Reliable Sarcoidosis Detection Using Chest X-rays with EfficientNets and Stain-Normalization Techniques
Abstract
:1. Introduction
2. Related Work
3. Research Contribution
4. Materials and Methods
4.1. Materials
4.2. Background
4.2.1. Training Convolutional Neural Networks (CNNs)
- m: the number of samples in the training dataset.
- : the sample with the label in the training dataset.
- : the probability of correct classification.
- : the weights for layer l at iteration t
- C: the cost of the mini-batch
- : the learning rate
- : the layer l learning rate
- : the rate of scheduling
- : the impact of lastly updated weights of neurons in the recent iteration.
4.2.2. Transfer-Learning-Based Convolutional Neural Network
EfficientNet
- Set = 1, assuming that twice as many resources are available, and apply a grid search for , , and .
- Set , , and as constants according to the values determined in the previous step and investigate with different values of . The different values of produce EfficientNets B0–B6. Table 2 shows the input sizes and the number of total parameters for each EfficientNet model.
VGG16
AlexNet
ResNet50
Inception V3
4.3. Methods
4.3.1. Overview
4.3.2. Pre-Processing
- Image Resizing: The X-ray image datasets for this study were obtained from multiple sources; therefore, the images were of various sizes. Each network only accepts a specific size of image. Each image was reduced to the specific sizes required by the networks while keeping its important features. The images were resized according to the recommended input size of each EfficientNet architecture, as shown in Table 2.
- Image Normalization: Different manufacturers of X-ray devices may provide different-looking X-ray images for the same patient. Overfitting to the device pixel distributions is quite a big problem in computer-aided diagnostic devices; therefore, it is standard practice to apply contrast normalization to minimize this problem. The general idea is to unify the distribution of pixels. This makes X-rays appear a little darker. This procedure generates a view that radiologists would not see in their standard workplace. Using the Reinhard and Macenko approaches, X-ray images were stain-normalized [43,48,49]. A reduction in the color discrepancies of X-ray images improves the classification accuracy of EfficientNet models.
- Data Augmentation: The normalized X-ray images were augmented before introduction into the EfficientNet model for training. The process of increasing the number of original images in a collection is known as data augmentation [38,50]. This strategy helps to eliminate the overfitting problem that arises when a model learns enough from the training data but cannot classify images of undetected X-rays. Table 3 illustrates the augmentation settings used on the stain-normalized X-ray images. In this study, the number of normal images was 1010, which is twice as many as the number of TB- and sarcoidosis-infected images. Therefore, the TB-infected images were augmented from 563 to 1126, and the sarcoidosis-infected images were increased from 231 to 462.
4.3.3. Classification Stage
4.3.4. Evaluation of the Classification Performance of the Proposed Methodology
5. Results and Discussion
6. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Class | Source | Number of Images |
---|---|---|
Normal | Kaggle | 360 |
NLM database | 400 | |
RSNA CXR dataset | 250 | |
TB | Belarus database | 169 |
NLM database | 394 | |
Sarcoidosis | Six national hospitals in Egypt | 231 |
EfficientNet Model | Input Image Size | Number Parameters |
---|---|---|
B0 | 224 × 224 | 4.3 |
B1 | 240 × 240 | 6.8 |
B2 | 260 × 260 | 8 |
B3 | 300 × 300 | 11 |
B4 | 380 × 380 | 17.9 |
B5 | 456 × 456 | 28.7 |
B6 | 528 × 528 | 41.1 |
