| Literature DB >> 34366576 |
Amar Kumar Verma1, Inturi Vamsi2, Prerna Saurabh3, Radhika Sudha1, Sabareesh G R2, Rajkumar S3.
Abstract
This paper proposes a wavelet and artificial intelligence-enabled rapid and efficient testing procedure for patients with Severe Acute Respiratory Coronavirus Syndrome (SARS-nCoV) through a deep learning approach from thoracic X-ray images. Presently, the virus infection is diagnosed primarily by a process called the real-time Reverse Transcriptase-Polymerase Chain Reaction (rRT-PCR) based on its genetic prints. This whole procedure takes a substantial amount of time to identify and diagnose the patients infected by the virus. The proposed research uses a wavelet-based convolution neural network architectures to detect SARS-nCoV. CNN is pre-trained on the ImageNet and trained end-to-end using thoracic X-ray images. To execute Discrete Wavelet Transforms (DWT), the available mother wavelet functions from different families, namely Haar, Daubechies, Symlet, Biorthogonal, Coiflet, and Discrete Meyer, were considered. Two-level decomposition via DWT is adopted to extract prominent features peripheral and subpleural ground-glass opacities, often in the lower lobes explicitly from thoracic X-ray images to suppress noise effect, further enhancing the signal to noise ratio. The proposed wavelet-based deep learning models of both, two-class instances (COVID vs. Normal) and four-class instances (COVID-19 vs. PNA bacterial vs. PNA viral vs. Normal) were validated from publicly available databases using k-Fold Cross Validation (k-Fold CV) technique. In addition to these X-ray images, images of recent COVID-19 patients were further used to examine the model's practicality and real-time feasibility in combating the current pandemic situation. It was observed that the Symlet 7 approximation component with two-level manifested the highest test accuracy of 98.87%, followed by Biorthogonal 2.6 with an efficiency of 98.73%. While the test accuracy for Symlet 7 and Biorthogonal 2.6 is high, Haar and Daubechies with two levels have demonstrated excellent validation accuracy on unseen data. It was also observed that the precision, the recall rate, and the dice similarity coefficient for four-class instances were 98%, 98%, and 99%, respectively, using the proposed algorithm.Entities:
Keywords: COVID-19; Medical imaging; Transfer learning; Wavelets; rRT-PCR
Year: 2021 PMID: 34366576 PMCID: PMC8327617 DOI: 10.1016/j.eswa.2021.115650
Source DB: PubMed Journal: Expert Syst Appl ISSN: 0957-4174 Impact factor: 6.954
Summary of the COVID-19 detection and diagnostic methods for thoracic X-ray and CT image.
| Authors | Image modality | Method used | COVID-19 positive cases | Accuracy (in %) |
|---|---|---|---|---|
| CT images | ResNet-18 + location attention | 219 (+) | 86.70 | |
| X-ray images | ResNet-18 + classification head + anomaly detection head | 100 (+) | 96.00 | |
| X-ray images | COVID-Net | 53 (+) | 92.40 | |
| X-ray images | ResNet50+SVM | 25 (+) | 95.38 | |
| CT images | DenseNet121 | 924 (+) | 80.12 | |
| X-ray images | Deep CNN ResNet-50 | 50 (+) | 98.00 | |
| CT images | ResNet-50 | 50 (+) | 94.00 | |
| X-ray images | VGG-19 | 244 (+) | 93.48 | |
| X-ray images | DeTrac | 105 (+) | 95.12 | |
| X-ray images | ResNet50+VGG16 | 135 (+) | 94.40 | |
| CT images | COVNet | 400 (+) | 90.00 | |
| CT images | DeCoVNet | 313 (+) | 90.00 | |
| CT images | DRE-Net | 777 (+) | 86.00 | |
| X-ray images | DarkCovidNet | 125 (+) | 87.02 | |
| X-ray images | CoroNet | 284 (+) | 89.60 | |
| CT images | M-Inception | 195 (+) | 82.90 | |
| X-ray images | CNN | 100 (+) | 93.20 | |
| X-ray images | VGG-16 based Fast R-CNN | 183 (+) | 97.36 | |
| CT images | FGCNet | 320 (+) | 97.71 | |
| CT images | CCSHNet | 284 (+) | 98.30 | |
| CT images | 7L-CNN-CD | 142 (+) | 94.44 |
Fig. 1Single-level decomposition through 2-D DWT.
Fig. 2Sample of thoracic X-ray image dataset for four-class instances.
Fig. 3Reconstructed thoracic X-ray image coefficient for db2 with DWT two-level approximation.
Fig. 4Reconstructed thoracic X-ray image coefficient for db2 with DWT two-level.
