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MACRO: Towards Classification of Co-Occurring Diseases in 12-Lead ECGs

Official PyTorch implementation of the paper "MACRO: A Multi-Head Attentional Convolutional Recurrent Network for Multi-Label Classification of Co-Occurring Diseases in 12-Lead ECGs"

Requirements

This project was developed using Python 3.10.12 and PyTorch 2.0.1. The requirements.txt contains all Python libraries that the project depends on, and can be installed using:

pip install -r requirements.txt

Important: The PYTHONPATH variable should be adapted to point to the project root directory to ensure that the modules can be imported correctly:

export PYTHONPATH=$PYTHONPATH:<root project path>

Model Architectures

MACRO

images/MACRO_detailed.png

Multi-Branch MACRO (MB-M)

images/multibranch_MACRO_detailed_v4.png

Datasets

CPSC 2018

The main dataset used in this study is the CPSC 2018 dataset, which contains 6877 ECG recordings. We preprocessed the dataset by resampling the ECG signals to 250 Hz and equalizing the ECG signal length to 60 seconds, yielding a signal length of T=15,000 data points per recording. For the hyperparameter study, we employed a fixed train-valid-test split with ratio 60-20-20, while for the final evaluations, including the comparison with the state-of-the-art methods and ablation studies, we used a 10-fold cross-validation strategy.

Our preprocessed data can be downloaded from FigShare and should be placed in the data directory at project root level while maintaining the folder structure. In case of using the fixed train-valid-test split, the validation set is automatically created from the training set during the training process.

Alternatively, the raw CPSC 2018 dataset can be downloaded from the PhysioNet/Computing in Cardiology Challenge 2020 website. The downloaded .mat and .hea files can be merged into a single folder and copied to data/CinC_CPSC/raw. Then, our preprocessing pipeline can be executed manually by running the preprocesssing/preprocess_cpsc.py script to get our preprocessed data and folder structure, including the data split and cross-validation folder.

PTB-XL (Super-Diag.)

To assess generalizability, we also utilize PTB-XL, a large multi-label dataset of 21,799 clinical 12-lead ECG records of 10 seconds each. PTB-XL contains 71 ECG statements, categorized into 44 diagnostic, 19 form, and 12 rhythmic classes. In addition, the diagnostic category can be divided into 24 sub- and 5 coarse-grained super-classes. For our experiments, we utilize the super-diagnostic labels for classification and the recommended train-valid-test splits, sampled at 100 Hz. We select only samples with at least one label in the super-diagnostic category, without applying any further preprocessing - the resulting dataset can be downloaded from FigShare or created manually by downloading the raw dataset from the PhysioNet/PTB-XL website and running the preprocesssing/preprocess_ptblxl.py script.

Device Preparation

To train the models, we recommend using a GPU. The GPU ID (device UUID) can be set in the configuration file global_config.py by adapting the CUDA_VISIBLE_DEVICES variable. For Nvidia GPUs, the UUID can be retrieved by running the following command:

nvidia-smi -q | grep UUID

Moreover, a path for creating the RayTune temporary directory should be set in the global_config.py file by adjusting the TUNE_TEMP_DIR variable.

Training and Testing with Fixed Data Split

To train one of the models with a fixed 60-20-20 data split, run the following command with the path to the corresponding configuration file of interest:

python train.py -c configs/single_run_examples/config_baseline.json

To evaluate a trained model on the test set, run the following command:

python test.py --resume <path_to_model_checkpoint>

Example resume path: <project_path>/savedVM/models/BaselineModel_SingleRun/<run_id>/model_best.pth

The path to the test set is automatically retrieved from the corresponding config file, which is saved to the model path during training. Under this path, the evaluation results are saved as well into a test_output folder.

Scope: This works for both, the fixed split on CPSC 2018 and the recommended PTB-XL split.

Training with Hyperparameter Tuning

To train the model with hyperparameter tuning via RayTune, run the following command with the path to the corresponding configuration file of interest and the --tune flag:

python train.py -c configs/param_study_examples/config.json --tune

Important: The hyperparameter search space can be defined in the tuning_params method of the train.py file. The metrics configured for the CLI Reporter in the train_fn method should match those defined in the config file. Depending on the GPU size and architecture, the number of parallel trials can be adjusted by setting the num_gpu variable to the desired value in the train_fn method.

