Precision Medicine for Apical Lesions and Peri-Endo Combined Lesions Based on Transfer Learning Using Periapical Radiographs
Abstract
:1. Introduction
2. Materials and Methods
2.1. Image Segmentation
2.1.1. Tooth Annotation
2.1.2. YOLOv8 OBB Model Training
2.1.3. Single-Tooth Cropping
- A.
- Image Rotation
- B.
- Coordinate Point Rotation
- C.
- Single-Tooth Cropping and Cropping Area Expansion
2.2. Image Processing
2.2.1. Grayscale
2.2.2. Gaussian High-Pass Filter
2.2.3. Adaptive Histogram Equalization
2.2.4. Flat-Field Correction
2.2.5. Linear Transformation
2.2.6. Negative Film Effect
2.3. CNN Training and Validation
2.3.1. CNN Architecture
2.3.2. Hyperparameter
2.3.3. Training and Validation
2.4. Object Detection Training and Validation
3. Results
3.1. YOLO Detection and Image Segmentation
3.2. CNN Training
- 1.
- Aspect 1: Black Padding
- 2.
- Aspect 2: Data Augmentation
- 3.
- Aspect 3: Expanding the Cropping Range
- 4.
- Aspect 4: Image Enhancement
3.3. YOLOv8
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Hardware Platform | Version | ||
CPU | 11 Gen Intel(R) Core(TM) [email protected] | ||
GPU | NVIDIA GeForce RTX 3070 8G | ||
DRAM | 32 GB | ||
Software Platform | Version | Software Platform | Version |
MATLAB | R2023b | Python | 3.11.8 |
Deep Network designer | R2023b | PyTorch | 2.2.1 + cu121 |
Deep Learning Toolbox | 23.2 | CUDA | 12.1 |
Layer | Filters/Neuron | Filter Size | Stride | Padding | Size of Feature Map | Activation Functions |
---|---|---|---|---|---|---|
Input | 227 × 227 × 3 | |||||
Conv 1 | 96 | 11 × 11 | 4 | 55 × 55 × 96 | ReLU | |
MaxPool 1 | 3 × 3 | 2 | 27 × 27 × 96 | |||
Conv 2 | 256 | 5 × 5 | 1 | 2 | 27 × 27 × 256 | ReLU |
MaxPool 2 | 3 × 3 | 2 | 13 × 13 × 256 | |||
Conv 3 | 384 | 3 × 3 | 1 | 1 | 13 × 13 × 384 | ReLU |
Conv 4 | 384 | 3 × 3 | 1 | 1 | 13 × 13 × 384 | ReLU |
Conv 5 | 356 | 3 × 3 | 1 | 1 | 13 × 13 × 256 | ReLU |
MaxPool 3 | 3 × 3 | 2 | 6 × 6 × 256 | |||
Dropout 1 | Rate = 0.7 | 6 × 6 × 256 | ||||
Fc 1 | 4096 | ReLU | ||||
Dropout 2 | Rate = 0.7 | 4096 | ||||
Fc 2 | 4096 | ReLU | ||||
Fc 3 | 3 | Softmax |
Hyperparameter | Value | Hyper Parameter | Model | Value |
---|---|---|---|---|
Initial Learning Rate | 0.0001 | Max Epoch | AlexNet | 30 |
Mini Batch Size | 16 | Places365-GoogLeNet | 20 | |
Learning Rate Drop Factor | 0.1 | VGG-16 | 6 | |
Learning Rate Drop Period | 10 | ResNet50 | 10 | |
Shuffle | Every-epoch | GoogLeNet | 20 | |
Validation Frequency | 100 | ConvNeXtv2_base | 10 |
Disease | Training Set | Validation Set | Total |
Normal | 53 | 14 | 67 |
Apical Lesion | 53 | 14 | 67 |
Peri-endo Combined Lesion | 53 | 14 | 67 |
Total | 159 | 42 | 201 |
Disease | Original | Augmentation |
Normal | 67 | 268 |
Apical Lesion | 67 | 268 |
Peri-endo Combined Lesion | 67 | 268 |
Hyperparameter | Value |
---|---|
Epoch | 100 |
Batch | 8 |
imgsize | 640 × 640 |
lr0 | 0.01 |
Number | No. 1 | No. 2 | No. 3 |
Ground Truth | Peri-endo Combined Lesion | Normal | Apical Lesion |
Validation | Peri-endo Combined Lesion | Normal | Apical Lesion |
Accuracy | 99.94% | 60.47% | 85.02% |