Fig. 5Network-based architecture for deep CNN using DWT featured thoracic X-ray images.
Image dataset description.
| SN. | Disease | Number of Images |
|---|---|---|
| 1 | Normal | 2398 |
| 2 | Pneumonia Viral | 3204 |
| 3 | Pneumonia Bacterial | 846 |
| 4 | COVID-19 | 1552 |
Accuracy (in%) for various wavelets.
| Wavelet | Level | |
|---|---|---|
| Level1 | Level2 | |
| Haar | 97.25 | 98.35 |
| Symlet | 96.62 | 98.87 |
| Biorthogonal | 95.92 | 98.73 |
| Coiflet | 96.25 | 98.31 |
| Daubechies | 98.18 | 98.43 |
| Discrete Meyer | 93.77 | 96.90 |
Accuracy (in%) with respect to the several wavelet families for two-levels of decomposition for DWT.
| Biorthogonal (%) | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| bior1.1 | bior1.3 | bior1.5 | bior2.2 | bior2.4 | bior2.6 | bior2.8 | bior3.1 | bior3.3 | bior3.5 | bior3.7 | bior3.9 | bior4.4 | bior5.5 | bior6.8 |
| 97.57 | 98.17 | 98.17 | 97.89 | 98.45 | 98.73 | 98.17 | 96.90 | 96.06 | 96.62 | 97.53 | 96.34 | 98.45 | 96.62 | 95.77 |
Fig. 6Accuracy with and without wavelet for three-class instances.
Descriptive statistics of the accuracy with and without wavelet for three-class instances.
| Descriptive Statistics | Mean | Standard Deviation | SE of mean | Lower 95% CI of Mean | Upper 95% CI of Mean | Min | Median | Max |
|---|---|---|---|---|---|---|---|---|
| Haar_Wavelet_Level1 | 97.14 | 1.57 | 0.47 | 96.08 | 98.20 | 92.82 | 97.61 | 98.45 |
| Haar_Wavelet_Level2 | 98.18 | 2.73 | 0.82 | 94.34 | 98.01 | 88.73 | 97.18 | 98.59 |
| Without Wavelet | 95.74 | 2.42 | 0.73 | 94.11 | 97.37 | 88.87 | 96.79 | 97.55 |
Performance comparison of Xception-I with and without wavelet for three-class instances.
| Model (Xception-I) | Time Taken Per Epoch | Time Taken Per Step | Training Loss | Training Accuracy | Validation Loss | Validation Accuracy |
|---|---|---|---|---|---|---|
| Haar_Wavelet_Level1 | 173 s | 605 ms | 0.0651 | 0.9776 | 0.0567 | 0.9845 |
| Haar_Wavelet_Level2 | 94 s | 330 ms | 0.0290 | 0.9912 | 0.0432 | 0.9859 |
| Without Wavelet | 89 s | 412 ms | 0.0316 | 0.9888 | 0.0822 | 0.9755 |
Fig. 7Xception-I demonstrates accuracy of DWT featured thoracic X-ray images for four-class instances.
Descriptive statistics of DWT featured thoracic X-ray images for four-class instances.
| Descriptive Statistics | Mean | Standard Deviation | SE of mean | Lower 95% CI of Mean | Upper 95% CI of Mean | Min | Median | Max |
|---|---|---|---|---|---|---|---|---|
| Haar_Wavelet_Level1 | 94.87 | 1.02 | 0.30 | 94.19 | 95.56 | 92.62 | 95.00 | 96.63 |
| Haar_Wavelet_Level2 | 96.57 | 0.99 | 0.29 | 95.90 | 97.24 | 94.81 | 96.96 | 97.85 |
| Haar_Wavelet_Level1, 2 | 96.09 | 1.40 | 0.42 | 95.14 | 97.03 | 93.46 | 96.54 | 97.74 |
Performance comparison of Xception-I for DWT featured thoracic X-ray images for four-class instances.
| Model (Xception-I) | Time Taken Per Epoch | Time Taken Per Step | Training Loss | Training Accuracy | Validation Loss | Validation Accuracy |
|---|---|---|---|---|---|---|
| Haar_Wavelet_Level1 | 120 s | 375 ms | 0.1087 | 0.9604 | 0.1030 | 0.9663 |
| Haar_Wavelet_Level2 | 105 s | 330 ms | 0.0414 | 0.9865 | 0.1216 | 0.9785 |
| Haar_Wavelet_Level1, 2 | 400 s | 625 ms | 0.0454 | 0.9856 | 0.0706 | 0.9774 |
Fig. 8Xception-I demonstrates accuracy concerning different epoch sizes for four-class instances.
