Automated Lung-Related Pneumonia and COVID-19 Detection Based on Novel Feature Extraction Framework and Vision Transformer Approaches Using Chest X-ray Images
Abstract
:1. Introduction
- This research offers a refined Chest X-ray Image Based Feature Extraction Framework for Lung Disease identification that is significantly discriminative in identifying Pneumonia, COVID-19, and Lung Cancer Diseases.
- We offer explainability-driven, medically explainable visuals that emphasize the crucial regions relevant to the model’s prediction of the input image.
- We established a novel technique for improving ensemble models by using the integration of global second-order pooling and multi-head self-attention.
- This work examined many pre-trained deep learning models, providing a unique ensemble deep learning model that acts as the suggested model backbone, tackling the problem of the requirement for large-scale data.
- We reported a well robust deep learning method in Accuracy, Specificity, Sensitivity, Precision, F1 Score, Confusion matrix, and AUC using receiver operating characteristics (ROC) for detecting Pneumonia, COVID-19, and Lung Cancer Diseases based on a detailed experimental evaluation of the proposed model and comparison with state-of-the-art results.
2. Materials and Methods
2.1. Dataset
2.1.1. Data_A
2.1.2. Data_B
2.2. Model Architecture
2.3. Feature Extraction
2.4. Evaluation Metrics
3. Results
3.1. Experimental Setup
3.2. Classification Results
3.2.1. Backbone Model Selection
3.2.2. Classification Results Using Data_A
3.2.3. Classification Results Using Data_B
4. Discussion
4.1. Ablation Studies of the Proposed Model
4.2. Comparison with the State-of-the-Art Based on Deep Learning Models
4.3. Limitations and Future Works
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Ref. | Architecture | Type | Result |
---|---|---|---|
[34] | Residual Blocks and Dilated Convolution | Pneumonia detection | Recall = 96.7% F1_score = 92.7% |
[32] | Transfer Learning Via VGG-16 And Xception Models | Accuracy = 87%(VGG) and 82% (Xception) | |
[33] | Transfer Learning Via Resnet152 Model | Accuracy = 97.4% | |
[35] | Convolutional Neural Network (CNN) | Accuracy = 93.73%. | |
[37] | RetinaNet And Mask R-CNN | Accuracy = 79.3% | |
[38] | Transfer Learning | Recall Rate = 96.7% F1_score = 92.7%. | |
VGG16 | Accuracy = 90.5%, Precision = 89.1%, Recall = 96.7%, and F1_score = 92.7% | ||
[39] | Transfer Learning | Accuracy = 96.4% | |
[40] | 18-Layer CNN | Accuracy = 93.75% | |
[41] | CNN-Based Transfer Learning | Accuracy = 95.62%, Recall = 95%, and Precision = 96% | |
[42] | Resnet34 | COVID-19 | Accuracy = 98.33% |
[43] | CNN-Based Transfer Learning | Accuracy = 96% | |
[44] | VGG-16 | Accuracy = 97.67% | |
[45] | COVIDXrayNet | Accuracy = 95.82% | |
[46] | Resnet-50 With TL+ PCA + Ensemble | Accuracy = 98% | |
[47] | SARS-Net | Accuracy = 97.60% | |
[48] | ResNet50 | Accuracy = 98% | |
[49] | COVID-Net | Accuracy = 92% |
Partition | Normal | Pneumonia | COVID-19 | Lung Opacity | Total | Total | |
---|---|---|---|---|---|---|---|
Data_A | Training | 3000 | 3000 | 3000 | 3000 | 12,000 | 14,400 |
Validation | 300 | 300 | 300 | 300 | 1200 | ||
Testing | 300 | 300 | 300 | 300 | 1200 | ||
Data_B | Training | 3500 | 3500 | 3500 | 10,500 | ||
Validation | 500 | 500 | 500 | 1500 | 1500 | ||
