Skin Deep Unlearning: Artefact and Instrument Debiasing in the Context of Melanoma Classification [PDF]

Method:

"Convolutional Neural Networks have demonstrated dermatologist-level performance in the classification of melanoma and other skin lesions, but prediction irregularities due to bias are an issue that should be addressed before widespread deployment is possible. In this work, we robustly remove bias and spurious variation from an automated melanoma classification pipeline using two leading bias 'unlearning' techniques: 'Learning Not to Learn' [1] (LNTL) and 'Turning a Blind Eye' [2] (TABE), as well as an additional hybrid of the two (CLGR) . We show that the biases introduced by surgical markings and rulers presented in previous studies can be reasonably mitigated using these bias removal methods. We also demonstrate the generalisation benefits of 'unlearning' spurious variation relating to the imaging instrument used to capture lesion images. The novel contributions of this work include a comparison of different debiasing techniques for artefact bias removal and the concept of instrument bias 'unlearning' for domain generalisation in melanoma detection. Our experimental results provide evidence that the effect of each of the aforementioned biases are notably reduced, with different debiasing techniques excelling at different tasks."

[Bevan and Atapour-Abarghouei, 2021]

Examples of artefacts seen in ISIC 2020 data. Top row shows images with surgical markings present, bottom row shows images with rulers present.

'Learning Not to Learn' architecture (left) and 'Turning a Blind Eye' architecture (right). Feature extractor, f, is implemented as a convolutional architecture such as ResNeXt or EfficientNet in this work. 'fc' denotes a fully connected layer.

Usage

Software used (see `requirements.txt` for package requirements):

Python 3.9.6

CUDA Version 11.3

Nvidia Driver Version: 465.31

PyTorch 1.8.1

Downloading the data:

A free account must be created to download The Interactive Atlas of Dermoscopy, available at this link: https://derm.cs.sfu.ca/Download.html. Place the release_v0.zip file into the data/raw_images directory (see below), from which it will be processed by the download.py script. The other datasets will be automatically downloaded and processed by the download.py script.

Melanoma-Bias  
└───Data
│   └───csv
│   |   │   asan.csv
│   |   │   atlas.csv
│   |   │   ...
│   |
|   └───images
|   |
|   └───raw_images
|       |   release_v0.zip
|
...

Run download.py to download, crop and resize the ISIC, ASAN, MClass clinical, MClass dermoscopic and Fitzpatrick17k datasaets. Have patience as it may take around an hour to complete. The 256x256 resized images are automatically placed into data/images as shown below. The manually downloaded Atlas data (data/raw_images/release_v0.zip) will also be processed by this script. Note this script clears the data/images directory before populating it, so if you want to put other images in there, do this after running the download.py script.

NOTE: The surgical markings/rulers test set from Heidelberg University [3] is not publicly available.

The data directory should now look as follows:

Melanoma-Bias  
└───Data
│   └───csv
│   |   │   asan.csv
│   |   │   atlas.csv
│   |   │   ...
│   |
|   └───images
|       |   asan_256
|       |   atlas_256
|       |   isic_19_train_256
|       |   isic_20_train_256
|       |   MClassC_256
|       |   MClassD_256
|
...

If you do wish to manually download the datasets, they are available at the following links:

ISIC 2020 data: https://www.kaggle.com/cdeotte/jpeg-melanoma-256x256
ISIC 2019/2018/2017 data: https://www.kaggle.com/cdeotte/jpeg-isic2019-256x256
Interactive Atlas of Dermoscopy: https://derm.cs.sfu.ca/Welcome.html
ASAN Test set: https://figshare.com/articles/code/Caffemodel_files_and_Python_Examples/5406223
MClassC/MClassD: https://skinclass.de/mclass/

Training and evaluation:

Training commands for the main experiments from the paper are below. Please see arguments.py for the full range of arguments if you wish to devise alternative experiments. Test results (plots, logs and weights) will autosave into the results directory, in subdirectories specific to the test number. Please contact me if you require trained weights for any model in the paper.