Scope: This was only used for the fixed split of CPSC 2018, not for PTB-XL.

Training with 10-Fold Cross-Validation (CV)

To train the model with 10-fold cross-validation, run the following command with the path to the corresponding configuration file of interest:

python train_with_cv.py -c configs/CV/config.json

Scope: We only used 10-fold CV for CPSC 2018. For PTB-XL, we only experimented with the recommended train-valid-test splits (cf. "Training and Testing with Fixed Data Split" above).

Machine Learning Classifiers (CPSC 2018)

To train and evaluate machine learning classifiers, the input and output tensors across all folds need to be retrieved, while maintaining the fold structure and data split. For this, run the following command to save the detached tensors to an output_logging subdirectory:

python ML_ensemble/retrieve_detached_cross_fold_tensors.py -p <path_to_trained_model>

Example path: <project_path>/savedVM/models/Multibranch_MACRO_CV/<run_id>/

Afterwards, the ML classifiers can be trained and evaluated based on these tensors by running the following command:

python ML_ensemble/train_ML_models_with_detached_tensors.py
 -p <path_to_trained_model>
 --strategy "gradient_boosting"

Example path: <project_path>/savedVM/models/Multibranch_MACRO_CV/<run_id>/

By default, all features from the Multi-Branch MACRO (MB-M) and all BranchNets are used (i.e., 117 features). For a reduced feature set, the following flags can be passed:

  • --individual_features : Predicted probabilities only for the class of interest (13 features)
  • --reduced_individual_features : Predicted probabilities only for the class of interest w/o MB-M (12 features)

Important: Since a parameter study is performed for each class' binary classifier per fold, the whole process can take a while, depending on the number of features used. After completion, the results are saved in a ML models/<ML setting> subdirectory. In order to get an improved, human-readable summary, you can use the summarize_cross_valid_batch.py script from the utils directory described below:

python utils/summarize_cross_valid_batch.py -p "savedVM/models/Multibranch_MACRO_CV/<run_id>/ML models"

For each ML setting, a summary file called cross_valid_runs_summary.tex is created in the corresponding subdirectory.

Scope: The above documentation describes the procedure for the cross-validation data on the CPSC 2018 dataset. For the fixed PTB-XL splits, other scripts are required: retrieve_detached_single_run_tensors.py and train_ML_models_with_detached_single_run_tensors.py

Script Utils

The utils directory contains scripts for the following tasks:

  • summarize_cross_valid_batch.py: Summarizes the results of multiple cross-validation runs within a folder, one run at a time. A path should be specified to the folder containing the cross-validation runs. Example usage: 
    python utils/summarize_cross_valid_batch.py -p "savedVM/models/BaselineWithMultiHeadAttention_CV"
  • summarize_cross_valid_for_paper.py: Fuses the results of the specified cross-validation runs in a suitable format for the publication. The paths can be specified at the beginning of the script.
  • summarize_tune_runs.py: Can be used to summarize the results of a hyperparameter tuning run within a folder. Details need to be configured at the beginning of the script.
  • tracker.py and util.py : Helper functions (used internally by other code segments)

The utils_bash directory contains scripts for the following tasks:

  • clear_all_ckpt_from_folder.sh : Removes all checkpoint files except model_best.pth from the folders specified in RELATIVE_PATHS_TO_FOLDERS, including single training runs, tune runs, and CV runs.
  • run-eval.sh : Evaluates all models in the specified folder on the test set. Should only be used with single training runs.
  • run-eval-tune.sh : Evaluates all models in the specified folder on the test set. Should only be used with RayTune runs.

Acknowledgements and License

This project is inspired by the PyTorch Template Project by Victor Huang. It is licensed under the MIT License (see LICENSE for more details).

References

Please acknowledge our work by citing our BHI2024 paper:

@inproceedings{borst2024MACRO,
title={{MACRO}: A Multi-Head Attentional Convolutional Recurrent Network for Multi-Label Classification of Co-Occurring Diseases in 12-Lead {ECGs}},
author={Vanessa Borst and Robert Leppich and Samuel Kounev},
booktitle={2024 IEEE EMBS International Conference on Biomedical and Health Informatics (BHI)},
pages={TBD},
year={2024},
organization={IEEE}
}