Testing | 1000 | 1000 | 1000 | 3000 |
Loss Function | Categorical Smooth Loss, Categorical Cross-Entropy |
---|---|
Optimizers | Adam |
Learning rate | 0.0001/0.001 |
Batch size | 8 |
Reduce Learning Rate | 0.2 |
Epsilon | 0.001 |
Patience | 10 |
Verbose | 1 |
Es-Callback (Patience) | 10 |
Clip Value | 0.2 |
Epoch | 100 |
Patch Size | (2, 2) |
Drop Rate | 0.01 |
Number of Heads | 8 |
Embed_dim | 64 |
Num_MLP | 256 |
Window Size | Window Size//2 |
Input Size | (224 × 224) |
Models | Accuracy (%) | Sensitivity (%) | Specificity (%) | Precision (%) | F1 Score | AUC |
---|---|---|---|---|---|---|
Learning Rate: 10−4 | ||||||
DenseNet201 | 0.9600 | 0.91981 | 0.97325 | 0.92453 | 0.92088 | 0.94651 |
EfficientNetB7 | 0.87333 | 0.74787 | 0.91542 | 0.83094 | 0.73639 | 0.83164 |
GoogleNet | 0.9300 | 0.86024 | 0.95322 | 0.86795 | 0.86188 | 0.90673 |
InceptResNetV2 | 0.94667 | 0.89385 | 0.96434 | 0.90298 | 0.89398 | 0.9291 |
VGG16 | 0.9100 | 0.81988 | 0.93985 | 0.87301 | 0.82008 | 0.87986 |
Xception | 0.9000 | 0.80032 | 0.93315 | 0.83420 | 0.80144 | 0.86674 |
Learning Rate: 10−3 | ||||||
DenseNet201 | 0.92333 | 0.84691 | 0.94880 | 0.86073 | 0.84883 | 0.8976 |
EfficientNetB7 | 0.85667 | 0.71337 | 0.90408 | 0.77687 | 0.72241 | 0.80872 |
GoogleNet | 0.89000 | 0.78094 | 0.92666 | 0.80353 | 0.78311 | 0.8538 |
InceptResNetV2 | 0.92667 | 0.85331 | 0.95097 | 0.86683 | 0.85618 | 0.90214 |
VGG16 | 0.89667 | 0.79374 | 0.93100 | 0.81953 | 0.79527 | 0.86237 |
Xception | 0.88667 | 0.77400 | 0.92428 | 0.80688 | 0.77546 | 0.84914 |
ROC (Area) | Macro-Average | Micro-Average | COVID-19 | Lung Opacity | Normal | Pneumonia |
---|---|---|---|---|---|---|
Learning Rate: 10−4 | ||||||
DenseNet201 | 0.95 | 0.95 | 0.95583 | 0.95061 | 0.93374 | 0.94595 |
EfficientNetB7 | 0.78 | 0.78 | 0.69737 | 0.93339 | 0.84445 | 0.85135 |
GoogleNet | 0.91 | 0.91 | 0.90296 | 0.93734 | 0.86772 | 0.91892 |
InceptResNetV2 | 0.93 | 0.93 | 0.86819 | 0.97321 | 0.92904 | 0.94595 |
VGG16 | 0.88 | 0.88 | 0.85526 | 0.97345 | 0.87993 | 0.81081 |
Xception | 0.87 | 0.87 | 0.78477 | 0.90588 | 0.8844 | 0.89189 |
Learning Rate: 10−3 | ||||||
DenseNet201 | 0.90 | 0.90 | 0.86372 | 0.91497 | 0.8938 | 0.91892 |
EfficientNetB7 | 0.81 | 0.81 | 0.73167 | 0.87862 | 0.80028 | 0.82432 |
GoogleNet | 0.85 | 0.85 | 0.80663 | 0.87515 | 0.82801 | 0.90541 |
InceptResNetV2 | 0.90 | 0.90 | 0.89427 | 0.92825 | 0.88064 | 0.90541 |
VGG16 | 0.86 | 0.86 | 0.81978 | 0.91521 | 0.84962 | 0.86486 |
Xception | 0.85 | 0.85 | 0.78031 | 0.91964 | 0.83177 | 0.86486 |
Precision-Recall (AP) | Micro-Average | COVID-19 | Lung Opacity | Normal | Pneumonia |
---|---|---|---|---|---|
Learning Rate: 10−4 | |||||
DenseNet201 | 0.87 | 0.87 | 0.89 | 0.81 | 0.92 |
EfficientNetB7 | 0.62 | 0.55 | 0.74 | 0.55 | 0.78 |
GoogleNet | 0.77 | 0.75 | 0.82 | 0.68 | 0.88 |
InceptResNetV2 | 0.82 | 0.75 | 0.90 | 0.75 | 0.92 |
VGG16 | 0.72 | 0.78 | 0.86 | 0.61 | 0.71 |
Xception | 0.69 | 0.62 | 0.76 | 0.62 | 0.84 |
Learning Rate: 10−3 | |||||
DenseNet201 | 0.76 | 0.73 | 0.76 | 0.69 | 0.88 |
EfficientNetB7 | 0.58 | 0.49 | 0.76 | 0.49 | 0.74 |
GoogleNet | 0.66 | 0.63 | 0.63 | 0.60 | 0.86 |
InceptResNetV2 | 0.76 | 0.75 | 0.82 | 0.67 | 0.86 |
VGG16 | 0.68 | 0.65 | 0.73 | 0.60 | 0.80 |
Xception | 0.65 | 0.60 | 0.75 | 0.56 | 0.80 |
Model | Accuracy (%) | Sensitivity (%) | Specificity (%) | Precision (%) | F1 Score | AUC |
