adversarial-medicine

This repository contains the code used to train the proof-of-concept models and adversarial attacks described in "Adversarial Attacks Against Medical Deep Learning Systems", an updated version of which is under consideration at a CS venue.

Data

Raw Images

All of the data used in the project is publically available, as outlined in the paper. The original sources are below:

CXR Data

DR Data

Melanoma Data

As outlined in the paper, regardless of any train/test splits in the original datasets, I merged all the images together and split by patient into ~80/20 train/test splits. The DR Kaggle repo in particular was way too test-heavy in their train/test split for my purposes.

Numpy Arrays

To make it easier to recreating the results in this repo, I also provide numpy arrays for the validation sets for each of the above datasets here. (Training sets are too big). These numpy validation sets, along with the keras models below, are sufficient to run the Jupyter notebooks generating the figures and python script generating the tables.

Models

Pretrained Keras models

If you want to skip the training steps, I provide the keras models (in the case of white-box models) and keras model weights (for the separately trained black-box models) for each of the three tasks here.

Note: please don't try to use these for any medical purposes. I noticed some big problems in these datasets and do not trust them for more than proofs of concept.

Code to recreate the models

train_model.py is a stand-alone python script that will train and save a model for one of the tasks. The model assumes that images are organized in folders at the locations images/trainand images/val relative to the python script's working directory. Alternatively, numpy data blobs of all the images in your training/test sets can be placed at (data/train_x.npy, 'data/train_y.npy', 'data/test_x.npy', 'data/test_y.npy').

The training script has a number of options, including whether to train inception or resnet models (in the paper I only report results for Resnet for simplicity, but results on Inception were ~identical), learning rates, early stopping, various data augmentations, etc. In practice, I got good enough results with the defaults I loaded in here so I didn't do much by way of hyperparameter tuning, so I'm sure a lot more performance could get squeezed out of the models.

Dependencies: requires Python3, keras, tensorflow, and numpy.

Recreating PGD Attacks and Figures

The pgd_attacks directory contains a craft_attacks.py script that builds the attacks, reports their success metrics, and saves the adversarial attacks themselves. This file assumes the white box model is located in models/wb_model.h5 and the weights for the black box model are located in models/bb_weights.hdf5", though there are command-line arguments to specify different locations.

The file generate_pgd_figures.ipynb is a Jupyter notebook that recreates the figures in the paper based on the files produced by craft_attacks.py.

Dependencies: see pgd_environment.yaml

Recreating Patch Attacks and Figures

The patch attacks were largely developed by Hyung Won Chung. The bulk of the functionality is developed in execute_patch_attacks.py and craft_attack_patch.py.

There are two options to explore the patch attack: Jupyter Notebook interface and directly running craft_attack_patch.py.

1. Notebook The file 0_generate_patch_results_derm.ipynb is a Jupyter notebook that generates the figures for the derm patches. The similarly named 1_generate_patch_results_cxr.ipynb and 1_generate_patch_results_dr.ipynb are similar notebooks that generate the results for DR and Chest-xrays.

2. craft_attack_patch.py. This file can be used stand-alone and does not require any command-line argument. So just run it via python craft_attack.py. To faciliate testing the functionality, we have included sample train and test images (8 images for each label) for Melanoma. For training the patch, use the full Data. We couldn't include the pretrained models object due to size. Create a directory models and put the model objects. For example, download the Pretrained Keras models and put both files in the models directory.

Dependencies: requires Python3, keras, tensorflow, cleverhans, numpy, scipy, sklearn.