Descriptive statistics of the accuracy in different epoch sizes for four-class instances.
| Epochs /Descriptive Statistics | Mean | Standard Deviation | SE of mean | Lower 95% CI of Mean | Upper 95% CI of Mean | Min | Median | Max |
|---|---|---|---|---|---|---|---|---|
| Accuracy_20epoch | 96.08 | 1.05 | 0.3179 | 95.37 | 96.79 | 94.05 | 96.33 | 97.34 |
| Accuracy_40epoch | 97.44 | 0.65 | 0.1969 | 97.00 | 97.88 | 96.08 | 97.34 | 98.35 |
| Accuracy_60epoch | 96.38 | 1.72 | 0.5190 | 95.23 | 97.54 | 92.53 | 96.84 | 98.61 |
| Accuracy_80epoch | 97.37 | 0.89 | 0.2704 | 96.77 | 97.97 | 95.82 | 97.72 | 98.48 |
| Accuracy_100epoch | 97.64 | 0.63 | 0.1904 | 97.21 | 98.06 | 96.58 | 97.85 | 98.61 |
Performance comparison of Xception-I for four-class instances over different epoch sizes.
| Model (Xception-I) | Time Taken Per Epoch | Time Taken Per Step | Training Loss | Training Accuracy | Validation Loss | Validation Accuracy |
|---|---|---|---|---|---|---|
| Accuracy_20epochs | 203 s | 633 ms | 0.0967 | 0.9699 | 0.1240 | 0.9734 |
| Accuracy_40epochs | 109 s | 342 ms | 0.0483 | 0.9856 | 0.0576 | 0.9835 |
| Accuracy_60epochs | 110 s | 341 ms | 0.0808 | 0.9731 | 0.0508 | 0.9861 |
| Accuracy_80epochs | 103 s | 322 ms | 0.0425 | 0.9884 | 0.0694 | 0.9848 |
| Accuracy_100epochs | 195 s | 610 ms | 0.0341 | 0.9912 | 0.0604 | 0.9861 |
Performance comparison of Xception-I for four-class instances over wavelet components.
| Wavelet Component | Time Taken Per Epoch | Training Loss | Training Accuracy | Validation Loss | Validation Accuracy | |
|---|---|---|---|---|---|---|
| Detail | Diagonal | 95 s | 1.0456 | 0.5408 | 1.0341 | 0.5535 |
| Vertical | 94 s | 0.7551 | 0.6948 | 0.6773 | 0.7514 | |
| Horizontal | 98 s | 0.6917 | 0.7289 | 0.6459 | 0.7634 | |
| Approximation | 188 s | 0.0803 | 0.9740 | 0.0507 | 0.9887 | |
Performance comparison of network-based pre-trained architectures.
| Model | Time Taken Per Epoch | Time Taken Per Step | Training Loss | Training Accuracy | Validation Loss | Validation Accuracy | Params (in M) |
|---|---|---|---|---|---|---|---|
| ResNet50V2 | 125 s | 393 ms | 0.1701 | 0.9390 | 0.6384 | 0.8392 | 36.22 |
| VGG16 | 84 s | 265 ms | 0.2609 | 0.9095 | 0.1941 | 0.9354 | 16.81 |
| Xception | 106 s | 332 ms | 0.0517 | 0.9852 | 0.0585 | 0.9785 | 36.62 |
| Xception-I | 109 s | 342 ms | 0.0483 | 0.9856 | 0.0576 | 0.9835 | 23.59 |
Fig. 9The accuracy and loss plots for different CNN architectures.
Average class-wise precision, recall, DSC for four-class instances.
| Class | Precision | Recall | DSC |
|---|---|---|---|
| Pneumonia Bacterial (PNA Bact.) | 0.98 | 0.93 | 0.97 |
| COVID-19 | 0.99 | 0.98 | 0.99 |
| Normal | 0.99 | 0.97 | 0.98 |
| Pneumonia Viral (PNA Viral) | 0.96 | 1.00 | 0.98 |
Fig. 10Confusion matrix for two-class instances with 5 and 10 fold CV.
Fig. 11Confusion matrix for four-class instances with 5 and 10 fold CV.
Evaluation assessment of Xception-I on each fold.
| Folds | Precision | Recall | DSC | Accuracy | Support |
|---|---|---|---|---|---|
| fold1 | 0.98 | 0.98 | 0.98 | 0.9800 | 400 X-ray |
| fold2 | 0.97 | 0.96 | 0.98 | 0.9700 | 400 X-ray |
| fold3 | 0.98 | 0.99 | 0.98 | 0.9850 | 400 X-ray |
| fold4 | 0.97 | 0.97 | 0.97 | 0.9725 | 400 X-ray |
| fold5 | 0.99 | 0.99 | 0.99 | 0.9825 | 400 X-ray |
| fold10 | 0.98 | 1.00 | 1.00 | 0.9950 | 400 X-ray |
| Weighted Average | 97.83 | 98.16 | 98.33 | 98.080 | |
Fig. 12Error estimation with respect to the k-Fold CV.
