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[Re] Deep Learning for ECG Analysis: Benchmarks and Insights from PTB-XL

A replication of Deep Learning for ECG Analysis: Benchmarks and Insights from PTB-XL by Strodthoff et al. 2021

This github repository comprises our code replicating the experiments reported in Deep Learning for ECG Analysis: Benchmarks and Insights from PTB-XL

Full reference to the original paper :

N. Strodthoff, P. Wagner, T. Schaeffter, and W. Samek, ‘Deep Learning for ECG Analysis: Benchmarks and Insights from PTB-XL’, IEEE Journal of Biomedical and Health Informatics, vol. 25, no. 5, pp. 1519–1528, May 2021, doi: 10.1109/JBHI.2020.3022989.

Original github repository: https://github.com/helme/ecg_ptbxl_benchmarking

The main goal of this project was to reproduce the results from Strodthoff et al (2021). In addition, we tested the robustness of the proposed models by adding random noise to the ECGs in the test set. Finally, we used the provided template to implement a new model and evaluated it on the six benchmark tasks described in Strodthoff et al.

Setup and requirements

To re-run our replication experiments, simply upload the notebook PTB_XL_experiments.ipynb to Google colab and run the code cells. In the second code cell you will be asked to mount your Google Drive to the Google colab notebook. This is not mandatory, but it is recommended if you want to store the results the experiments.

Data

The dataset (PTB-XL) will be downloaded from the original data repository in the 5th code cell of the PTB_XL_experiments.ipynb notebook.

Dependencies

A custom version of Fast AI was created to make the original repository compatible with Google Colab notebooks. This is taken care of in code cell 11 in PTB_XL_experiments.ipynb.

Hyperparameter search

To perform hyperparameter search for our Inception Time model we first made a file describing all parameter combinations using make_gridsearch_file.ipynb, resulting in gridsearch_params.csv. Furthermore, we use this .csv file in Gridsearch.ipynb.

Results

Replicating results from Strodthoff et al.

The table presented below show the replicated results of Strodthoff et al. The results are obtained taking the mean of repeated (3 times) bootstrapping on the test set.

Method All Diagnostic Subdiagnostic Superdiagnostic Form Rhythm
fastai_inception1d 0.926 0.930 0.930 0.918 0.891 0.953
fastai_xresnet1d101 0.925 0.934 0.926 0.929 0.898 0.959
fastai_resnet1d_wang 0.919 0.932 0.932 0.929 0.873 0.943
fastai_fcn_wang 0.913 0.927 0.922 0.926 0.868 0.928
fastai_lstm 0.906 0.926 0.928 0.927 0.849 0.950
fastai_lstm_bidir 0.915 0.929 0.924 0.924 0.856 0.949
Wavelet+NN 0.837 0.834 0.847 0.871 0.765 0.879
ensemble 0.927 0.937 0.935 0.934 0.901 0.966

Noise

To be able to add noise to the test data we modified the prepare() method in the SCP_Experiment class, defined in ./code/experiments/scp_experiment.py. prepare() takes the arguments add_noise=Boolean, noise_mean=Float, noise_std_dev=Float.

The image below show an example of a ECG with noise_mean = 0 and noise_std_dev= 0, 0.1, 0.5 and 1

ECG with noise

The figures bellow show how the performance (in AUROC) decrease when more noise are added to the test ECGs.

Implementing a new model

The following tables presents the results obtained in the original paper as well as the results obtained by the Inception Time model (bold) in this work.

The model code for this model can be found in ./code/models/your_model.py and the configurations for the different benchmark tasks are located here: ./code/configs/your_configs.py. Finally, it also has to be specified in ./code/reproduce_results.py which models that should be used and which benchmark tasks.

1. PTB-XL: all statements

Model AUC ↓ paper/source code
Inception Time 0.926(08) our work this repo
inception1d 0.925(08) original work code
xresnet1d101 0.925(07) original work code
resnet1d_wang 0.919(08) original work code
fcn_wang 0.918(08) original work code
lstm_bidir 0.914(08) original work code
lstm 0.907(08) original work code
Wavelet+NN 0.849(13) original work code

2. PTB-XL: diagnostic statements

Model AUC ↓ paper/source code
xresnet1d101 0.937(08) original work code
resnet1d_wang 0.936(08) original work code
lstm_bidir 0.932(07) original work code
inception1d 0.931(09) original work code
Inception Time 0.929(09) our work this repo
lstm 0.927(08) original work code
fcn_wang 0.926(10) original work code
Wavelet+NN 0.855(15) original work code

3. PTB-XL: Diagnostic subclasses

Model AUC ↓ paper/source code
inception1d 0.930(10) original work code
xresnet1d101 0.929(14) original work code
lstm 0.928(10) original work code
resnet1d_wang 0.928(10) original work code
fcn_wang 0.927(11) original work code
Inception Time 0.927(08) our work this repo
lstm_bidir 0.923(12) original work code
Wavelet+NN 0.859(16) original work code

4. PTB-XL: Diagnostic superclasses

Model AUC ↓ paper/source code
resnet1d_wang 0.930(05) original work code
xresnet1d101 0.928(05) original work code
lstm 0.927(05) original work code
fcn_wang 0.925(06) original work code
Inception Time 0.922(06) our work this repo
inception1d 0.921(06) original work code
lstm_bidir 0.921(06) original work code
Wavelet+NN 0.874(07) original work code

5. PTB-XL: Form statements

Model AUC ↓ paper/source code
inception1d 0.899(22) original work code
xresnet1d101 0.896(12) original work code
resnet1d_wang 0.880(15) original work code
lstm_bidir 0.876(15) original work code
fcn_wang 0.869(12) original work code
lstm 0.851(15) original work code
Inception Time 0.840(11) our work this repo
Wavelet+NN 0.757(29) original work code

6. PTB-XL: Rhythm statements

Model AUC ↓ paper/source code
xresnet1d101 0.957(19) original work code
inception1d 0.953(13) original work code
lstm 0.953(09) original work code
lstm_bidir 0.949(11) original work code
resnet1d_wang 0.946(10) original work code
fcn_wang 0.931(08) original work code
Inception Time 0.923(32) our work this repo
Wavelet+NN 0.890(24) original work code