ECG_Classification

ECG-DualNet: Atrial Fibrillation Classification in Electrocardiography using Deep Learning

This repository includes the code of the ECG-DualNet for ECG classification proposed in the paper Exploring Novel Algorithms for Atrial Fibrillation Detection by Driving Graduate Level Education in Medical Machine Learning (Physiological Measurement).

This repository includes the code of the follow-up work On the Atrial Fibrillation Detection Performance of ECG-DualNet (EMBC 2023, short paper).

This work was done original as part of the competition “Wettbewerb künstliche Intelligenz in der Medizin” at TU Darmstadt (KIS*MED, Prof. Hoog Antink).

A report on the project is available here. Slides of the final presentation are available here. LaTeX code of both the report and the slides is also available.

If you find this research useful in your work, please cite our papers:

@article{Rohr2022,
        title={{Exploring Novel Algorithms for Atrial Fibrillation Detection by Driving Graduate Level Education in Medical Machine Learning}},
        author={Rohr, Maurice and Reich, Christoph and H{\"o}hl, Andreas and Lilienthal, Timm and Dege, Tizian and Plesinger, Filip and Bulkova, Veronika and Clifford, Gari D and Reyna, Matthew A and Antink, Christoph Hoog},
        journal={{Physiological Measurement}},
        year={2022},
        publisher={IOP Publishing}
}

@article{Reich2023,
	title={{On the Atrial Fibrillation Detection Performance of ECG-DualNet}},
	author={Reich, Christoph and Rohr, Maurice and Kircher, Tim and Hoog Antink, Christoph},
	journal={{45th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 1-Page Paper, medRxiv}},
	year={2023}
}

Installation

All dependencies can be installed by running the following commands:

git clone https://github.com/ChristophReich1996/ECG_Classification
cd ECG_Classification
pip install --no-deps -r requirements.txt -f https://download.pytorch.org/whl/torch_stable.html
cd ecg_classification/pade_activation_unit/cuda
python setup.py install
cd ../../../

The implementation was tested Gentoo Linux 5.10.7, Python 3.8.5, and CUDA 11.1. To perform training and validation a CUDA device is recommended! This is due to the PAU implementation, which provides an efficient CUDA implementation. Training and inference on the CPU is supported but not recommended. The functionality of this repository can not be guaranteed for other system configurations.

If only CUDA 11.0 is available the code can also be executed with PyTorch 1.7.1 and Torchaudio 0.7.2 see.

Used Packages and Implementations

ECG-DualNet is implemented with PyTorch 1.8.1 and Torchaudio 0.8.1. All required packages can be seen in the requirements.txt file. For the Pade Activation Unit, the implementation (cuda extension) from the authors were adopted [1].

Docker

This repository also offers a Dockerfile to install all dependencies.

To build the Docker image run:

docker build --tag ecg_classification .

To execute the container run (with all available GPUs):

docker run -it --gpus all --rm --name user_name ecg_classification

This Dockerfile does not use the PAU CUDA extension, which leads to higher memory usage and an increased runtime.

A Dockerfile based on the Nvidia NGC container, supporting the PAU CUDA extension, is also available.

Results

Three different training runs are always reported. Weights of the best-performing model are provided.

The following validation results for the custom training/validation split on the 2017 PhysioNet Challenge dataset [2] (without pre-training) were achieved.

