| Literature DB >> 34121811 |
Kai Hu1,2, Yingjie Huang1, Wei Huang3, Hui Tan1, Zhineng Chen4, Zheng Zhong3, Xuanya Li5, Yuan Zhang1, Xieping Gao1,6.
Abstract
The outbreak and rapid spread of coronavirus disease 2019 (COVID-19) has had a huge impact on the lives and safety of people around the world. Chest CT is considered an effective tool for the diagnosis and follow-up of COVID-19. For faster examination, automatic COVID-19 diagnostic techniques using deep learning on CT images have received increasing attention. However, the number and category of existing datasets for COVID-19 diagnosis that can be used for training are limited, and the number of initial COVID-19 samples is much smaller than the normal's, which leads to the problem of class imbalance. It makes the classification algorithms difficult to learn the discriminative boundaries since the data of some classes are rich while others are scarce. Therefore, training robust deep neural networks with imbalanced data is a fundamental challenging but important task in the diagnosis of COVID-19. In this paper, we create a challenging clinical dataset (named COVID19-Diag) with category diversity and propose a novel imbalanced data classification method using deep supervised learning with a self-adaptive auxiliary loss (DSN-SAAL) for COVID-19 diagnosis. The loss function considers both the effects of data overlap between CT slices and possible noisy labels in clinical datasets on a multi-scale, deep supervised network framework by integrating the effective number of samples and a weighting regularization item. The learning process jointly and automatically optimizes all parameters over the deep supervised network, making our model generally applicable to a wide range of datasets. Extensive experiments are conducted on COVID19-Diag and three public COVID-19 diagnosis datasets. The results show that our DSN-SAAL outperforms the state-of-the-art methods and is effective for the diagnosis of COVID-19 in varying degrees of data imbalance.Entities:
Keywords: COVID-19; Classification; Data imbalance; Deep supervised learning; Self-adaptive auxiliary loss
Year: 2021 PMID: 34121811 PMCID: PMC8180474 DOI: 10.1016/j.neucom.2021.06.012
Source DB: PubMed Journal: Neurocomputing ISSN: 0925-2312 Impact factor: 5.719
The number of samples of each class in the datasets with CT scans.
| Literature | Samples |
|---|---|
| Wang et al. | 325 COVID-19 |
| 740 Viral pneumonia | |
| He et al. | 349 COVID-19 |
| 397 non-COVID-19 | |
| Soares et al. | 1252 COVID-19 |
| 1229 non-COVID-19 | |
| Xu et al. | 219 COVID-19 |
| 224 Influenza-A | |
| 175 Normal | |
| Ying et al. | 777 COVID-19 |
| 505 Bacterial pneumonia | |
| 708 Normal | |
| Gunraj et al. | 21395 COVID-19 |
| 36856 Common pneumonia | |
| 45758 Normal | |
Fig. 1Overview of the proposed COVID-19 diagnosis method.
Fig. 2The architecture of the proposed deep supervised network with self-adaptive auxiliary loss.
Dataset split of our COVID19-Diag.
| Item | Class | Training | Testing |
|---|---|---|---|
| Cases | COVID-19 | 43 | 18 |
| Normal | 67 | 28 | |
| Bacterial Pneumonia | 48 | 21 | |
| Images | COVID-19 | 1256 | 513 |
| Normal | 2674 | 1150 | |
| Bacterial Pneumonia | 980 | 409 | |
Fig. 3Samples of normal (top row), bacterial pneumonia (middle row), and COVID-19 (bottom row).
Performance comparison of DSN-SAAL with other classification models on our COVID19-Diag dataset. The best results are highlighted in bold.
| Model | ACC | F1-score | G-mean |
|---|---|---|---|
| VGG-16 | 0.836 | 0.748 | 0.849 |
| ResNet-50 | 0.837 | 0.763 | 0.838 |
| DenseNet-169 | 0.844 | 0.767 | 0.862 |
| MobileNet-V2 | 0.867 | 0.797 | 0.873 |
| ResNeXt-50 | 0.846 | 0.765 | 0.850 |
| Self-Trans | 0.909 | 0.866 | 0.896 |
| Transfer-CheXNet | 0.899 | 0.848 | 0.885 |
| Meta-Weight-Net | 0.888 | 0.825 | 0.868 |
Fig. 4The ROC curves of our DSN-SAAL and some popular models.
Performance comparison of whether to add auxiliary supervision in classification models on our COVID19-Diag dataset.
| Model | Method | ACC | F1-score | G-mean | Params |
|---|---|---|---|---|---|
| VGG-16 | Baseline | 0.836 ± 0.013 | 0.748 ± 0.018 | 0.849 ± 0.008 | 134.28 M |
| 134.32 M | |||||
| ResNet-50 | Baseline | 0.837 ± 0.009 | 0.763 ± 0.017 | 0.838 ± 0.017 | 23.51 M |
| 23.59 M | |||||
| DenseNet-169 | Baseline | 0.844 ± 0.002 | 0.767 ± 0.004 | 0.862 ± 0.001 | 12.48 M |
| 12.49 M | |||||
| ResNeXt-50 | Baseline | 0.846 ± 0.012 | 0.765 ± 0.017 | 0.850 ± 0.007 | 22.98 M |
| 23.06 M | |||||
Performance comparison of VGG-16 with different loss functions to solve the data imbalance on our COVID19-Diag dataset.
