Concept-level Debugging of Part-Prototype Networks

Implementation of the paper

Bontempelli, A., Teso, S., Giunchiglia, F., & Passerini, A. (2023). Concept-level Debugging of Part-Prototype Networks.

Accepted for publication at ICLR 2023 (slides, Poster).

The code in this repository is an adaptation of the code in the following repositories:

	Repository	License
ProtoPNet	https://github.com/cfchen-duke/ProtoPNet	See License
IAIA-BL loss	https://github.com/alinajadebarnett/iaiabl	See License
Covid data processing and data loaders	https://github.com/suinleelab/cxr_covid	See License

Used datasets:

CUB-200-2011: Wah, C., Branson, S., Welinder, P., Perona, P., & Belongie, S. (2022). CUB-200-2011 (1.0) [Data set]. CaltechDATA. https://doi.org/10.22002/D1.20098
CUB-200-2011 Segmentations: Farrell, R. (2022). CUB-200-2011 Segmentations (1.0) [Data set]. CaltechDATA. https://doi.org/10.22002/D1.20097
ChestX-ray14: Xiaosong Wang, Yifan Peng, Le Lu, Zhiyong Lu, MohammadhadiBagheri, Ronald M. Summers.ChestX-ray8: Hospital-scale Chest X-ray Database and Benchmarks on Weakly-Supervised Classification and Localization of Common Thorax Diseases, IEEE CVPR, pp. 3462-3471,2017
GitHub-COVID: COVID-19 Image Data Collection: Prospective Predictions Are the Future Joseph Paul Cohen and Paul Morrison and Lan Dao and Karsten Roth and Tim Q Duong and Marzyeh Ghassemi arXiv:2006.11988, https://github.com/ieee8023/covid-chestxray-dataset, 2020
PadChest: Aurelia Bustos, Antonio Pertusa, Jose-Maria Salinas, and Maria de la Iglesia-Vayá. Padchest: A large chest x-ray image dataset with multi-label annotated reports. Medical Image Analysis, 66:101797, 2020. ISSN 1361-8415. doi: https://doi.org/10.1016/j.media.2020.101797. URL https://www.sciencedirect.com/science/article/pii/S1361841520301614.
bimcv+: Maria de la Iglesia Vayá, Jose Manuel Saborit, Joaquim Angel Montell, Antonio Pertusa, Aurelia Bustos, Miguel Cazorla, Joaquin Galant, Xavier Barber, Domingo Orozco-Beltrán, Francisco García-García, Marisa Caparrós, Germán González, and Jose María Salinas. Bimcv covid-19+: a large annotated dataset of rx and ct images from covid-19 patients. 2020. doi: 10.48550/ARXIV.2006.01174. URL https://arxiv.org/abs/2006.01174.

Requirements

Python 3.9.7
Pytorch 1.11.0
cudatoolkit=11.3

Installation

Clone the repository

git clone https://github.com/abonte/protopdebug  ProtoPDebug
cd ProtoPNet

Create a new environment with Conda

conda env create -f environment.yml
conda activate protopnet

Repository structure

.
├── conf                   // experiment configuration used by Hydra
├── data                   // data processing scripts
├── datasets               // COVID and CUB200 datasets are preprocessed in this folder
├── extract_confound.py    // give supervision about the prototypes
├── global_analysis.py     // find the nearest patch to each prototype, compute activation precision
├── local_analysis.py      // find the nearest prototypes to all test images
├── old_code               // code of the original repository, but not used in this
├── plot_stat.py           // plot statistics about an experiment
├── pretrained_models      // pre-trained model downloaded during the training
├── saved_models           // results of the experiments
├── settings.py            // default values of the models and datasets parameters
├── tests                  // test suite
├── user_experiment        // data about the experiment with real users
└── visualization          // script for plotting