Some useful arguments to tweak the below commands:

Adjust --CUDA_VISIBLE_DEVICES and num-workers to suit the available GPUs and CPU cores respectively on your machine.
To run in debug mode add --DEBUG (limits epochs to 3 batches).
To chnage the random seed (default 0), use --seed argument.
To run on different architechtures, use --arch argument to choose from resnext101, enet, resnet101, densenet or inception (default=resnext101).
Add --cv to perform cross validation.
Add --test-only if you wish to load weights and run testing only (loads weights of whatever --test-no argument is passed).

Instrument debiasing for domain generalisation:

Baseline: python train.py --test-no 9 --n-epochs 4 --CUDA_VISIBLE_DEVICES 0,1
LNTL: python train.py --test-no 10 --n-epochs 4 --debias-config LNTL --GRL --instrument --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8
TABE: python train.py --test-no 11 --n-epochs 4 --debias-config TABE --instrument --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8
CLGR: python train.py --test-no 12 --n-epochs 4 --debias-config TABE --GRL --instrument --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8

Surgical marking bias removal (REQUIRES PRIVATE HEIDELBERG UNIVERSITY DATASET):

Baseline: python train.py --test-no 1 --arch enet --enet-type efficientnet_b3 --n-epochs 15 --marked --CUDA_VISIBLE_DEVICES 0,1 --skew --heid-test_marked
LNTL: python train.py --test-no 2 --arch enet --enet-type efficientnet_b3 --n-epochs 15 --debias-config LNTL --GRL --marked --CUDA_VISIBLE_DEVICES 0,1 --skew --heid-test_marked
TABE: python train.py --test-no 3 --arch enet --enet-type efficientnet_b3 --n-epochs 15 --debias-config TABE --marked --CUDA_VISIBLE_DEVICES 0,1 --skew --heid-test_marked
CLGR: python train.py --test-no 4 --arch enet --enet-type efficientnet_b3 --n-epochs 15 --debias-config TABE --GRL --marked --CUDA_VISIBLE_DEVICES 0,1 --skew --heid-test_marked

Ruler bias removal (REQUIRES PRIVATE HEIDELBERG UNIVERSITY DATASET):

Baseline: python train.py --test-no 5 --arch enet --enet-type efficientnet_b3 --n-epochs 15 --rulers --CUDA_VISIBLE_DEVICES 0,1 --skew --heid-test_rulers
LNTL: python train.py --test-no 6 --arch enet --enet-type efficientnet_b3 --n-epochs 15 --debias-config LNTL --GRL --rulers --CUDA_VISIBLE_DEVICES 0,1 --skew --heid-test_rulers
TABE: python train.py --test-no 7 --arch enet --enet-type efficientnet_b3 --n-epochs 15 --debias-config TABE --rulers --CUDA_VISIBLE_DEVICES 0,1 --skew --heid-test_rulers
CLGR: python train.py --test-no 8 --arch enet --enet-type efficientnet_b3 --n-epochs 15 --debias-config TABE --GRL --rulers --CUDA_VISIBLE_DEVICES 0,1 --skew --heid-test_rulers

Double headers (removing instrument and surgical marking bias):

TABE (instrument) + TABE (marks): python train.py --test-no 21 --n-epochs 4 --debias-config doubleTABE --instrument --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8 --lr-class 0.0003
CLGR (instrument) + CLGR (marks): python train.py --test-no 22 --n-epochs 4 --debias-config doubleTABE --GRL --instrument --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8 --lr-class 0.0003
LNTL (instrument) + CLGR (marks): python train.py --test-no 23 --n-epochs 4 --debias-config both --GRL --instrument --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8 --lr-class 0.0003
CLGR (instrument) + LNTL (marks): python train.py --test-no 24 --n-epochs 4 --debias-config both --GRL --instrument --CUDA_VISIBLE_DEVICES 0,1 --num-aux2 8 --switch-heads --lr-class 0.0003
LNTL (instrument) + TABE (marks): python train.py --test-no 25 --n-epochs 4 --debias-config both --instrument --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8 --lr-class 0.0003
TABE (instrument) + LNTL (marks): python train.py --test-no 26 --n-epochs 4 --debias-config both --instrument --CUDA_VISIBLE_DEVICES 0,1 --num-aux2 8 --switch-heads --lr-class 0.0003
LNTL (instrument) + LNTL (marks): python train.py --test-no 27 --n-epochs 4 --debias-config doubleLNTL --instrument --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8 --lr-class 0.0003

