Classification and Visualisation of Normal and Abnormal Radiographs; A Comparison between Eleven Convolutional Neural Network Architectures
<p>Eight examples of radiographs without abnormalities (considered negative) of the Musculoskeletal Radiographs (MURA) dataset [<a href="#B59-sensors-21-05381" class="html-bibr">59</a>]. (<b>a</b>) Elbow, (<b>b</b>) Forearm, (<b>c</b>) Shoulder, (<b>d</b>) Wrist (lateral view), (<b>d</b>) Lateral view of Wrist, (<b>e</b>) Finger, (<b>f</b>) Hand, (<b>g</b>) Humerus, (<b>h</b>) Wrist. It should be noted the variability of the images in terms of dimensions, quality, contrast and the large number of labels (i.e., R for right and L for left), which appear in various locations.</p> "> Figure 2
<p>Eight examples of radiographs with abnormalities (considered positive) of the Musculoskeletal Radiographs (MURA) dataset [<a href="#B59-sensors-21-05381" class="html-bibr">59</a>]. (<b>a</b>) Elbow, (<b>b</b>) Forearm, (<b>c</b>) Shoulder, (<b>d</b>) Wrist (lateral view), (<b>d</b>) Lateral view of Wrist, (<b>e</b>) Finger, (<b>f</b>) Hand, (<b>g</b>) Humerus, (<b>h</b>) Wrist. As for the cases without abnormalities, it should be noted the variability of the images and in addition the abnormalities themselves. There are cases of metallic implants some of which are smaller (<b>a</b>) than others (<b>b</b>), as well as fractures.</p> "> Figure 3
<p>Block diagram which illustrates the classification of the wrist radiographs with 11 different convolutional neural network (CNN) architectures. 9752 images from Musculoskeletal Radiographs (MURA) Wrist dataset were used for training CNN architectures and 659 images were used for validation. Two different metrics, Accuracy (<math display="inline"><semantics> <mrow> <mi>A</mi> <mi>c</mi> </mrow> </semantics></math>) and Cohen’s kappa (<math display="inline"><semantics> <mi>κ</mi> </semantics></math>) were computed to assess the performance of 11 pre-trained CNNs. Image data augmentation was used during training and different number of epochs and mini batch sizes were tested.</p> "> Figure 4
<p>Schematic illustration of the X-ray classification process and class activation mapping through layer-wise activation maps across different dense blocks. At each level, a series of feature maps are generated, the resolution decreases progress through the blocks. Colours indicate the range of activation: blue corresponds to low activation, red for highly activated features. The final output, visualised here using class activation mapping, which highlights the area(s) where abnormalities can be located.</p> "> Figure 5
<p>Illustration of classification results for lateral (LA) views of wrist radiographs. (<b>a</b>) Corresponds to positive (abnormal) diagnosis image but predicted as negative (normal), (<b>b</b>) Abnormal diagnosis and abnormal prediction. (<b>c</b>) Normal diagnosis image and normal prediction. (<b>d</b>) Normal diagnosis and abnormal prediction. Notice that the errors in classification may have been biased by artefact elements on the images.</p> "> Figure 6
<p>Illustration of classification results for postero-anterior (PA) views of wrist radiographs. (<b>a</b>) corresponds to a positive (abnormal) diagnosis image that is predicted as negative (normal); (<b>b</b>) to abnormal diagnosis and abnormal prediction; (<b>c</b>) to normal diagnosis image and normal prediction; and (<b>d</b>) to normal diagnosis and abnormal prediction. Notice again that the errors in classification may have been biased by artefactual elements on the images.</p> "> Figure 7
<p>Illustration of activation maps overlaid over the eight radiographs without abnormalities of <a href="#sensors-21-05381-f001" class="html-fig">Figure 1</a> to indicate the regions of the image that activated a ResNet 50 architecture. (<b>a</b>) Elbow, (<b>b</b>) Forearm, (<b>c</b>) Shoulder, (<b>d</b>) Wrist (lateral view), (<b>d</b>) Lateral view of Wrist, (<b>e</b>) Finger, (<b>f</b>) Hand, (<b>g</b>) Humerus, (<b>h</b>) Wrist. As these cases are positive (no abnormality), the regions of activation are not as critical as those with abnormalities.</p> "> Figure 8