| Method | ACC | F1-score | G-mean |
|---|---|---|---|
| CE | 0.836 ± 0.013 | 0.748 ± 0.018 | 0.849 ± 0.008 |
| Focal Loss | 0.851 ± 0.007 | 0.766 ± 0.011 | 0.855 ± 0.008 |
| CB Loss | 0.861 ± 0.005 | 0.782 ± 0.007 | 0.868 ± 0.006 |
| SCE | 0.856 ± 0.014 | 0.804 ± 0.014 | 0.885 ± 0.010 |
Performance comparison of DSN-SAAL with the baseline under both balanced and imbalanced distributions of our COVID19-Diag dataset.
| Imbalanced | ACC | F1-score | G-mean | SEN | SPE | |||||
|---|---|---|---|---|---|---|---|---|---|---|
| Base. | D.S. | Base. | D.S. | Base. | D.S. | Base. | D.S. | Base. | D.S. | |
| Stand. split | 0.836 ± 0.013 | 0.748 ± 0.018 | 0.849 ± 0.008 | 0.822 ± 0.009 | 0.877 ± 0.018 | |||||
| 25% of COVID-19 | 0.837 ± 0.004 | 0.719 ± 0.005 | 0.803 ± 0.006 | 0.702 ± 0.013(-0.120) | 0.918 ± 0.006 | |||||
| 10% of COVID-19 | 0.832 ± 0.003 | 0.692 ± 0.014 | 0.758 ± 0.008 | 0.602 ± 0.012(-0.220) | 0.955 ± 0.009 | |||||
| 5% of COVID-19 | 0.804 ± 0.005 | 0.581 ± 0.015 | 0.666 ± 0.011 | 0.464 ± 0.015(-0.358) | 0.956 ± 0.005 | |||||
| 1% of COVID-19 | 0.731 ± 0.010 | 0.141 ± 0.030 | 0.278 ± 0.033 | 0.080 ± 0.018(-0.742) | 0.983 ± 0.005 | |||||
Base.: Baseline; D.S.: DSN-SAAL
Fig. 5Confusion matrix for DSN-SAAL on our COVID19-Diag dataset. Fig. 5a–d are the results with 25, 10, 5 and 1 of COVID-19 samples respectively.
Fig. 6Examples of the diagnostic results obtained using our DSN-SAAL.
Fig. 7Visualization of raw images with COVID-19 (the first row), the input images (the second row), and CAMs obtained by VGG-16 with CE (the third row) and our DSN-SAAL (the fourth row).
Comparison with the state-of-the-art methods on the COVIDx-CT dataset.
| Section | Method | ACC | SEN (Normal/CP/NCP) | PRE (Normal/CP/NCP) |
|---|---|---|---|---|
| Stand.split | COVIDNet-CT | 0.9911 | 1.0000/0.9904/0.9731 | 0.9940/0.9844/0.9969 |
| VisionPro | 0.9960 | 0.9992/0.9922/0.9959 | 0.9962/0.9966/0.9947 | |
| 5% of training set | COVID-CT-Mask-Net | 0.9166 | 0.9110/0.9162/0.9080 | 0.9433/0.8708/0.9475 |
| Two Stage Model | 0.9564 | 0.9691/0.9506/0.9388 | 0.9766/0.9300/0.9588 | |
| Lightweight Model | 0.9395 | 0.9698/0.9163/0.9135 | – | |
| One Shot Model | – | 0.9927/0.9813/0.9574 | – | |
| COVIDNet-CT | 0.9757 | –/–/0.9249 | – | |
Comparison with the state-of-the-art methods on the COVID19-CT dataset.
| Method | ACC | F1-score | AUC |
|---|---|---|---|
| VGG-16 | 0.76 | 0.76 | 0.82 |
| ResNet-50 | 0.80 | 0.81 | 0.88 |
| DenseNet-169 | 0.83 | 0.81 | 0.87 |
| Self-Trans | 0.86 | 0.85 | |
| Contrastive-COVIDNet | 0.79 | 0.79 | 0.85 |
| Transfer-CheXNet | 0.87 | 0.75 | |
| Cross-Datasets Analysis | 0.91 | ||
| 0.87 | 0.91 |
Comparison with the state-of-the-art methods on the SARS-CoV-2 CT-scan dataset.
| Method | ACC | F1-score | AUC | PRE | SEN |
|---|---|---|---|---|---|
| AdaBoost | 0.9516 | 0.9514 | 0.9519 | 0.9363 | 0.9671 |
| Decision Tree | 0.7944 | 0.7984 | 0.7951 | 0.7681 | 0.8313 |
| AlexNet | 0.9375 | 0.9361 | 0.9368 | 0.9498 | 0.9228 |
| VGG-16 | 0.9496 | 0.9497 | 0.9496 | 0.9402 | 0.9543 |
| GoogleNet | 0.9173 | 0.9182 | 0.9179 | 0.9020 | 0.9350 |
| ResNet | 0.9496 | 0.9503 | 0.9498 | 0.9300 | 0.9715 |
| xDNN | 0.9738 | 0.9731 | 0.9736 | 0.9916 | 0.9553 |
| Contrastive-COVIDNet | 0.9083 | 0.9087 | 0.9624 | 0.9575 | 0.8589 |
| Cross-Datasets Analysis | 0.9889 | – | – | 0.9920 | 0.9880 |
| MADE-DBM | 0.9837 | 0.9814 | 0.9832 | 0.9874 | 0.9887 |
| 1: Net |
| 2: |
| 3: |
| 4: |
| 5: |
| 6: |
| 7: |
| 8: |
| 9: |
| 10: |
| 11: |
| 12: |
| 13: |
| 14: |
| 15: |
| 16: |
| 17: |