CPSC2021

Paroxysmal Atrial Fibrillation Events Detection from Dynamic ECG Recordings: The 4th China Physiological Signal Challenge 2021

Offline generated training data

CPSC2021-sliced on Kaggle.

Graphical Abstract of the Solution

Main files

<details> <summary>Click to view!</summary>

• Files required by the submission system
  • entry_2021.py: entry file of the challenge
  • score_2021.py: scoring function of the challenge
• Files of the solution:
  • cfg.py: configurations for the preprocessing, augmentation, model, trainer, etc.
  • data_reader.py: contains a class which makes reading data, annotations, etc. more easy
  • dataset.py: torch Dataset which generates tensors for training the models
  • model.py: models, adjustification of the architecture is highly flexible
  • trainer.py: contains a trainer class
• Files for analyzing and visualizing experiments:
  • gather_results.py
• Test files:
  • test_entry.py
• Notebooks (the filenames imply the usages):
  • inspect_data.ipynb
  • train_models.ipynb
  • aggregate_val_res.ipynb

</details>

Remember to change BaseCfg.db_dir to your local data directory.

Results (Rankings)

Results on the hidden test set

<details> <summary>Click to view!</summary> <table class="table w-100 table-bordered text-center"> <tbody><tr class="table-primary font-weight-bold"><td style="width:12%">Name</td><td style="width:25%">Affiliation</td><td style="width:30%">Team Members</td><td style="width:10%">Test_I</td><td>Test_II</td><td>Average</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/1-usstmed.zip" target="_blank">usstmed</a></td><td>University of Shanghai for Science and Technology</td><td>Wenjie Cai, Fanli Liu, Bolin Xu, Xuan Wang, Yufeng Ji</td><td>2.0629</td><td>4.3921</td><td>3.2275</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/2-CeZIS.zip" target="_blank">CeZIS</a></td><td>^1.VSL Software, a.s., Košice, Slovakia;<br>^2.Pavol Jozef Šafárik University in Košice, Slovakia</td><td>Peter Bugata¹, Peter Bugata Jr.¹, David Gajdos¹, David Hudak¹,Vladimira Kmecova¹, Monika Stankova¹, Lubomir Antoni², Erik Bruoth², Simon Horvat², Richard Stana², Alexander Szabari², Gabriela Vozarikova²</td><td>2.1128</td><td>3.5716</td><td>2.8422</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/3-UNIWA.zip" target="_blank">UNIWA</a></td><td>University of West Attica, Greece</td><td>Lampros Kokkalas, Nicolas A. Tatlas, Stelios M. Potirakis</td><td>2.0144</td><td>3.3833</td><td>2.6989</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/4-lingshui_BME.zip" target="_blank">lingshui_BME</a></td><td>^1.Dalian University of Technology;<br>^2.RWTH Aachen University</td><td>Yating Hu¹, Tengfei Feng², Hong Tang¹</td><td>1.8754</td><td>3.5116</td><td>2.6935</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/5-Taozi.zip" target="_blank">Taozi</a></td><td>Tianjin Medical University, Beihang University</td><td>Jingsu Kang, Hao Wen </td><td>1.9972</td><td>3.0907</td><td>2.5440</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/6-Metformin-121.zip" target="_blank">Metformin-121</a></td><td>National Taiwan University; Academia Sinica; Taiwan Artificial Intelligence Academy Foundation</td><td>Tsai-Min Chen, Yi-Dar Tang, Huan-Hsin Tseng, Wei Luok Ngu, Le-Yin Hsu, Miao-Chen Chiang, Yu-Te Ku, Ming-Yi Hong, Yu Tsao</td><td>1.6277</td><td>2.6649</td><td>2.1463</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/7-MVTECH.zip" target="_blank">MVTECH</a></td><td>Shanghai Medical Vision Technology Co. Ltd.</td><td>Yang Hou, Jinlei Li</td><td>1.7966</td><td>2.4346</td><td>2.1156</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/8-FUDU_Car.zip" target="_blank">FUDU_Car</a></td><td>Fudan University</td><td>Sen Liu, Ya‘nan Wang, Haijun Jia </td><td>1.9147</td><td>1.9473</td><td>1.9310</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/9-WHS.zip" target="_blank">WHS</a></td><td> ^1.Central South University<br>^2.China University of Geosciences</td><td>Lebing Pan, Jiechen Tang</td><td>1.8585</td><td>1.9236</td><td>1.8911</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/10-Muhammad%20Uzair%20Zahid.zip" target="_blank">Muhammad Uzair Zahid</a></td><td>^1. Tampere University, Finland;<br>^2. Qatar University, Qatar</td><td>Muhammad Uzair Zahid¹, Mustafa Serkan Kiranyaz², Moncef Gabbouj¹</td><td>1.8192</td><td>1.9469</td><td>1.8831</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/11-DaBin.zip" target="_blank">DaBin</a></td><td>Beijing University of Technology</td><td>Fengya Liu, Rui Yu, Shuicai Wu, Guangyu Bin,Zhuhuang Zhou ,Qian Wang</td><td>1.8352</td><td>0.9728</td><td>1.4040</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/12-Lastone.zip" target="_blank">Lastone</a></td><td>King's College London, UK</td><td>Xinqi Bao, Fenghe Hu</td><td>0.9616</td><td>1.6430</td><td>1.3023</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/13-BSU%E5%B7%A5%E7%A8%8B%E5%B0%8F%E5%88%86%E9%98%9F(1).zip" target="_blank">BSU工程小分队</a></td><td>Beijing Sport University</td><td>Kuan Tao, Lixin Sun</td><td>1.2384</td><td>1.1710</td><td>1.2047</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/14-CUTCM.zip" target="_blank">CUTCM</a></td><td>City University of Hong Kong</td><td>Marshall</td><td>0.6706</td><td>1.3854</td><td>1.0280</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/15-AZ-unet.zip" target="_blank">AZ-unet</a></td><td>AstraZeneca</td><td>Hannes Whittingham, Long Luu</td><td>1.1168</td><td>0.7788</td><td>0.9478</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/16-AIBI_LAB.zip" target="_blank">AIBI_LAB</a></td><td>Ludong University</td><td>Shuhong Wei, Yipeng Wang, Yu Ji, Yinhao Sun</td><td>0.7837</td><td>1.1006</td><td>0.9422</td></tr> <tr><td><a href="https://opensz.oss-cn-beijing.aliyuncs.com/icbeb2021/file/cpsc/17-CPSC_eie.zip" target="_blank">CPSC_eie</a></td><td>Zhejiang University of Technology, China</td><td>Xinyuan Ying, Qing Pan, Ziyou Zhang</td><td>0.8555</td><td>0.9629</td><td>0.9092</td></tr> <tr><td>Baseline</td><td>/</td><td>/</td><td>0.6819</td><td>0.6485</td><td>0.6652</td></tr> </tbody></table> </details>