Model	ACC	F1	# Parameters	best
ECG-DualNet S (CNN + LSTM)	0.8527; 0.8410; 0.8455	0.8049; 0.7923; 0.7799	1840210	weights
ECG-DualNet M (CNN + LSTM)	0.8560; 0.8442; 0.8495	0.7938; 0.7955; 0.7928	4269618	weights
ECG-DualNet L (CNN + LSTM)	0.8508; 0.8213; 0.8514	0.8097; 0.7515; 0.8038	6176498	weights
ECG-DualNet XL (CNN + LSTM)	0.7702; 0.8612; 0.7866	0.6899; 0.8164; 0.7162	20683122	weights
ECG-DualNet++ S (AxAtt + Trans.)	0.7323; 0.8174; 0.7912	0.6239; 0.7291; 0.7127	1785186	weights
ECG-DualNet++ M (AxAtt + Trans.)	0.8226; 0.8259; 0.7938	0.7544; 0.7730; 0.6947	2589714	weights
ECG-DualNet++ L (AxAtt + Trans.)	0.8449; 0.8442; 0.8396	0.7859; 0.7750; 0.7671	3717426	weights
ECG-DualNet++ XL (AxAtt + Trans.)	0.8593; 0.8351; 0.8501	0.8051; 0.7799; 0.7851	8212658	weights
ECG-DualNet++ 130M (AxAtt + Trans.)	0.8475; 0.8534; 0.8462	0.7878; 0.7963; 0.7740	127833010	weights

Note that for the weights of ECG-DualNet XL and ECG-DualNet++ 130M an external link is provided.

For training on the Icentia11k dataset [3] we achieved the following results:

Model	ACC	F1	# Parameters	best	20 epochs
ECG-DualNet XL (CNN + LSTM)	0.8989	0.5135	20683122	weights	weights
ECG-DualNet++ XL (AxAtt + Trans.)	0.8899	0.5017	8212658	weights	weights

If fine-tuning the pretrained networks on the PhysioNet dataset [2] the following results were achieved:

Model	ACC	F1	# Parameters	best
ECG-DualNet XL (CNN + LSTM)	0.8455; 0.7664; 0.8468	0.7911; 0.5880; 0.8014	20683122	weights
ECG-DualNet++ XL (AxAtt + Trans.)	0.8475; 0.8481; 0.8469	0.7828; 0.7817; 0.7899	8212658	weights

In the challenge setting (pretrained weights used) the following results were achieved:

Model	ACC	F1	# Parameters	best
ECG-DualNet XL (CNN + LSTM)	0.8840; 0.8820; 0.8080	0.8549; 0.8449; 0.7360	20683122	weights
ECG-DualNet++ XL (AxAtt + Trans.)	0.8720; 0.8800; 0.8680	0.8276; 0.8494; 0.8403	8212658	weights

In the two class challenge setting (pretrained weights used) the following results were achieved:

Model	ACC	F1	# Parameters	best
ECG-DualNet XL (CNN + LSTM)	0.9800	0.9288	20683122	weights
ECG-DualNet++ XL (AxAtt + Trans.)	0.9760	0.9146	8212658	weights

Usage

Training and Ablations

To reproduce the presented results simply run (a single GPU is needed):

sh run_experiments.sh

This script trains all models listed in the table above except ECG-DualNet++ 130M. During training all logs are saved in the experiments folder (produced automatically). Most logs are stored in the PyTorch tensor format .pt and can be loaded by loss:torch.Tensor = torch.load("loss.pt""). Network weights are stored as a state dict and can be loaded by state_dict:Dict[str, torch.Tensor] = torch.load("best_model.pt").

To train the biggest ECG-DualNet++ with 130M parameters run:

python -W ignore train.py --cuda_devices "0, 1, 2, 3" --epochs 100 --batch_size 24 --physio_net --dataset_path "data/training2017/" --network_config "ECGAttNet_130M" --data_parallel

Four GPUs with 16GB are recommended. Reducing the batch size is a possible workaround if limited GPU memory is available.

To train ECG-DualNet++ with 130M parameters on two A6000 GPUs run:

python -W ignore train.py --cuda_devices "0, 1" --epochs 100 --batch_size 32 --physio_net --dataset_path "data/training2017/" --network_config "ECGAttNet_130M" --data_parallel

To reproduce the presented ablation studies run:

sh run_ablations.sh

To perform pretraining on the Icentia11k dataset [3] run:

python -W ignore train.py --cuda_devices "0" --batch_size 100 --dataset_path "/dataset/icentia11k" --icentia11k --network_config "ECGAttNet_XL" --epochs 20

Pretraining with a batch size of 100 requres a GPU with at least 32GB. If a batch size of 50 is utilized a 16GB GPU is needed. Batch size can only be set in steps of 50.