<p>Illustration of activation maps overlaid over the eight radiographs with abnormalities of <a href="#sensors-21-05381-f002" class="html-fig">Figure 2</a> to indicate the regions of the image that activated a ResNet 50 architecture. (<b>a</b>) Elbow, (<b>b</b>) Forearm, (<b>c</b>) Shoulder, (<b>d</b>) Wrist (lateral view), (<b>d</b>) Lateral view of Wrist, (<b>e</b>) Finger, (<b>f</b>) Hand, (<b>g</b>) Humerus, (h) Wrist. The activation maps illustrate the location of the abnormalities, e.g., (<b>a</b>,<b>e</b>), but appears spread in other cases (<b>b</b>,<b>g</b>) where the abnormality is detected together with a neighbouring region. In other cases (<b>c</b>), the abnormality is not detected.</p> "> Figure 9
<p>Illustration of activation maps overlaid over the eight radiographs without abnormalities of <a href="#sensors-21-05381-f001" class="html-fig">Figure 1</a> to indicate the regions of the image that activated an Inception-ResNet-v2 architecture. (<b>a</b>) Elbow, (<b>b</b>) Forearm, (<b>c</b>) Shoulder, (<b>d</b>) Wrist (lateral view), (<b>e</b>) Finger, (<b>f</b>) Hand, (<b>g</b>) Humerus, (<b>h</b>) Wrist. It should be noted that the activation regions are more localised than those of the ResNet 50.</p> "> Figure 10
<p>Illustration of activation maps overlaid over the eight radiographs with abnormalities of <a href="#sensors-21-05381-f002" class="html-fig">Figure 2</a> to indicate the regions of the image that activated an Inception-ResNet-v2 architecture. As for the cases without abnormalities, the activation regions are more located, e.g., ((<b>c</b>) Shoulder,(<b>d</b>) Lateral view of Wrist, and (<b>h</b>) Posterior-Anterior view of Wrist)) and in addition, the abnormalities are better located, e.g., ((<b>a</b>) Elbow, (<b>b</b>) Forearm, (<b>e</b>) Finger, (<b>f</b>) Hand, and (<b>g</b>) Humerus).</p> "> Figure 11
<p>Illustration of the class Activation Maps overlaid on the four classification results for (<b>a</b>,<b>b</b>) Postero-anterior and (<b>c</b>,<b>d</b>) Lateral views shown in <a href="#sensors-21-05381-f005" class="html-fig">Figure 5</a> and <a href="#sensors-21-05381-f006" class="html-fig">Figure 6</a> for ResNet 50 (<b>a,c</b>) and Inception-ResNet-v2 (<b>b,d</b>). In general Inception-Resnet-v2 presented more focused and smaller activation maps. It should also be noted that whilst for correct classifications, the highlighted regions are similar, for some incorrect classifications (<b>c,d</b>, top left and bottom right) the activations are quite different, which suggest that the architectures may not be confusing salient regions that are not related with the condition of normal or abnormal.</p> "> Figure 12
<p>Illustration of the effect of the number of layers of architectures against the two metrics used in this paper Accuracy and Cohen’s Kappa. Each architecture is represented by a circle, except those with augmentation that are represented by an asterisk. For visualisation purposes, numbers are added and these correspond to the order of <a href="#sensors-21-05381-t007" class="html-table">Table 7</a> (1 GoogleNet, 2 VGG-19, 3 AlexNet, 4 SqueezeNet, 5 ResNet-18, 6 Inception-v3, 7 ResNet-50, 8 VGG-16, 9 ResNet-101, 10 DenseNet-201, 11 Inception-ResNet-v2, 12 ResNet-50 (augmentation), 13 Inception-ResNet-v2 (augmentation)). Notice the slight improvement provided by deeper networks and the significant improvement that corresponds to data augmentation.</p> ">
Abstract
:1. Introduction
2. Materials and Methods
2.1. Materials
2.2. Convolutional Neural Network
2.3. Experiments
2.4. Further Processing with Data Augmentation
2.5. Class Activation Mapping
2.6. Performance Metrics
2.7. Implementation Details
3. Results
4. Discussion
- 1.
