pocovidnet

pocovidnet

A simple package to train deep learning models on ultrasound data for COVID19.

Train/test split

Due to multiple papers that used our dataset incorrectly, we are adding the following disclaimer: Please make sure to create a meaningful train/test data split. Do not split the data on a frame-level, but on a video/patient-level. The task becomes trivial otherwise because consecutive LUS frames are extremely correlated. We provide scripts to create a cross-validation split for you. See the instructions here.

Installation

The library itself has few dependencies (see setup.py) with loose requirements.

To run the code, just install the package pocovidnet in editable mode:

git clone https://github.com/BorgwardtLab/covid19_ultrasound.git
cd covid19_ultrasound/pocovidnet/
pip install -e .

Training the model

Set up database

A lot of data is directly provided in this repository in the data folder.

Web data

Parts of our database are videos/images from online sources that are not licensed for redistribution. This includes publications with restrictive licenses (e.g. from Elsevier) or data from commercial websites. These samples are not provided within our repo but we provide a script to download and preprocess this data automatically:

cd ../data
sh get_and_process_web_data.sh

This will take a while, but afterwards more data will be in the data folder.

Videos to images

First, we have to merge the videos and images to create an image dataset. You can use the script cross_val_splitter.py to copy from pocus images and pocus videos. It will cope the images automatically and process all videos (read the frames and save every x-th frame dependent on the framerate supplied in args).

Note: In the script, it is hard-coded that only convex POCUS data is taken, and only the classes covid, pneumonia, regular (there is not enough data for viralyet). You can change this selection in the script.

From the directory of this README, execute:

python3 scripts/build_image_dataset.py

Now, your data folder should contain a new folder image_dataset with folders covid, pneumonia, regular and viral or a subset of those dependent on your selection.

Cross validation splitting

The next step is to perform the datat split. You can use the script cross_val_splitter.py to perform a 5-fold cross validation (it will use the data from data/image_dataset by default):

From the directory of this README, execute:

python3 scripts/cross_val_splitter.py --splits 5

Now, your data folder should contain a new folder cross_validation with folders fold_1, fold_2. Each folder contains only the test data for that specific fold.

Uninformative data

If you want to add data from an uninformative class, see here.

Train the model

Afterwards you can train the model by:

python3 scripts/train_covid19.py --data_dir ../data/cross_validation/ --fold 0 --epochs 2

NOTE: train_covid19.py will automatically utilize the data from all other folds for training.

Test the model

Given a pre-trained model, it can be evaluated on a cross validations split (--data) with the following command:

python scripts/test.py [-h] [--data DATA] [--weights WEIGHTS] [--m_id M_ID] [--classes CLASSES] [--folds FOLDS] [--save_path SAVE_PATH]

Video classification

We have explored method for video classification to exploit temporal information in the videos. With the following instructions one can train a video classifier based on 3D convolutions.

python scripts/eval_vid_classifier.py [-h] [--json ../data/video_input_data/cross_val.json] [--genesis_weights GENESIS_WEIGHTS][--cam_weights CAM_WEIGHTS] [--videos ../data/pocus_videos/convex]

A json file is provided that corresponds to the cross validation split in data/cross_validation. To train a 3D CNN on a split, cd into the folder of this README and run

python scripts/video_classification.py --output models --fold 0 --epoch 40  

The models will be saved to the directory specified in the output flag.

Our results

To see our results, please have a look at our paper.

Pretrained models

To access the pre-trained models, have a look here. The default configuration in the evaluation class Evaluator in evaluate_covid19.py uses the vgg_base model which is stored in the Google Drive folder trained_models_vgg. You can place the 5 folders named fold_1 ... fold_5 into pocovidnet/trained_models and should be ready to go to use the Evaluator class.

Contact

• If you experience problems with the code, please open an issue.
• If you have questions about the project, please reach out: [email protected].

Citation

An abstract of our work was published in Thorax as part of the BTS Winter Meeting 2021. The full paper is available via the COVID-19 special issue of Applied Sciences. Please cite these in favor of our deprecated POCOVID-Net preprint.

Please use the following bibtex entries:

@article{born2021accelerating,
  title={Accelerating Detection of Lung Pathologies with Explainable Ultrasound Image Analysis}, 
  author={Born, Jannis and Wiedemann, Nina and Cossio, Manuel and Buhre, Charlotte and Brändle, Gabriel and Leidermann, Konstantin and      Aujayeb, Avinash and Moor, Michael and Rieck, Bastian and Borgwardt, Karsten}, 
  volume={11}, ISSN={2076-3417}, 
  url={http://dx.doi.org/10.3390/app11020672}, 
  DOI={10.3390/app11020672}, 
  number={2}, 
  journal={Applied Sciences}, 
  publisher={MDPI AG}, 
  year={2021}, 
  month={Jan}, 
  pages={672}
}

@article {born2021l2,
  author = {Born, J and Wiedemann, N and Cossio, M and Buhre, C and Br{\"a}ndle, G and Leidermann, K and Aujayeb, A and Rieck, B and Borgwardt, K},
  title = {L2 Accelerating COVID-19 differential diagnosis with explainable ultrasound image analysis: an AI tool},
  volume = {76},
  number = {Suppl 1},
  pages = {A230--A231},
  year = {2021},
  doi = {10.1136/thorax-2020-BTSabstracts.404},
  publisher = {BMJ Publishing Group Ltd},
  issn = {0040-6376},
  URL = {https://thorax.bmj.com/content/76/Suppl_1/A230.2},
  eprint = {https://thorax.bmj.com/content/76/Suppl_1/A230.2.full.pdf},
  journal = {Thorax}
}