Performance comparison of CNN architecture Xception-I from literature.
| Authors | Image modality | Method used | COVID-19 cases | Acc (%) |
|---|---|---|---|---|
| Xu et al. | CT images | ResNet-18 + location attention | 219 (+) | 86.70 |
| Zhang et al. | X-ray images | ResNet-18 + classification head + anomaly detection head | 100 (+) | 96.00 |
| Wang et al. | X-ray images | COVID-Net | 53 (+) | 92.40 |
| Sethy et al. | X-ray images | ResNet50+SVM | 25 (+) | 95.38 |
| Wang et al. | CT images | DenseNet121 | 924 (+) | 80.12 |
| Narin et al. | X-ray images | Deep CNN ResNet-50 | 50 (+) | 98.00 |
| Gozes et al. | CT images | ResNet-50 | 50 (+) | 94.00 |
| Apostolopoulos et al. | X-ray images | VGG-19 | 244 (+) | 93.48 |
| Hemdan et al. | X-ray images | COVIDX-Net | 25 (+) | 90.00 |
| Abbas et al. | X-ray images | DeTrac | 105 (+) | 95.12 |
| Hall et al. | X-ray images | ResNet50+VGG16 | 135 (+) | 94.40 |
| Li et al. | CT images | COVNet | 400 (+) | 90.00 |
| Zheng et al. | CT images | DeCoVNet | 313 (+) | 90.00 |
| Song et al. | CT images | DRE-Net | 777 (+) | 86.00 |
| Ozturk et al. | X-ray images | DarkCovidNet | 125 (+) | 87.02 |
| Khan et al. | X-ray images | CoroNet | 284 (+) | 89.60 |
| Wang et al. | CT images | M-Inception | 195 (+) | 82.90 |
| Hassantabar et al. | X-ray images | CNN | 100 (+) | 93.20 |
| Shibly et al. | X-ray images | VGG-16 based Fast R-CNN | 183 (+) | 97.36 |
Fig. 13Misaligned thoracic X-ray images from collected dataset.
Fig. 14Error estimation with respect to the k-Fold CV.
Xception architecture.
| Layer (Type) | Output Shape | Param # |
|---|---|---|
| Xception (Model) | (None, 5, 5, 2048) | 20861480 |
| flatten_1 (Flatten) | (None, 51200) | 0 |
| dropout_1 (Dropout) | (None, 51200) | 0 |
| dense_2 (Dense) | (None, 256) | 15360300 |
| dense_3 (Dense) | (None, 4) | 1204 |
| Total params: 36,222,984 |
VGG-16 architecture.
| Layer (Type) | Output Shape | Param # |
|---|---|---|
| vgg16 (Model) | (None, 4, 4, 512) | 14714688 |
| flatten_1 (Flatten) | (None, 51200) | 0 |
| dropout_1 (Dropout) | (None, 51200) | 0 |
| dense_2 (Dense) | (None, 256) | 15360300 |
| dense_3 (Dense) | (None, 4) | 1204 |
| Total params: 16,813,124 | ||
Inception_ResNet50V2 architecture.
| Layer (Type) | Output Shape | Param # |
|---|---|---|
| resnet50v2 (Model) | (None, 5, 5, 2048) | 23564800 |
| flatten_1 (Flatten) | (None, 51200) | 0 |
| dropout_1 (Dropout) | (None, 51200) | 0 |
| dense_2 (Dense) | (None, 256) | 15360300 |
| dense_3 (Dense) | (None, 4) | 1204 |
| Total params: 36,673,284 | ||
Wavelet-featured deep CNN Xception-I architecture.
| Layer (Type) | Output Shape | Param # |
|---|---|---|
| Xception (Model) | (None, 5, 5, 2048) | 20861480 |
| flatten_1 (Flatten) | (None, 51200) | 0 |
| dropout_1 (Dropout) | (None, 51200) | 0 |
| dense (Dense) | (None, 50) | 2560050 |
| dense_1 (Dense) | (None, 100) | 5100 |
| dense_2 (Dense) | (None, 150) | 15150 |
| dense_3 (Dense) | (None, 200) | 30200 |
| dense_4 (Dense) | (None, 250) | 50250 |
| dense_5 (Dense) | (None, 300) | 75300 |
| dense_6 (Dense) | (None, 4) | 1204 |
| Total params: 23,598,734 | ||