- Data Pre-Processing: In addition to a grid search of the hyper-parameters, image pre-processing to remove irrelevant features (e.g., text labels) may help the network to target its attention. Appropriate data augmentations (e.g., rotation, reflection, etc.) will allow better pattern recognition to be trained and, in turn, provides higher prediction accuracy.
- 2.
- Post Training Evaluation: class activation map provides an interpretable visualisation for clinicians and radiologists to understand how a prediction was made. It allows the model to be re-trained with additional data to mitigate any model bias and discrepancy. Having a clear association of the key features with the prediction classes [70] will aid in developing a more trustworthy CNN-based classification especially in a clinical setting.
- 3.
- 4.
- Domain Knowledge: The knowledge of anatomy (e.g., bone structure in elbow or hands [73]) or the location/orientation of bones [28] can be supplemented in a CNN-based classification to provide further fine tuning in anomaly detection as well as guiding the attention of the network for better results [74].
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
Ac | Accuracy |
A&E | Accidents and Emergency |
AI | Artificial Intelligence |
CAM | Class Activation Mapping |
CNN | Convolutional Neural Network |
CT | Computed Tomography |
ILSVRC | ImageNet Large Scale Visual Recognition Challenge |
MUA | Manipulation under Anaesthesia |
MURA | Musculoskeletal Radiographs |
ORIF | Open Reduction and Internal Fixation |
ReLU | Rectified Linear Unit |
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No. | Study | Train | Validation | Total | ||
---|---|---|---|---|---|---|
Normal | Abnormal | Normal | Abnormal | |||
1 | Elbow | 1094 | 660 | 92 | 66 | 1912 |
2 | Finger | 1280 | 655 | 92 | 83 | 2110 |
3 | Hand | 1497 | 521 | 101 | 66 | 2185 |
4 | Humerus | 321 | 271 | 68 | 67 | 727 |
5 | Forearm | 590 | 287 | 69 | 64 | 1010 |
6 | Shoulder | 1364 | 1457 | 99 | 95 | 3015 |
7 | Wrist | 2134 | 1326 | 140 | 97 | 3697 |
Total | 8280 | 5177 | 661 | 538 | 14,656 |
Wrist-Train Dataset | Abnormal | Normal |
---|---|---|
Study 1 | 3920 | 5282 |
Study 2 | 64 | 425 |
Study 3 | 3 | 45 |
Study 4 | 0 | 13 |
Total | 3987 | 5765 |
Total Wrist Train Images | 9752 | |
Wrist-Valid Dataset | Abnormal | Normal |
Study 1 | 287 | 293 |
Study 2 | 5 | 59 |
Study 3 | 3 | 9 |
Study 4 | 0 | 3 |
Total | 295 | 364 |
Total Wrist Valid Images | 659 | |
Total Images of Wrist | 10,411 |
No. | Network | Depth | Image Input Size | Reference |
---|---|---|---|---|
1 | GoogleNet | 22 | 224-by-224 | [61] |
2 | VGG-19 | 19 | 224-by-224 | [62] |
3 | AlexNet | 8 | 227-by-227 | [60] |
4 | SqueezeNet | 18 | 227-by-227 | [65] |
5 | ResNet-18 | 18 | 224-by-224 | [63] |
6 | Inception-v3 | 48 | 299-by-299 | [64] |
7 | ResNet-50 | 50 | 224-by-224 | [63] |
8 | VGG-16 | 16 | 224-by-224 | [62] |