---|---|---|---|---|---|---|
Learning Rate: 10−4, Loss Function: categorical_smooth_loss | ||||||
Backbone | 0.95333 | 0.90701 | 0.96891 | 0.91419 | 0.90736 | 0.93796 |
Proposed Method | 0.96000 | 0.91945 | 0.97325 | 0.92783 | 0.91934 | 0.94635 |
Learning Rate: 10−3, Loss Function: categorical_smooth_loss | ||||||
Backbone | 0.94000 | 0.87909 | 0.95986 | 0.89431 | 0.88056 | 0.91948 |
Proposed Method | 0.96667 | 0.93314 | 0.97772 | 0.93895 | 0.93391 | 0.95543 |
Learning Rate: 10−4, Loss Function: categorical cross-entropy | ||||||
Backbone | 0.96333 | 0.92656 | 0.97551 | 0.93172 | 0.92677 | 0.95104 |
Proposed Method | 0.98000 | 0.96017 | 0.98665 | 0.96209 | 0.9603 | 0.97341 |
Learning Rate: 10−3, Loss Function: categorical cross-entropy | ||||||
Backbone | 0.83667 | 0.67372 | 0.89098 | 0.78304 | 0.65383 | 0.78235 |
Proposed Method | 0.98000 | 0.94965 | 0.98992 | 0.95508 | 0.95216 | 0.96976 |
ROC (Area) | Macro-Average | Micro-Average | COVID-19 | Lung Opacity | Normal | Pneumonia |
---|---|---|---|---|---|---|
Optimizer: Adaptive Moment Estimation, Learning Rate: 10−4, Loss Function: categorical_smooth_loss | ||||||
Backbone | 0.94 | 0.94 | 0.94737 | 0.96903 | 0.90742 | 0.92801 |
Proposed Method | 0.95 | 0.95 | 0.99107 | 0.97764 | 0.92481 | 0.89189 |
Learning Rate: 10−3, Loss Function: categorical_smooth_loss | ||||||
Backbone | 0.92 | 0.92 | 0.94690 | 0.89656 | 0.92904 | 0.90541 |
Proposed Method | 0.96 | 0.96 | 0.95606 | 0.98206 | 0.95559 | 0.92801 |
Learning Rate: 10−4, Loss Function: categorical cross-entropy | ||||||
Backbone | 0.95 | 0.95 | 0.95606 | 0.99115 | 0.94243 | 0.91449 |
Proposed Method | 0.97 | 0.97 | 0.96053 | 0.99558 | 0.96898 | 0.96855 |
Learning Rate: 10−3, Loss Function: categorical cross-entropy | ||||||
Backbone | 0.78 | 0.78 | 0.67975 | 0.89333 | 0.8266 | 0.72973 |
Proposed Method | 0.94 | 0.94 | 0.90158 | 0.97534 | 0.94884 | 0.94354 |
Precision-Recall (AP) | Micro-Average | COVID-19 | Lung Opacity | Normal | Pneumonia |
---|---|---|---|---|---|
Learning Rate: 10−4, Loss Function: categorical_smooth_loss | |||||
Backbone | 0.85 | 0.92 | 0.84 | 0.77 | 0.87 |
Proposed Method | 0.87 | 0.95 | 0.93 | 0.77 | 0.84 |
Learning Rate: 10−3, Loss Function: categorical_smooth_loss | |||||
Backbone | 0.80 | 0.83 | 0.81 | 0.75 | 0.86 |
Proposed Method | 0.89 | 0.92 | 0.95 | 0.83 | 0.87 |
Learning Rate: 10−4, Loss Function: categorical cross-entropy | |||||
Backbone | 0.88 | 0.92 | 0.95 | 0.81 | 0.85 |
Proposed Method | 0.93 | 0.94 | 0.97 | 0.89 | 0. 93 |
Learning Rate: 10−3, Loss Function: categorical cross-entropy | |||||
Backbone | 0.54 | 0.50 | 0.64 | 0.52 | 0.59 |
Proposed Method | 0.90 | 0.97 | 0.95 | 0.80 | 0.87 |
Models | Accuracy (%) | Sensitivity (%) | Specificity (%) | Precision (%) | F1_score | AUC | ||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Learning Rate: 10−4, Loss Function: categorical_smooth_loss | ||||||||||||
Proposed Model | 0.9819 | 0.9729 | 0.9864 | 0.9729 | 0.9729 | 0.9810 | ||||||
Backbone | 0.9720 | 0.9580 | 0.9790 | 0.9583 | 0.9580 | 0.9686 | ||||||
ROC | Macro-Average Area | Micro-Average Area | Class 0 Area | Class 1 Area | Class 2 Area | |||||||
Proposed Model | 0.98 | 0.98 | 0.9842 | 0.9700 | 0.9848 | |||||||
Backbone | 0.97 | 0.97 | 0.9771 | 0.9541 | 0.9741 | |||||||
