jeromerony, updated 🕥 2023-03-06 13:11:17

Pytorch 1.10.0 code for:

Deep Weakly-Supervised Learning Methods for Classification and Localization in Histology Images: A Survey. Webpage, PDF

Citation:

@article{rony2023deep, title ={Deep Weakly-Supervised Learning Methods for Classification and Localization in Histology Images: A Survey}, author={Rony, J. and Belharbi, S. and Dolz, J. and Ben Ayed, I. and McCaffrey, L. and Granger, E.}, journal = "Machine Learning for Biomedical Imaging", volume = "2", year = "2023", pages = "96--150" }

Issues:

Please create a github issue.

Content:

Method:

view

taxonomy

Installed methods: - GAP - Max-Pooling - LSE - CAM - HaS - WILDCAT - ACoL - SPG - Deep MIL - PRM - ADL - CutMix - TS-CAM - MAXMIN - NEGEV - GradCAM - GradCAM++ - Smooth-GradCAM++ - LayerCAM - U-Net

Results:

localization performance

localization performance and its sensitivity to thresholding

Impact of model selection over localization performance

localization GLAS dataset, Benign.

localization GLAS dataset, Malignant.

localization Camelyon16 dataset, Normal.

localization Camelyon16 dataset, Metastatic.

Requirements:

  • Python 3.7.10
  • Pytorch 1.10.0
  • torchvision 0.11.1 shell pip install torch==1.10.0 -f https://download.pytorch.org/whl/cu111/torch-1.10.0%2Bcu111-cp37-cp37m-linux_x86_64.whl pip install torchvision==0.11.1 -f https://download.pytorch.org/whl/cu111/torchvision-0.11.1%2Bcu111-cp37-cp37m-linux_x86_64.whl
  • Full dependencies
  • Build and install CRF:
    • Install Swig
    • CRF (not used in this work, but it is part of the code.)

shell cdir=$(pwd) cd dlib/crf/crfwrapper/bilateralfilter swig -python -c++ bilateralfilter.i python setup.py install cd $cdir cd dlib/crf/crfwrapper/colorbilateralfilter swig -python -c++ colorbilateralfilter.i python setup.py install

Download datasets :

2.1. Links to dataset:

2.2. Download datasets:

You find the splits in ./folds.

2.3 Code for datasets split/sampling (+ patches sampling from WSI):

Run code :

  • CAM-method: CAM over GLAS using ResNet50: shell cudaid=$1 export CUDA_VISIBLE_DEVICES=$cudaid getfreeport() { freeport=$(python -c 'import socket; s=socket.socket(); s.bind(("", 0)); print(s.getsockname()[1]); s.close()') } export OMP_NUM_THREADS=50 export NCCL_BLOCKING_WAIT=1 plaunch=$(python -c "from os import path; import torch; print(path.join(path.dirname(torch.__file__), 'distributed', 'launch.py'))") getfreeport torchrun --nnodes=1 --node_rank=0 --nproc_per_node=1 \ --master_port=$freeport main_wsol.py \ --local_world_size=1 \ --task STD_CL \ --encoder_name resnet50 \ --arch STDClassifier \ --runmode final-mode \ --opt__name_optimizer sgd \ --batch_size 32 \ --eval_checkpoint_type best_localization \ --opt__step_size 250 \ --opt__gamma 0.1 \ --max_epochs 1000 \ --freeze_cl False \ --support_background True \ --method CAM \ --spatial_pooling WGAP \ --dataset GLAS \ --fold 0 \ --cudaid 0 \ --debug_subfolder None \ --amp True \ --opt__lr 0.003 \ --exp_id 11_19_2021_09_32_36_109051__423849

Issues

Bump notebook from 5.7.4 to 6.4.10 in /datasets-split/dependencies

opened on 2022-04-06 18:54:50 by dependabot[bot]

Bumps notebook from 5.7.4 to 6.4.10.

Dependabot compatibility score

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) - `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language - `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language - `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language - `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/jeromerony/survey_wsl_histology/network/alerts).

Bump pillow from 5.4.1 to 9.0.1 in /datasets-split/dependencies

opened on 2022-03-12 00:05:11 by dependabot[bot]

Bumps pillow from 5.4.1 to 9.0.1.

Release notes

Sourced from pillow's releases.

9.0.1

https://pillow.readthedocs.io/en/stable/releasenotes/9.0.1.html

Changes

  • In show_file, use os.remove to remove temporary images. CVE-2022-24303 #6010 [@​radarhere, @​hugovk]
  • Restrict builtins within lambdas for ImageMath.eval. CVE-2022-22817 #6009 [radarhere]

9.0.0

https://pillow.readthedocs.io/en/stable/releasenotes/9.0.0.html

Changes

... (truncated)

Changelog

Sourced from pillow's changelog.