9 | ResNet-101 | 101 | 224-by-224 | [63] |
10 | DenseNet-201 | 201 | 224-by-224 | [66] |
11 | Inception-ResNet-v2 | 164 | 299-by-299 | [67] |
1 | GoogleNet | Optimiser | SGDM | ADAM | RMSprop |
Epoch | 30 | 30 | 30 | ||
Mini batch size | 64 | 64 | 64 | ||
Init. Learn. R. | 0.01 | 0.001 | 0.001 | ||
Momentum | 0.9000 | - | - | ||
L2 Reg. | 0.0001 | 0.0001 | 0.0001 | ||
2 | VGG-19 | Optimiser | SGDM | ADAM | RMSprop |
Epoch | 30 | 30 | 30 | ||
Mini batch size | 64 | 64 | 64 | ||
Init. Learn. R. | 0.001 | 0.001 | 0.001 | ||
Momentum | 0.9000 | - | - | ||
L2 Reg. | 0.0001 | 0.0001 | 0.0001 | ||
3 | AlexNet | Optimiser | SGDM | ADAM | RMSprop |
Epoch | 50 | 50 | 50 | ||
Mini batch size | 128 | 128 | 128 | ||
Init. Learn. R. | 0.001 | 0.001 | 0.001 | ||
Momentum | 0.9000 | - | - | ||
L2 Reg. | 0.0001 | 0.0001 | 0.0001 | ||
4 | SqueezeNet | Optimiser | SGDM | ADAM | RMSprop |
Epoch | 30 | 30 | 30 | ||
Mini batch size | 64 | 64 | 64 | ||
Init. Learn. R. | 0.001 | 0.0001 | 0.0001 | ||
Momentum | 0.9000 | - | - | ||
L2 Reg. | 0.0001 | 0.0001 | 0.0001 | ||
5 | ResNet-18 | Optimiser | SGDM | ADAM | RMSprop |
Epoch | 30 | 30 | 30 | ||
Mini batch size | 64 | 64 | 64 | ||
Init. Learn. R. | 0.001 | 0.0001 | 0.0001 | ||
Momentum | 0.9000 | - | - | ||
L2 Reg. | 0.0001 | 0.0001 | 0.0001 | ||
6 | Inception-v3 | Optimiser | SGDM | ADAM | RMSprop |
Epoch | 10 | 10 | 10 | ||
Mini batch size | 64 | 64 | 64 | ||
Init. Learn. R. | 0.001 | 0.0001 | 0.0001 | ||
Momentum | 0.9000 | - | - | ||
L2 Reg. | 0.0001 | 0.0001 | 0.0001 | ||
7 | ResNet-50 | Optimiser | SGDM | ADAM | RMSprop |
Epoch | 30 | 30 | 30 | ||
Mini batch size | 64 | 64 | 64 | ||
Init. Learn. R. | 0.001 | 0.0001 | 0.0001 | ||
Momentum | 0.9000 | - | - | ||
L2 Reg. | 0.0001 | 0.0001 | 0.0001 |
8 | VGG-16 | Optimiser | SGDM | ADAM | RMSprop |
Epoch | 30 | 30 | 30 | ||
Mini batch size | 128 | 128 | 128 | ||
Init. Learn. R. | 0.001 | 0.0001 | 0.0001 | ||
Momentum | 0.9000 | - | - | ||
L2 Reg. | 0.0001 | 0.0001 | 0.0001 | ||
9 | ResNet-101 | Optimiser | SGDM | ADAM | RMSprop |
Epoch | 30 | 30 | 30 | ||
Mini batch size | 32 | 32 | 32 | ||
Init. Learn. R. | 0.001 | 0.0001 | 0.0001 | ||
Momentum | 0.9000 | - | - | ||
L2 Reg. | 0.0001 | 0.0001 | 0.0001 | ||
10 | DenseNet-201 | Optimiser | SGDM | ADAM | RMSprop |
Epoch | 30 | 30 | 30 | ||
Mini batch size | 32 | 32 | 32 | ||
Init. Learn. R. | 0.001 | 0.0001 | 0.0001 | ||
Momentum | 0.9000 | - | - | ||
L2 Reg. | 0.0001 | 0.0001 | 0.0001 | ||
11 | Inception-ResNet-v2 | Optimiser | SGDM | ADAM | RMSprop |
Epoch | 30 | 30 | 30 | ||
Mini batch size | 32 | 32 | 32 | ||
Init. Learn. R. | 0.001 | 0.0001 | 0.0001 | ||
Momentum | 0.9000 | - | - | ||
L2 Reg. | 0.0001 | 0.0001 | 0.0001 |
No. | CNNs | SGDM | ADAM | Rms Prop | Mean | Epoch | Mini-Batch Size |
---|---|---|---|---|---|---|---|
1 | GoogleNet | 0.650 | 0.671 | 0.640 | 0.654 | 30 | 64 |
2 | VGG-19 | 0.680 | 0.681 | 0.590 | 0.650 | 30 | 64 |