To train the pretrained models on the 2017 PhysioNet dataset [2] run:

python -W ignore train.py --cuda_devices "0" --epochs 100 --batch_size 24 --physio_net --dataset_path "data/training2017/" --network_config "ECGAttNet_XL" --load_network "experiments/20_05_2021__18_32_19ECGAttNet_XL_icentia11k_dataset/models/20.pt"

or

python -W ignore train.py --cuda_devices "0" --epochs 100 --batch_size 24 --physio_net --dataset_path "data/training2017/" --network_config "ECGCNN_XL" --load_network "experiments/21_05_2021__12_15_06ECGCNN_XL_icentia11k_dataset/models/20.pt"

The challenge submission can be reproduced by setting the additional flag --challange. For the two class challenge submission add the flag --two_classes.

Pleas note that the dataset or model paths as well as the cuda devices might change for different systems!

To run custom training the train.py script can be used. This script takes the following commands:

Argument	Default Value	Info
--cuda_devices	“0”	String of cuda device indexes to be used. Indexes must be separated by a comma.
--no_data_aug	False	Binary flag. If set no data augmentation is utilized.
--data_parallel	False	Binary flag. If set data parallel is utilized.
--epochs	100	Number of epochs to perform while training.
--lr	1e-03	Learning rate to be employed.
--physio_net	False	Binary flag. Utilized PhysioNet dataset instead of default one.
--batch_size	24	Number of epochs to perform while training.
--dataset_path	False	Path to dataset.
--network_config	“ECGCNN_M”	Type of network configuration to be utilized.
--load_network	None	If set given network (state dict) is loaded.
--no_signal_encoder	False	Binary flag. If set no signal encoder is utilized.
--no_spectrogram_encoder	False	Binary flag. If set no spectrogram encoder is utilized.
--icentia11k	False	Binary flag. If set icentia11k dataset is utilized.
--challange	False	Binary flag. If set challange split is utilized.
--two_classes	False	Binary flag. If set two classes are utilized. Can only used with PhysioNet dataset and challange flag.

All network hyperparameters can be found and adjusted in the config.py file.

Challenge Submission

The following files for the challenge submission are taken form the 18-ha-2010-pj repo by Maurice Rohr and Prof. Hoog Antink. wettbewerb.py, predict_pretrained.py, predict_trained.py, and score.py.

Please not that the weights linked in the results have to be downloaded and put in the correct directories. For detailed information pleas have a look at the predict.py file. Additionally, the publicly available PhysioNet [2] samples have to be downloaded for training.

Data

The cleaned data of the challenge (also coming from [2]) as well as the publicly available PhysioNet [2] samples can be downloaded here.

The Icentia11k dataset [3] used for pretraining can be downloaded here.

Latex Files (Report and Presentation)

For compiling the report please use pdfLaTeX. To compile the presentation slides LuaLaTeX is requred.

References

[1] @article{Molina2019,
        title={Pad\'{e} Activation Units: End-to-end Learning of Flexible Activation Functions in Deep Networks},
        author={Molina, Alejandro and Schramowski, Patrick and Kersting, Kristian},
        journal={preprint arXiv:1907.06732},
        year={2019}
}

[2] @inproceedings{Clifford2017,
        title={{AF Classification from a Short Single Lead ECG Recording: the
        PhysioNet/Computing in Cardiology Challenge 2017}},
        author={Clifford, Gari D and Liu, Chengyu and Moody, Benjamin and Li-wei, H Lehman and Silva, Ikaro and Li, Qiao and Johnson, AE and Mark, Roger G},
        booktitle={2017 Computing in Cardiology (CinC)},
        pages={1--4},
        year={2017},
        organization={IEEE}
}

[3] @article{Tan2019,
        title={Icentia11k: An unsupervised representation learning dataset for arrhythmia subtype discovery},
        author={Tan, Shawn and Androz, Guillaume and Chamseddine, Ahmad and Fecteau, Pierre and Courville, Aaron and Bengio, Yoshua and Cohen, Joseph Paul},
        journal={preprint arXiv:1910.09570},
        year={2019}
}