Data preparation

CUB-200

Download the dataset CUB-200-2011 from https://data.caltech.edu/records/20098 (1.1 GB).
Extract CUB_200_2011.tgz in the datasets folder.
Download the image masks from https://data.caltech.edu/records/20097
Extract it in datasets/CUB-200-2011

CUB-200 artificial confound

Run the following command to add the synthetic confound to the first five classes.

python data_preprocessing.py --seed 0 bird -i datasets/CUB_200_2011 --classes 001 002 003 004 005

The data pipeline performs the following operations:

Crop the images using information from bounding_boxes.txt (included in the dataset)
Split the cropped images into training and test sets, using train_test_split.txt (included in the dataset)
Put the cropped training images in the directory ./datasets/cub200_cropped/train_cropped/
Put the cropped test images in the directory ./datasets/cub200_cropped/test_cropped/
Augment the training set and create an augmented training set in ./datasets/cub200_cropped/train_cropped_augmented/
Add artificial confound (colored box) on three classes

CUB-200 natural confound

python data_preprocessing.py cub200_shuffled_bg
./copy_top_20.sh

The scripts, in addition to the operations from 1 to 5 in the previous section, change the backgrounds of the test set images by shifting the background of one class to the next one (e.g., the background of class 1 becomes the background of class 2). A the end of the process, the modified images are placed in the directory ./datasets/cub200_cropped/test_cropped_shuffled.

At the end of the data preparation, you should have the following structure in the dataset folder

./datasets/
   cub200_cropped/
      clean_5_classes/
         ...
      clean_top_20/
         ...
      confound_artificial/
         ...

COVID datasets

Data processing of the COVID data set is based on the code of the paper "AI for radiographic COVID-19 detection selects shortcuts over signal". Follow the instruction in the README.md of the repository https://github.com/suinleelab/cxr_covid. Use the scripts make_csv_bimcv_negative.py and make_h5.py of this repository instead of the ones in the original repository. Put the resulting *.h5 in the corresponding folders in the datasets/covid folder.

Only a subset of the data has been used, see the following list of which parts have been downloaded:

ChestX-ray14: images_001.tar.gz, images_002.tar.gz
GitHub-COVID: the complete repository
PadChest: 0.zip
BIMCV-COVID+: bimcv_covid19_posi_subjects_<1-10>.tgz

./datasets/
   covid/
      ChestX-ray14/
         ...
      GitHub-COVID/
         ...
      PadChest/
         ...
      bimcv+/
         ...

Running

Training

Configurations are managed by Hydra and a basic tutorial can be found here. The structure of the configuration is in settings.py, which contains the default values. The actual hyperparameters used for each experiment are in the conf folder.

Run main.py passing the following arguments:

experiment_name=<<NAME_OF_THE_EXPERIMENT>> choose an experiment name
+experiment=natural_base load a configuration file from the conf directory

Example:

python main.py experiment_name=firstExperiment +experiment=natural_base

You can override the loaded configuration values from the command line. For instance,

python main.py experiment_name=firstExperiment +experiment=natural_base epochs=30

To see the current configuration

python main.py --cfg job

The experiments can be tracked on Weights and Biases. To enable this feature, add wandb=true to the command line when running the script.

Evaluation

./plot.sh <PATH-TO-MODEL> "<LIST-OF-CLASSES>"

Substitute PATH-TO-MODEL with the path to the model you want to analyze. Specify the list of (0-based) index of the classes to use for the evaluation (Cub200: "0 8 14 6 15", Covid dataset: "0 1").