3 | AlexNet | 0.674 | 0.690 | 0.657 | 0.674 | 50 | 128 |
4 | SqueezeNet | 0.683 | 0.657 | 0.690 | 0.677 | 30 | 64 |
5 | ResNet-18 | 0.704 | 0.709 | 0.668 | 0.693 | 30 | 64 |
6 | Inception-v3 | 0.710 | 0.689 | 0.707 | 0.702 | 10 | 64 |
7 | ResNet-50 | 0.686 | 0.718 | 0.716 | 0.707 | 30 | 64 |
8 | VGG-16 | 0.692 | 0.713 | 0.716 | 0.707 | 30 | 128 |
9 | ResNet-101 | 0.715 | 0.706 | 0.701 | 0.707 | 30 | 32 |
10 | DenseNet-201 | 0.733 | 0.695 | 0.722 | 0.717 | 30 | 32 |
11 | Inception-ResNet-v2 | 0.712 | 0.747 | 0.710 | 0.723 | 30 | 32 |
12 | ResNet-50 (augmentation) | 0.835 | 0.854 | 0.847 | 0.845 | 30 | 64 |
13 | Inception-ResNet-v2 (augmentation) | 0.842 | 0.869 | 0.860 | 0.857 | 30 | 32 |
No. | CNNs | SGDM | ADAM | Rms Prop | Mean | Epoch | Mini-Batch Size |
---|---|---|---|---|---|---|---|
1 | GoogleNet | 0.373 | 0.412 | 0.358 | 0.381 | 30 | 64 |
2 | VGG-19 | 0.433 | 0.446 | 0.335 | 0.404 | 30 | 64 |
3 | AlexNet | 0.420 | 0.450 | 0.390 | 0.420 | 50 | 128 |
4 | SqueezeNet | 0.438 | 0.390 | 0.448 | 0.425 | 30 | 64 |
5 | ResNet-18 | 0.474 | 0.484 | 0.408 | 0.455 | 30 | 64 |
6 | Inception-v3 | 0.487 | 0.450 | 0.482 | 0.473 | 10 | 64 |
7 | ResNet-50 | 0.441 | 0.496 | 0.494 | 0.477 | 30 | 64 |
8 | VGG-16 | 0.453 | 0.491 | 0.492 | 0.479 | 30 | 128 |
9 | ResNet-101 | 0.495 | 0.475 | 0.472 | 0.481 | 30 | 32 |
10 | DenseNet-201 | 0.524 | 0.458 | 0.507 | 0.497 | 30 | 32 |
11 | Inception-ResNet-v2 | 0.485 | 0.548 | 0.484 | 0.506 | 30 | 32 |
12 | ResNet-50 (augmentation) | 0.655 | 0.696 | 0.683 | 0.678 | 30 | 64 |
13 | Inception-ResNet-v2 (augmentation) | 0.670 | 0.728 | 0.711 | 0.703 | 30 | 32 |
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Ananda, A.; Ngan, K.H.; Karabağ, C.; Ter-Sarkisov, A.; Alonso, E.; Reyes-Aldasoro, C.C. Classification and Visualisation of Normal and Abnormal Radiographs; A Comparison between Eleven Convolutional Neural Network Architectures. Sensors 2021, 21, 5381. https://doi.org/10.3390/s21165381
Ananda A, Ngan KH, Karabağ C, Ter-Sarkisov A, Alonso E, Reyes-Aldasoro CC. Classification and Visualisation of Normal and Abnormal Radiographs; A Comparison between Eleven Convolutional Neural Network Architectures. Sensors. 2021; 21(16):5381. https://doi.org/10.3390/s21165381
Chicago/Turabian StyleAnanda, Ananda, Kwun Ho Ngan, Cefa Karabağ, Aram Ter-Sarkisov, Eduardo Alonso, and Constantino Carlos Reyes-Aldasoro. 2021. "Classification and Visualisation of Normal and Abnormal Radiographs; A Comparison between Eleven Convolutional Neural Network Architectures" Sensors 21, no. 16: 5381. https://doi.org/10.3390/s21165381
APA StyleAnanda, A., Ngan, K. H., Karabağ, C., Ter-Sarkisov, A., Alonso, E., & Reyes-Aldasoro, C. C. (2021). Classification and Visualisation of Normal and Abnormal Radiographs; A Comparison between Eleven Convolutional Neural Network Architectures. Sensors, 21(16), 5381. https://doi.org/10.3390/s21165381