Augmentation Type | Value |
---|---|
Rescaling | According to each EfficientNet model |
Rotation range | and |
Range of width shifts | 0.1 |
Range of height shift | 0.1 |
Hyper-Parameter | Setting |
---|---|
Patience | 5 |
Learning rate | 0.001 |
Size of mini-batch | 32 |
Optimizer | SGD |
Activation function | Softmax |
EfficientNet Architectures | Precision | Sensitivity | ||
---|---|---|---|---|
Reinhard | Macenko | Reinhard | Macenko | |
B0 | 94.88 | 92.9 | 94.56 | 92.9 |
B1 | 95.16 | 93.69 | 95.82 | 93.48 |
B2 | 95.16 | 93.69 | 95.82 | 93.48 |
B3 | 93.49 | 93.05 | 92.78 | 92.78 |
B4 | 98.67 | 97.11 | 98.36 | 96.9 |
B5 | 90.74 | 94.1 | 90.63 | 93.97 |
B6 | 91.34 | 91.15 | 90.36 | 90.21 |
Test Type | Indication for Tuberculosis | Indication for Sarcoidosis | Proposed Approach |
---|---|---|---|
Physical examination | Coughing for three or more weeks, coughing up blood or mucus, chest pain, weight loss, fatigue and fever [52] | Fatigue, fever, weight loss, and erythema nodosum [53] | Not required |
Peripheral blood count | High lymphocyte count [54] | ||
Renal function tests | Unclear for tuberculosis diagnosis [55] | High level of calcium, urea, and creatinine [56] | |
Urine analysis | Urine analysis currently offers little utility for the diagnosis of tuberculosis [57] | Hypercalciurea [53] | |
Pulmonary function tests | Just used to indicate pulmonary involvement and disease severity, but not to determine whether TB or sarcoidosis is present [53] | ||
Tissue biopsy | This method is probably the most useful one for the diagnosis of bone and joint tuberculosis [58] | For the presence of granuloma (lungs, lymph node, skin, salivary gland, conjunctiva) [53] | |
Bronchial biopsy | Transbronchial lung biopsy (TBLB) is a helpful examination for pulmonary tuberculosis [59] | Flexible bronchoscopy has a very high diagnostic yield in all stages of suspected sarcoidosis [53] | |
Tuberculin skin test (Mantoux) | Determining whether a person is infected with mycobacterium tuberculosis [60] | Negative in most sarcoidosis patients [53] | |
Electrocardiogram (ECG) | Patients with pulmonary tuberculosis often have a normal ECG [61] | Repolarization disturbances, ectopic beats, and rhythm abnormalities [62] | |
MRI | MRI is the most sensitive modality for early diagnosis and follow-up of spinal TB [63] | Detect neurological involvement, spinal cord, meninges, skull vault, and pituitary lesions [53] | Not investigated to improve diagnostic accuracy |
Chest X-ray | A posterior-anterior chest radiograph is used to detect chest abnormalities [53] | Required |
Cases | Number of Actual Cases | EfficientNet-B4 | Committees of Consultants |
---|---|---|---|
Normal | 2 | 2 (100%) | 2 (100%) |
Tuberculosis | 3 | 2 (67%) | 1 (33%) |
Sarcoidosis | 5 | 3 (60%) | 0 (0%) |
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Baghdadi, N.; Maklad, A.S.; Malki, A.; Deif, M.A. Reliable Sarcoidosis Detection Using Chest X-rays with EfficientNets and Stain-Normalization Techniques. Sensors 2022, 22, 3846. https://doi.org/10.3390/s22103846
Baghdadi N, Maklad AS, Malki A, Deif MA. Reliable Sarcoidosis Detection Using Chest X-rays with EfficientNets and Stain-Normalization Techniques. Sensors. 2022; 22(10):3846. https://doi.org/10.3390/s22103846
Chicago/Turabian StyleBaghdadi, Nadiah, Ahmed S. Maklad, Amer Malki, and Mohanad A. Deif. 2022. "Reliable Sarcoidosis Detection Using Chest X-rays with EfficientNets and Stain-Normalization Techniques" Sensors 22, no. 10: 3846. https://doi.org/10.3390/s22103846
APA StyleBaghdadi, N., Maklad, A. S., Malki, A., & Deif, M. A. (2022). Reliable Sarcoidosis Detection Using Chest X-rays with EfficientNets and Stain-Normalization Techniques. Sensors, 22(10), 3846. https://doi.org/10.3390/s22103846