9.0.1 (2022-02-03)

  • In show_file, use os.remove to remove temporary images. CVE-2022-24303 #6010 [radarhere, hugovk]

  • Restrict builtins within lambdas for ImageMath.eval. CVE-2022-22817 #6009 [radarhere]

9.0.0 (2022-01-02)

  • Restrict builtins for ImageMath.eval(). CVE-2022-22817 #5923 [radarhere]

  • Ensure JpegImagePlugin stops at the end of a truncated file #5921 [radarhere]

  • Fixed ImagePath.Path array handling. CVE-2022-22815, CVE-2022-22816 #5920 [radarhere]

  • Remove consecutive duplicate tiles that only differ by their offset #5919 [radarhere]

  • Improved I;16 operations on big endian #5901 [radarhere]

  • Limit quantized palette to number of colors #5879 [radarhere]

  • Fixed palette index for zeroed color in FASTOCTREE quantize #5869 [radarhere]

  • When saving RGBA to GIF, make use of first transparent palette entry #5859 [radarhere]

  • Pass SAMPLEFORMAT to libtiff #5848 [radarhere]

  • Added rounding when converting P and PA #5824 [radarhere]

  • Improved putdata() documentation and data handling #5910 [radarhere]

  • Exclude carriage return in PDF regex to help prevent ReDoS #5912 [hugovk]

  • Fixed freeing pointer in ImageDraw.Outline.transform #5909 [radarhere]

... (truncated)

Commits
  • 6deac9e 9.0.1 version bump
  • c04d812 Update CHANGES.rst [ci skip]
  • 4fabec3 Added release notes for 9.0.1
  • 02affaa Added delay after opening image with xdg-open
  • ca0b585 Updated formatting
  • 427221e In show_file, use os.remove to remove temporary images
  • c930be0 Restrict builtins within lambdas for ImageMath.eval
  • 75b69dd Dont need to pin for GHA
  • cd938a7 Autolink CWE numbers with sphinx-issues
  • 2e9c461 Add CVE IDs
  • Additional commits viewable in compare view


Dependabot compatibility score

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) - `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language - `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language - `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language - `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/jeromerony/survey_wsl_histology/network/alerts).

Bump ipython from 7.2.0 to 7.16.3 in /datasets-split/dependencies

opened on 2022-01-21 20:06:16 by dependabot[bot]

Bumps ipython from 7.2.0 to 7.16.3.

Commits


Dependabot compatibility score

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) - `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language - `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language - `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language - `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/jeromerony/survey_wsl_histology/network/alerts).

Bump dask from 1.1.1 to 2021.10.0 in /datasets-split/dependencies

opened on 2021-10-27 18:56:59 by dependabot[bot]

Bumps dask from 1.1.1 to 2021.10.0.

Commits


Dependabot compatibility score

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) - `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language - `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language - `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language - `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/jeromerony/survey_wsl_histology/network/alerts).

Bump pygments from 2.3.1 to 2.7.4 in /datasets-split/dependencies

opened on 2021-03-29 20:57:23 by dependabot[bot]

Bumps pygments from 2.3.1 to 2.7.4.

Release notes

Sourced from pygments's releases.

2.7.4

  • Updated lexers:

    • Apache configurations: Improve handling of malformed tags (#1656)

    • CSS: Add support for variables (#1633, #1666)

    • Crystal (#1650, #1670)

    • Coq (#1648)

    • Fortran: Add missing keywords (#1635, #1665)

    • Ini (#1624)

    • JavaScript and variants (#1647 -- missing regex flags, #1651)

    • Markdown (#1623, #1617)

    • Shell

      • Lex trailing whitespace as part of the prompt (#1645)
      • Add missing in keyword (#1652)

    • SQL - Fix keywords (#1668)

    • Typescript: Fix incorrect punctuation handling (#1510, #1511)

  • Fix infinite loop in SML lexer (#1625)

  • Fix backtracking string regexes in JavaScript/TypeScript, Modula2 and many other lexers (#1637)

  • Limit recursion with nesting Ruby heredocs (#1638)

  • Fix a few inefficient regexes for guessing lexers

  • Fix the raw token lexer handling of Unicode (#1616)

  • Revert a private API change in the HTML formatter (#1655) -- please note that private APIs remain subject to change!

  • Fix several exponential/cubic-complexity regexes found by Ben Caller/Doyensec (#1675)

  • Fix incorrect MATLAB example (#1582)

Thanks to Google's OSS-Fuzz project for finding many of these bugs.

2.7.3

... (truncated)

Changelog

Sourced from pygments's changelog.

Version 2.7.4

(released January 12, 2021)

  • Updated lexers:

    • Apache configurations: Improve handling of malformed tags (#1656)

    • CSS: Add support for variables (#1633, #1666)

    • Crystal (#1650, #1670)

    • Coq (#1648)

    • Fortran: Add missing keywords (#1635, #1665)

    • Ini (#1624)

    • JavaScript and variants (#1647 -- missing regex flags, #1651)

    • Markdown (#1623, #1617)

    • Shell

      • Lex trailing whitespace as part of the prompt (#1645)
      • Add missing in keyword (#1652)

    • SQL - Fix keywords (#1668)

    • Typescript: Fix incorrect punctuation handling (#1510, #1511)

  • Fix infinite loop in SML lexer (#1625)

  • Fix backtracking string regexes in JavaScript/TypeScript, Modula2 and many other lexers (#1637)

  • Limit recursion with nesting Ruby heredocs (#1638)

  • Fix a few inefficient regexes for guessing lexers

  • Fix the raw token lexer handling of Unicode (#1616)

  • Revert a private API change in the HTML formatter (#1655) -- please note that private APIs remain subject to change!