Average Precision | Micro-Average Precision-Recall | Class 0 AP | Class 1 AP | Class 2 AP | ||||||||
Proposed Model | 0.96 | 0.9796 | 0.9606 | 0.9785 | ||||||||
Backbone | 0.93 | 0.9461 | 0.9077 | 0.9574 |
Reference | Year | Model | Accuracy | Precision | Sensitivity | F1_score |
---|---|---|---|---|---|---|
Khan et al. (Strategy 1) [73] | 2022 | EfficientNetB1 | 92 | 91.75 | 94.50 | 92.75 |
NasNetMobile | 89.30 | 89.25 | 91.75 | 91 | ||
MobileNetV2 | 90.03 | 92.25 | 92 | 91.75 | ||
Khan et al. (Strategy 2) [73] | 2022 | EfficientNetB1 | 96.13 | 97.25 | 96.50 | 97.50 |
NasNetMobile | 94.81 | 95.50 | 95 | 95.25 | ||
MobileNetV2 | 93.96 | 94.50 | 95 | 94.50 | ||
Mondal et al. [71] | 2022 | Local Global Attention Network | 95.87 | 95.56 | 95.99 | 95.74 |
Shi et al. [72] | 2021 | Teacher Student Attention | 91.38 | 91.65 | 90.86 | 91.24 |
Li et al. [70] | 2021 | Mag-SD | 92.35 | 92.50 | 92.20 | 92.34 |
Khan et al. [69] | 2020 | CoroNet | 89.6 | 90.0 | 96.4 | 89.8 |
Shi et al. [72] | 2020 | COVIDNet | 90.78 | 91.1 | 90.56 | 90.81 |
Ours | 2022 | 98.00 | 96.21 | 96.02 | 96.03 |
Reference | Year | Architecture | Accuracy | Precision | Recall | F1_score |
---|---|---|---|---|---|---|
Naralasetti et al. [74] | 2021 | Deep CNN | 91% | - | - | - |
Dokur et al. [75] | 2020 | CNN Ensemble | 78% 75% | 80% 77% | 78% 75% | 78% 75% |
Hammoudi et al. [36] | 2020 | VGG19 ResNet+RNN1 ResNet+RNN2 DenseNet169 | 83% 78% 80% 96% | - - - - | - - - - | - - - - |
Windodo et al. [76] | 2021 | UBNetV1 UBNetV2 | 88% 88% | 89% 89% | 86% 85% | 86% 86% |
Kermany et al. [77] | 2021 | AutoML | 86% | 82% | 84% | 84% |
Ibrahim et al. [78] | 2020 | AlexNet | 97.40% | - | - | - |
Ours | 2022 | 98.19% | 97.29% | 97.29% | 97.29% |
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Ukwuoma, C.C.; Qin, Z.; Heyat, M.B.B.; Akhtar, F.; Smahi, A.; Jackson, J.K.; Furqan Qadri, S.; Muaad, A.Y.; Monday, H.N.; Nneji, G.U. Automated Lung-Related Pneumonia and COVID-19 Detection Based on Novel Feature Extraction Framework and Vision Transformer Approaches Using Chest X-ray Images. Bioengineering 2022, 9, 709. https://doi.org/10.3390/bioengineering9110709
Ukwuoma CC, Qin Z, Heyat MBB, Akhtar F, Smahi A, Jackson JK, Furqan Qadri S, Muaad AY, Monday HN, Nneji GU. Automated Lung-Related Pneumonia and COVID-19 Detection Based on Novel Feature Extraction Framework and Vision Transformer Approaches Using Chest X-ray Images. Bioengineering. 2022; 9(11):709. https://doi.org/10.3390/bioengineering9110709
Chicago/Turabian StyleUkwuoma, Chiagoziem C., Zhiguang Qin, Md Belal Bin Heyat, Faijan Akhtar, Abla Smahi, Jehoiada K. Jackson, Syed Furqan Qadri, Abdullah Y. Muaad, Happy N. Monday, and Grace U. Nneji. 2022. "Automated Lung-Related Pneumonia and COVID-19 Detection Based on Novel Feature Extraction Framework and Vision Transformer Approaches Using Chest X-ray Images" Bioengineering 9, no. 11: 709. https://doi.org/10.3390/bioengineering9110709
APA StyleUkwuoma, C. C., Qin, Z., Heyat, M. B. B., Akhtar, F., Smahi, A., Jackson, J. K., Furqan Qadri, S., Muaad, A. Y., Monday, H. N., & Nneji, G. U. (2022). Automated Lung-Related Pneumonia and COVID-19 Detection Based on Novel Feature Extraction Framework and Vision Transformer Approaches Using Chest X-ray Images. Bioengineering, 9(11), 709. https://doi.org/10.3390/bioengineering9110709