The script performs the following operations:

plot the statistics of the experiment;
plot the prototypes projected at the same epoch of the supplied model;
find the nearest patches to each prototype
plot a grid of the nearest patches

Reproducibility

Experiment 1

./run_artificial_confound.sh

Experiment 2

ProtoPDebug

Since human intervention is required in the debugging loop, follow these steps to run ProtoPDebug:

First round, without any human supervision

python main.py experiment_name=\"first_round\" +experiment=natural_base

Give supervision to the learned prototypes.

a) find the nearest patches to each prototype, substitute <PATH-TO-MODEL> with the path to the model of the previous round
```
python global_analysis.py <PATH-TO-MODEL>
```
b) manually select the patches that represent the confounds you want to forbid
```
python extract_confound.py interactive <PATH-TO-MODEL> -classes 0 8 14 6 15 -n-img 10
```
Only the prototypes of the specified classes are presented for the debugging step. (See main paper for the details on how have been selected these 5 classes). The command extracts the most activated patches from the most activate images of each prototype associated to the 5 classes. For each patch, you will have to choose one of these options:
- y (yes) the prototype activation overlays exclusively (or very nearly so) the background. The activation cut-out is added to the forbidden concepts
- n (next) the prototype activation overlays some part of the bird. No action is performed and go to the next patch
- r (remember) the prototype activation overlays some part of the bird and the concept is added to the concepts to be remembered (useful when you use the remembering loss).
The cut-out of the selected patched are placed in two folders tmp_forbidden_conf and tmp_remember_patch, inside the experiment folder. The patches from the images selected with y or r must be extracted manually and saved in the same folder.

c) move the patches in the dataset folder
```
python extract_confound.py move <PATH-TO-MODEL-FOLDER>
```
The script takes the patches in tmp_forbidden_conf and tmp_remember_patch (the filenames must contain class, prototype and image id formatted like c=0_p=1_i=2.png) and adds them to datasets/cub200_cropped/clean_top_20/forbidden_prototypes and datasets/cub200_cropped/clean_top_20/remembering_prototypes respectively.
Subsequent rounds, with the supervision on the confounds. The training will start from the model of the previous round by substituting <<PATH_TO_MODEL>> with the path to the saved model of the previous round.
```
python main.py experiment_name=\"second_round\" +experiment=natural_aggregation debug.path_to_model=\"<<PATH_TO_MODEL>>\"
```
Go back to 2) and repeat.

IAIA-BL, ProtoPNet clean, ProtoPNet

Run:

./run_natural_confound.sh

Experiment 3

Follow the same steps of Experiment 2

First round:

python main.py experiment_name=first_round +experiment=covid_base

Subsequent rounds:

python main.py experiment_name=\"second_round\"
                    +experiment=covid_aggregation
                    debug.path_to_model=\"<PATH_TO_MODEL>\"

User experiment

The generated images and the answers of the experiment with real user are in the user_experiment folder. The csv files contains the answers for each image:

1: 'some part of the bird'
0: 'exclusively (or very nearly so) the background'

The image names follow the pattern <number_of_the_question>Hexp_c=<idx_of_the_class>_p=<idx_of_the_prototype>_i=<idx_of_the_image>.png. For instance, 01Hexp_c=0_p=0_i=2_c.png. The folder user_experiment/cuts contains the cut-out for each image.

Results

The learned models can be accessed on Zenodo at https://zenodo.org/record/7181267. The zip file contains the models for each of the three experiments. These files can be found in the run folders:

config.json: configuration file
stat.pickle: statistics about the run (e.g., F1, loss,...)
img: projection of prototypes at different epochs
prototypes_activation_precision_testset.pickle: activation precision values on test set
*.pth.tar: the trained model
forbidden_prototypes: the supervision given to the model about the patches to forget
remembering_prototypes: the supervision given to the model about the patches to remember

To reproduce the figures in the paper, run

./plot_zenodo_results.sh

How to cite

@inproceedings{
   bontempelli2023conceptlevel,
   title={Concept-level Debugging of Part-Prototype Networks},
   author={Andrea Bontempelli and Stefano Teso and Katya Tentori and Fausto Giunchiglia and Andrea Passerini},
   booktitle={The Eleventh International Conference on Learning Representations },
   year={2023},
   url={https://openreview.net/forum?id=oiwXWPDTyNk}
}