  • Fix several exponential/cubic-complexity regexes found by Ben Caller/Doyensec (#1675)

  • Fix incorrect MATLAB example (#1582)

Thanks to Google's OSS-Fuzz project for finding many of these bugs.

Version 2.7.3

(released December 6, 2020)

... (truncated)

Commits
  • 4d555d0 Bump version to 2.7.4.
  • fc3b05d Update CHANGES.
  • ad21935 Revert "Added dracula theme style (#1636)"
  • e411506 Prepare for 2.7.4 release.
  • 275e34d doc: remove Perl 6 ref
  • 2e7e8c4 Fix several exponential/cubic complexity regexes found by Ben Caller/Doyensec
  • eb39c43 xquery: fix pop from empty stack
  • 2738778 fix coding style in test_analyzer_lexer
  • 02e0f09 Added 'ERROR STOP' to fortran.py keywords. (#1665)
  • c83fe48 support added for css variables (#1633)
  • Additional commits viewable in compare view


Dependabot compatibility score

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) - `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language - `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language - `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language - `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/jeromerony/survey_wsl_histology/network/alerts).

Bump jinja2 from 2.10 to 2.11.3 in /datasets-split/dependencies

opened on 2021-03-20 02:09:07 by dependabot[bot]

Bumps jinja2 from 2.10 to 2.11.3.

Release notes

Sourced from jinja2's releases.

2.11.3

This contains a fix for a speed issue with the urlize filter. urlize is likely to be called on untrusted user input. For certain inputs some of the regular expressions used to parse the text could take a very long time due to backtracking. As part of the fix, the email matching became slightly stricter. The various speedups apply to urlize in general, not just the specific input cases.

2.11.2

2.11.1

This fixes an issue in async environment when indexing the result of an attribute lookup, like {{ data.items[1:] }}.

2.11.0

This is the last version to support Python 2.7 and 3.5. The next version will be Jinja 3.0 and will support Python 3.6 and newer.

2.10.3

2.10.2

2.10.1

Changelog

Sourced from jinja2's changelog.

Version 2.11.3

Released 2021-01-31

  • Improve the speed of the urlize filter by reducing regex backtracking. Email matching requires a word character at the start of the domain part, and only word characters in the TLD. :pr:1343

Version 2.11.2

Released 2020-04-13

  • Fix a bug that caused callable objects with __getattr__, like :class:~unittest.mock.Mock to be treated as a :func:contextfunction. :issue:1145
  • Update wordcount filter to trigger :class:Undefined methods by wrapping the input in :func:soft_str. :pr:1160
  • Fix a hang when displaying tracebacks on Python 32-bit. :issue:1162
  • Showing an undefined error for an object that raises AttributeError on access doesn't cause a recursion error. :issue:1177
  • Revert changes to :class:~loaders.PackageLoader from 2.10 which removed the dependency on setuptools and pkg_resources, and added limited support for namespace packages. The changes caused issues when using Pytest. Due to the difficulty in supporting Python 2 and :pep:451 simultaneously, the changes are reverted until 3.0. :pr:1182
  • Fix line numbers in error messages when newlines are stripped. :pr:1178
  • The special namespace() assignment object in templates works in async environments. :issue:1180
  • Fix whitespace being removed before tags in the middle of lines when lstrip_blocks is enabled. :issue:1138
  • :class:~nativetypes.NativeEnvironment doesn't evaluate intermediate strings during rendering. This prevents early evaluation which could change the value of an expression. :issue:1186

Version 2.11.1

Released 2020-01-30

  • Fix a bug that prevented looking up a key after an attribute ({{ data.items[1:] }}) in an async template. :issue:1141

... (truncated)

Commits


Dependabot compatibility score

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

Dependabot commands and options
You can trigger Dependabot actions by commenting on this PR: - `@dependabot rebase` will rebase this PR - `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it - `@dependabot merge` will merge this PR after your CI passes on it - `@dependabot squash and merge` will squash and merge this PR after your CI passes on it - `@dependabot cancel merge` will cancel a previously requested merge and block automerging - `@dependabot reopen` will reopen this PR if it is closed - `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually - `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) - `@dependabot use these labels` will set the current labels as the default for future PRs for this repo and language - `@dependabot use these reviewers` will set the current reviewers as the default for future PRs for this repo and language - `@dependabot use these assignees` will set the current assignees as the default for future PRs for this repo and language - `@dependabot use this milestone` will set the current milestone as the default for future PRs for this repo and language You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/jeromerony/survey_wsl_histology/network/alerts).
Jérôme Rony

PhD student at ÉTS (École de Technologie Supérieure - Montréal, Canada) in machine learning and computer vision.

GitHub Repository