Method | Metrics | AlexNet | Places365-GoogLeNet | VGG16 | ResNet50 | GoogLeNet | ConvNeXtv2 |
Original | Accuracy | 80.95% | 79.19% | 71.43% | 71.43% | 80.95% | 76.19% |
Training time | 54 s | 1 m 20 s | 26 s | 1 m 19 s | 1 m 19 s | 6 m 4 s | |
After padding | Accuracy | 83.33% | 80.95% | 80.95% | 73.81% | 85.71% | 85.71% |
Training time | 48 s | 1 m 29 s | 24 s | 1 m 19 s | 1 m 17 s | 5 m 46 s |
Method | Metrics | AlexNet | Places365-GoogLeNet | VGG16 | ResNet50 | GoogLeNet | ConvNeXtv2 |
Padding | Accuracy | 83.33% | 80.95% | 80.95% | 73.81% | 85.71% | 85.71% |
Training time | 48 s | 1 m 29 s | 24 s | 1 m 19 s | 1 m 17 s | 5 m 46 s | |
Padding + Enhancement | Accuracy | 88.69% | 88.69% | 88.69% | 88.69% | 86.90% | 87.50% |
Training time | 2 m 49 s | 5 m 17 s | 1 m 2 s | 4 m 33 s | 5 m 26 s | 21 m 58 s |
Method | Metrics | AlexNet | Places365-GoogLeNet | VGG16 | ResNet50 | GoogLeNet | ConvNeXtv2 |
Original YOLOv8 cropping | Accuracy | 88.69% | 88.69% | 88.69% | 88.69% | 86.90% | 87.50% |
Training time | 2 m 49 s | 5 m 17 s | 1 m 21 s | 4 m 33 s | 5 m 26 s | 21 m 58 s | |
Expand x = 20 pixels, y = 0 pixels | Accuracy | 91.67% | 89.29% | 90.48% | 85.71% | 89.29% | 89.28% |
Training time | 1 m 30 s | 4 m 8 s | 1 m 37 s | 3 m 20 s | 4 m 39 s | 21 m 13 s | |
Expand x = 0 pixels, y = 40 pixels | Accuracy | 88.10% | 91.67% | 90.48% | 88.10% | 88.69% | 88.09% |
Training time | 2 m 38 s | 1 m 23 s | 1 m 16 s | 3 m 22 s | 5 m 31 s | 22 m 4 s | |
Expand x = 20 pixels, y = 40 pixels | Accuracy | 89.29% | 89.88% | 88.10% | 89.88% | 88.10% | 91.07% |
Training time | 2 m 1 s | 4 m 50 s | 1 m 29 s | 4 m 28 s | 4 m 37 s | 20 m 35 s |
Method | Metrics | AlexNet | Places365- GoogLeNet | VGG16 | ResNet50 | GoogLeNet | Conv NeXtv2 |
Original (padding, enhancement) | Accuracy | 88.69% | 88.69% | 88.69% | 88.69% | 86.90% | 87.50% |
Training time | 2 m 49 s | 5 m 17 s | 1 m 21 s | 4 m 33 s | 5 m 26 s | 21 m 58 s | |
Gaussian high-pass filter | Accuracy | 92.26% | 93..45% | 91.67% | 89.29% | 92.26% | 89.29% |
Training time | 2 m 50 s | 6 m 3 s | 1 m 16 s | 4 m 3 s | 5 m 33 s | 20 m 53 s | |
Adaptive histogram equalization | Accuracy | 88.10% | 92.86% | 92.26% | 91.07% | 89.88% | 95.23% |
Training time | 50 s | 1 m 16 s | 1 m 21 s | 4 m 1 s | 5 m 14 s | 55 m 40 s | |
Gaussian high-pass filter with adaptive histogram equalization | Accuracy | 93.45% | 91.07% | 92.86% | 90.48% | 88.10% | 93.45% |
Training time | 2 m 24 s | 5 m 37 s | 1 m 30 s | 3 m 55 s | 5 m 48 s | 22 m 2 s |
Disease | Actual | |||
Normal | Apical Lesion | Peri-endo Combined Lesion | ||
Predicted | Normal | 56 | 4 | 0 |
Apical Lesion | 0 | 49 | 1 | |
Peri-endo Combined Lesion | 0 | 3 | 55 |
Method | The Best Model in this Study | Method in [8] | Method in [23] | |||
Model | ConvNeXtv2 | U-Net Model | Decision Tree | |||
Disease | Normal | Apical Lesion | Peri-endo Combined Lesion | Total | Apical Lesion | Apical Lesion |
Accuracy | 95.23% | No data | No data | |||
Precision | 93.33% | 98.00% | 94.82% | 95.38% | No data | No data |
Recall | 99.75% | 87.50% | 98.21% | 95.23% | No data | No data |