See the official website for more details.

Results on the validation set

Raw results are gathered into one zip file, the val_res.zip in the results folder

| Network(s) | Merge Rule | Score on Partial Hidden Test Set | Score on Validation Set| |-------------------|---------------|----------------------------------|------------------------| | LSTM | NA | 1.9392 | 2.0621 | | SeqTag | NA | 1.9781 | 2.1577 | | U-Net | NA | 1.3699 | NA | | LSTM + U-Net | Union | 1.7829 | NA | | LSTM + SeqTag | Intersection | 1.9287 | NA | | LSTM + SeqTag | Union | 1.9766 | 2.1682 | | LSTM + SeqTag | New Union | 1.9972 | 2.2179 |

Confusion matrices of the LSTM model and the SeqTag model

<p align="middle"> <img src="/images/rr-lstm-confusion-matrix.svg" width="33%" /> &nbsp; &nbsp; &nbsp; &nbsp;&nbsp; &nbsp; &nbsp; &nbsp; <img src="/images/seq-tag-confusion-matrix.svg" width="33%" /> </p>

More detailed analysis using pandas

<p align="middle"> <img src="/images/res_ana_1.png" width="60%" /> <img src="/images/res_ana_2.png" width="110%" /> </p>

Citation

See the file CITATIONS.bib. Also at sciencedirect.

References

See the references listed on the sciencedirect webpage.