uark-aicv/ecg_ssl_12lead

[IEEE BHI 2022] Multimodality Multi-Lead ECG Arrhythmia Classification using Self-Supervised Learning

1. Download datasets from the PhysioNet 2020 Competition. Put in the folder ./data_folder/datasets and extract all of them . https://physionetchallenges.github.io/2020/

2. Preparing the data python data_preparation/data_extraction_without_preprocessing.py python data_preparation/reformat_memmap.py

3. Training base models python experiments/run_signal.py --batch_size 128 --lr_rate 5e-3 --num_epoches 100 --gpu 0 --save_folder ./checkpoints/base_signal python experiments/run_spectrogram.py --batch_size 256 --lr_rate 5e-3 --num_epoches 200 --gpu 0 --save_folder ./checkpoints/base_spectrogram (without gating fusion) python experiments/run_ensembled.py --batch_size 128 --lr_rate 5e-3 --num_epoches 100 --gpu 0 --save_folder ./checkpoints/base_ensemble_wogating (with gating fusion) python experiments/run_ensembled.py --batch_size 128 --lr_rate 5e-3 --num_epoches 100 --gpu 0 --gating --save_folder ./checkpoints/base_ensemble_wgating

4. Self-supervised learning for pretrained models (SimCLR) python experiments/SIMCLR_signal.py (BYOL) python experiments/BYOL_signal.py (DINO) python experiments/DINO_signal.py python experiments/DINO_spectrogram.py

5. Finetuning the main model based on the self-supervised pretrained models (SimCLR) python experiments/SIMCLR_signal_finetune.py (BYOL) python experiments/BYOL_signal_finetune.py (DINO) python experiments/run_signal.py --batch_size 128 --lr_rate 5e-3 --num_epoches 100 --gpu 0 --finetune ./checkpoints/DINO_signal_student.pth --save_folder ./checkpoints/finetune_signal python experiments/run_spectrogram.py --batch_size 256 --lr_rate 5e-3 --num_epoches 200 --gpu 0 --finetune ./checkpoints/DINO_spectrogram_student.pth --save_folder ./checkpoints/finetune_spectrogram (without gating fusion) python experiments/run_ensembled.py --batch_size 128 --lr_rate 5e-3 --num_epoches 100 --gpu 0 --finetune ./checkpoints --save_folder ./checkpoints/finetune_ensemble_wogating (with gating fusion) python experiments/run_ensembled.py --batch_size 128 --lr_rate 5e-3 --num_epoches 100 --gpu 0 --finetune ./checkpoints --gating --save_folder ./checkpoints/finetune_ensemble_wgating

6. Searching the thresholds of classes for best Challenge score python experiments/threshold_search.py --model_type signal --best-type PRC --gpu 0 --weight_folder ./checkpoints/base_signal