F1-Score | 96.55% | 92.45% | 96.49% | 95.16% | 74.2% | 89% |
Disease | Training Set | Validation Set | Total |
Normal | 194 | 58 | 252 |
Apical Lesion | 106 | 20 | 126 |
Peri-endo Combined Lesion | 70 | 15 | 85 |
Total | 370 | 93 | 463 |
Method | Metrics | Normal | Apical Lesion | Peri-Endo Combined Lesion | Total |
Original | mAP50 | 0.871 | 0.742 | 0.928 | 0.847 |
Accuracy | 75.00% | ||||
Original with data enhancement | mAP50 | 0.906 | 0.878 | 0.927 | 0.904 |
Accuracy | 84.70% |
Method | Metrics | Normal | Apical Lesion | Peri-Endo Combined Lesion | Total |
Linear Transformation with Adaptive histogram equalization | mAP50 | 0.904 | 0.876 | 0.957 | 0.912 |
Accuracy | 85.16% | ||||
Flat-Field Correction with Adaptive histogram equalization | mAP50 | 0.888 | 0.857 | 0.971 | 0.905 |
Accuracy | 87.79% | ||||
Gaussian high-pass filter with Negative Film Effect | mAP50 | 0.918 | 0.913 | 0.923 | 0.918 |
Accuracy | 92.13% |
Disease | Actual | |||
Normal | Apical Lesion | Peri-endo Combined Lesion | ||
Predicted | Normal | 143 | 3 | 2 |
Apical Lesion | 6 | 55 | 5 | |
Peri-endo Combined Lesion | 2 | 2 | 36 |
Method | The Best Models of this Study Method | Method in [24] | Method in [25] | |||
Model | YOLOv8 | YOLOv5x | YOLOv3 Darknet | |||
Disease | Normal | Apical Lesion | Peri-endo Combined Lesion | Total | Apical Lesion | Apical Lesion |
Accuracy | 92.13% | No data | No data | |||
Precision | 69.3% | 91% | 86.4% | 82.2% | 83% | 56% |
Recall | 84.2% | 95% | 91.7% | 90% | No data | 98% |
mAP50 | 0.918 | 0.913 | 0.923 | 0.918 | 0.88 | No data |
F1-Score | 87.46% | 80.13% | 88.49% | 85.92% | 87% | 71% |
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Wu, P.-Y.; Mao, Y.-C.; Lin, Y.-J.; Li, X.-H.; Ku, L.-T.; Li, K.-C.; Chen, C.-A.; Chen, T.-Y.; Chen, S.-L.; Tu, W.-C.; et al. Precision Medicine for Apical Lesions and Peri-Endo Combined Lesions Based on Transfer Learning Using Periapical Radiographs. Bioengineering 2024, 11, 877. https://doi.org/10.3390/bioengineering11090877
Wu P-Y, Mao Y-C, Lin Y-J, Li X-H, Ku L-T, Li K-C, Chen C-A, Chen T-Y, Chen S-L, Tu W-C, et al. Precision Medicine for Apical Lesions and Peri-Endo Combined Lesions Based on Transfer Learning Using Periapical Radiographs. Bioengineering. 2024; 11(9):877. https://doi.org/10.3390/bioengineering11090877
Chicago/Turabian StyleWu, Pei-Yi, Yi-Cheng Mao, Yuan-Jin Lin, Xin-Hua Li, Li-Tzu Ku, Kuo-Chen Li, Chiung-An Chen, Tsung-Yi Chen, Shih-Lun Chen, Wei-Chen Tu, and et al. 2024. "Precision Medicine for Apical Lesions and Peri-Endo Combined Lesions Based on Transfer Learning Using Periapical Radiographs" Bioengineering 11, no. 9: 877. https://doi.org/10.3390/bioengineering11090877
APA StyleWu, P. -Y., Mao, Y. -C., Lin, Y. -J., Li, X. -H., Ku, L. -T., Li, K. -C., Chen, C. -A., Chen, T. -Y., Chen, S. -L., Tu, W. -C., & Abu, P. A. R. (2024). Precision Medicine for Apical Lesions and Peri-Endo Combined Lesions Based on Transfer Learning Using Periapical Radiographs. Bioengineering, 11(9), 877. https://doi.org/10.3390/bioengineering11090877