this commit: 7c121a0 I, bala93 <[email protected]>, hereby add my Signed-off-by to this commit: dccde47 Signed-off-by: bala93 <[email protected]>

DCO Remediation Commit for Balamurali <[email protected]> I, Balamurali <[email protected]>, hereby add my Signed-off-by to this commit: bc6b995 Signed-off-by: Balamurali <[email protected]>

Signed-off-by: Balamurali <[email protected]>

I, bala93 <[email protected]>, hereby add my Signed-off-by to this commit: 3a00aec Signed-off-by: bala93 <[email protected]>

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Bala93 · 2024-08-05T23:48:32Z

Hi @Bala93 I have a few further comments, the fixes for the mypy issues should be minor and the DCO page tells you how to address that. Thanks!

Hi @ericspod, Thanks for your feedback. I have addressed all the issues. I will work on using the monai functions (for the gaussian, and mean) in some time. Until then, is it possible to merge it with the dev branch and make the loss function available ? Thank you.

docs/source/losses.rst

Co-authored-by: YunLiu <[email protected]> Signed-off-by: Balamurali <[email protected]>

KumoLiu

Thanks for the contribution! Overall looks good to me. Several minor inline comments.

monai/losses/nacl_loss.py

tests/test_nacl_loss.py

* Modify the code with MeanFilter, and GaussianFilter of MONAI layers * Add Doc string explaining the mask preparation Signed-off-by: Balamurali <[email protected]>

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Bala93 · 2024-08-07T05:32:37Z

Hi @KumoLiu @ericspod. I have addressed the comments with the latest commit. Please feel free to resolve the comments if deemed solved. Thanks for your prompt response.

KumoLiu

Thanks for the quick update, few further comments inline.

monai/losses/nacl_loss.py

Co-authored-by: YunLiu <[email protected]> Signed-off-by: Balamurali <[email protected]>

ericspod · 2024-08-07T16:13:07Z

Looks good now to me with the last minor comments addressed.

Signed-off-by: Balamurali <[email protected]>

…nto model-calibration

DCO Remediation Commit for Balamurali <[email protected]> I, Balamurali <[email protected]>, hereby add my Signed-off-by to this commit: 7deb2cc Signed-off-by: Balamurali <[email protected]>

KumoLiu

Thanks for the quick update, looks good to me now. Will trigger more tests and try to merge this one.

KumoLiu · 2024-08-08T06:45:20Z

/build

Bala93 and others added 10 commits June 1, 2024 22:11

Initial commit -- Adding calibration loss specific to segmentation

8fbec82

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Update __init__.py

b2ec62b

Fix the order of loss function in import statement

Update segcalib.py

93ee114

Fixed the formatting and minor issues.

Update segcalib.py

42e732b

Reorder import statements

Update segcalib.py

187053d

Reorder system imports.

Update segcalib.py

1d27ec5

isort inferred one

Update segcalib.py

d499134

Updated class name according to standard

Update segcalib.py

1e3f755

Fixed the inline comment

Update segcalib.py

9dedfba

Add datatype in functions and classes

ericspod reviewed Jun 13, 2024

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ericspod requested a review from KumoLiu June 13, 2024 14:34

Bala93 and others added 18 commits June 14, 2024 06:32

Update monai/losses/segcalib.py

59959ce

Co-authored-by: Eric Kerfoot <[email protected]> Signed-off-by: Balamurali <[email protected]>

Update monai/losses/segcalib.py

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Co-authored-by: Eric Kerfoot <[email protected]> Signed-off-by: Balamurali <[email protected]>

[pre-commit.ci] auto fixes from pre-commit.com hooks

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Update segcalib.py

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Add model description.

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Add specific to gaussian for both 2d and 3d

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Merge branch 'Project-MONAI:dev' into model-calibration

0067953

Add mean loss and resolve formatting

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Merge branch 'dev' into model-calibration

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Update segcalib.py

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Fixed the initialization issues with return types

[pre-commit.ci] auto fixes from pre-commit.com hooks

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Update segcalib.py

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Use Any instead of tensor

Update segcalib.py

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Import typing

Update segcalib.py

6dbd53d

Update segcalib.py

354056c

Update segcalib.py

7eb911f

Fix return type formatting

Bala93 and others added 7 commits August 5, 2024 14:25

Formatting check with monai

3a00aec

DCO Remediation Commit for Balamurali <[email protected]> I, Balamurali <[email protected]>, hereby add my Signed-off-by to this commit: bc6b995 Signed-off-by: Balamurali <[email protected]>

Update test_nacl_loss.py

818b42b

DCO Remediation Commit for Balamurali <[email protected]> I, Balamurali <[email protected]>, hereby add my Signed-off-by to this commit: bc6b995 Signed-off-by: Balamurali <[email protected]>

Added mypy fixes

6647708

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DCO Remediation Commit for bala93 <[email protected]>

7e579dd

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Bala93 requested a review from ericspod August 5, 2024 23:50

KumoLiu reviewed Aug 6, 2024

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Co-authored-by: YunLiu <[email protected]> Signed-off-by: Balamurali <[email protected]>

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Bala93 and others added 2 commits August 7, 2024 01:24

* Include test cases covering more cases

747681d

* Modify the code with MeanFilter, and GaussianFilter of MONAI layers * Add Doc string explaining the mask preparation Signed-off-by: Balamurali <[email protected]>

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Bala93 and others added 2 commits August 7, 2024 06:27

Update monai/losses/nacl_loss.py

877139c

Co-authored-by: YunLiu <[email protected]> Signed-off-by: Balamurali <[email protected]>

Update monai/losses/nacl_loss.py

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Co-authored-by: YunLiu <[email protected]> Signed-off-by: Balamurali <[email protected]>

Bala93 added 6 commits August 7, 2024 10:32

* Add docstring with better explanations

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Signed-off-by: Balamurali <[email protected]>

* Maintain the dimension consistency.

d33f435

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Update nacl_loss.py

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Update nacl_loss.py

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Signed-off-by: Balamurali <[email protected]>

Merge branch 'model-calibration' of https://github.com/Bala93/MONAI i…

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…nto model-calibration

Modify docstring

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DCO Remediation Commit for Balamurali <[email protected]> I, Balamurali <[email protected]>, hereby add my Signed-off-by to this commit: 7deb2cc Signed-off-by: Balamurali <[email protected]>

Bala93 requested a review from KumoLiu August 8, 2024 06:32

Merge branch 'dev' into model-calibration

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KumoLiu merged commit 660891f into Project-MONAI:dev Aug 8, 2024
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Initial commit -- Adding calibration loss specific to segmentation #7819

Initial commit -- Adding calibration loss specific to segmentation #7819

Bala93 commented Jun 2, 2024 •

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Initial commit -- Adding calibration loss specific to segmentation #7819

Initial commit -- Adding calibration loss specific to segmentation #7819

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