Double headers (removing instrument and ruler bias):

TABE (instrument) + TABE (rulers): python train.py --test-no 21 --n-epochs 4 --debias-config doubleTABE --instrument --rulers --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8 --lr-class 0.0003
CLGR (instrument) + CLGR (rulers): python train.py --test-no 22 --n-epochs 4 --debias-config doubleTABE --GRL --instrument --rulers --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8 --lr-class 0.0003
LNTL (instrument) + CLGR (rulers): python train.py --test-no 23 --n-epochs 4 --debias-config both --GRL --instrument --rulers --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8 --lr-class 0.0003
CLGR (instrument) + LNTL (rulers): python train.py --test-no 24 --n-epochs 4 --debias-config both --GRL --instrument --rulers --CUDA_VISIBLE_DEVICES 0,1 --num-aux2 8 --switch-heads --lr-class 0.0003
LNTL (instrument) + TABE (rulers): python train.py --test-no 25 --n-epochs 4 --debias-config both --instrument --rulers --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8 --lr-class 0.0003
TABE (instrument) + LNTL (rulers): python train.py --test-no 26 --n-epochs 4 --debias-config both --instrument --rulers --CUDA_VISIBLE_DEVICES 0,1 --num-aux2 8 --switch-heads --lr-class 0.0003
LNTL (instrument) + LNTL (rulers): python train.py --test-no 27 --n-epochs 4 --debias-config doubleLNTL --instrument --rulers --CUDA_VISIBLE_DEVICES 0,1 --num-aux 8 --lr-class 0.0003

Reference:

Skin Deep Unlearning: Artefact and Instrument Debiasing in the Context of Melanoma Classification (P. Bevan, A. Atapour-Abarghouei) [pdf]


@InProceedings{pmlr-v162-bevan22a,
  title = 	 {Skin Deep Unlearning: Artefact and Instrument Debiasing in the Context of Melanoma Classification},
  author =       {Bevan, Peter and Atapour-Abarghouei, Amir},
  booktitle = 	 {Proceedings of the 39th International Conference on Machine Learning},
  pages = 	 {1874--1892},
  year = 	 {2022},
  editor = 	 {Chaudhuri, Kamalika and Jegelka, Stefanie and Song, Le and Szepesvari, Csaba and Niu, Gang and Sabato, Sivan},
  volume = 	 {162},
  series = 	 {Proceedings of Machine Learning Research},
  month = 	 {17--23 Jul},
  publisher =    {PMLR},
  pdf = 	 {https://proceedings.mlr.press/v162/bevan22a/bevan22a.pdf},
  url = 	 {https://proceedings.mlr.press/v162/bevan22a.html},
}

Name		Name	Last commit message	Last commit date
Latest commit History 47 Commits
data		data
images		images
misc_code		misc_code
results		results
.gitignore		.gitignore
LICENSE		LICENSE
README.md		README.md
arguments.py		arguments.py
dataset.py		dataset.py
download.py		download.py
globalbaz.py		globalbaz.py
models.py		models.py
preprocessing.py		preprocessing.py
requirements.txt		requirements.txt
test.py		test.py
train.py		train.py
train_epoch_variations.py		train_epoch_variations.py

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Skin Deep Unlearning: Artefact and Instrument Debiasing in the Context of Melanoma Classification [PDF]

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Downloading the data:

Training and evaluation:

Reference:

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Skin Deep Unlearning: Artefact and Instrument Debiasing in the Context of Melanoma Classification [PDF]

Method:

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Software used (see requirements.txt for package requirements):

Downloading the data:

Training and evaluation:

Reference:

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