Prediction of Mismatch Repair Status in Endometrial Cancer from Histological Slide Images Using Various Deep Learning-Based Algorithms
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethical Compliance
2.2. Patients and Specimens
2.3. Immunohistochemistry Staining and Evaluation of MMR Status
2.4. Pre-Processing of Whole-Slide Images
2.5. Hardware and Software Libraries Used
2.6. Data Split and Training Data Preparation
2.7. Classification Model Construction Using Convolutional Neural Networks
2.8. Classification Model Construction Using Attention Networks and Our API-Net-Based Model
2.9. Evaluation of Constructed Model Performance
3. Results
3.1. Pre-Processing of Data Set before Model Training
3.2. Validation of Model Performance in Various Hyperparameter and Classification Models
3.3. Performance of the Models for Unseen Test Data Set
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Accuracy | Precision | Recall | F-Score | AUROC | |||
---|---|---|---|---|---|---|---|
Pre-processing | Ratio | Original | 0.74 | 0.55 | 0.09 | 0.15 | 0.74 |
Down-sampled | 0.80 | 0.76 | 0.88 | 0.81 | 0.89 | ||
Data augmentation | None | 0.80 | 0.76 | 0.88 | 0.81 | 0.89 | |
Rotate | 0.76 | 0.70 | 0.90 | 0.79 | 0.87 | ||
Flip | 0.75 | 0.73 | 0.77 | 0.75 | 0.84 | ||
Rotate and flip | 0.77 | 0.77 | 0.76 | 0.77 | 0.86 | ||
Hyper-parameter | Batch | 8 | 0.80 | 0.76 | 0.88 | 0.81 | 0.89 |
16 | 0.72 | 0.70 | 0.74 | 0.72 | 0.80 | ||
32 | 0.69 | 0.70 | 0.67 | 0.68 | 0.77 | ||
Epoch | 30 | 0.80 | 0.76 | 0.88 | 0.81 | 0.89 | |
60 | 0.78 | 0.75 | 0.84 | 0.79 | 0.88 | ||
90 | 0.80 | 0.79 | 0.81 | 0.80 | 0.88 | ||
120 | 0.75 | 0.69 | 0.89 | 0.78 | 0.87 | ||
Learning rate | 1 × 10−2 | 0.80 | 0.76 | 0.88 | 0.81 | 0.89 | |
1 × 10−3 | 0.70 | 0.68 | 0.75 | 0.71 | 0.78 | ||
1 × 10−4 | 0.69 | 0.64 | 0.86 | 0.74 | 0.78 |
Accuracy | Precision | Recall | F-Score | AUROC | ||
---|---|---|---|---|---|---|
Convolutional neural network | GoogLeNet | 0.74 | 0.72 | 0.79 | 0.75 | 0.83 |
VGG_19_BN | 0.79 | 0.86 | 0.68 | 0.76 | 0.85 | |
ResNet50 | 0.80 | 0.76 | 0.88 | 0.81 | 0.89 | |
ResNet101 | 0.81 | 0.78 | 0.88 | 0.82 | 0.89 | |
wideResNet101-2 | 0.77 | 0.88 | 0.62 | 0.73 | 0.88 | |
EfficientNet-B7 | 0.74 | 0.77 | 0.68 | 0.72 | 0.81 | |
Attention mechanism | ViT_B16 | 0.57 | 0.59 | 0.43 | 0.50 | 0.62 |
ViT_B32 | 0.67 | 0.61 | 0.89 | 0.73 | 0.76 | |
API-Net-based model | 0.81 | 0.81 | 0.81 | 0.81 | 0.89 |
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Share and Cite
Umemoto, M.; Mariya, T.; Nambu, Y.; Nagata, M.; Horimai, T.; Sugita, S.; Kanaseki, T.; Takenaka, Y.; Shinkai, S.; Matsuura, M.; et al. Prediction of Mismatch Repair Status in Endometrial Cancer from Histological Slide Images Using Various Deep Learning-Based Algorithms. Cancers 2024, 16, 1810. https://doi.org/10.3390/cancers16101810
Umemoto M, Mariya T, Nambu Y, Nagata M, Horimai T, Sugita S, Kanaseki T, Takenaka Y, Shinkai S, Matsuura M, et al. Prediction of Mismatch Repair Status in Endometrial Cancer from Histological Slide Images Using Various Deep Learning-Based Algorithms. Cancers. 2024; 16(10):1810. https://doi.org/10.3390/cancers16101810
Chicago/Turabian StyleUmemoto, Mina, Tasuku Mariya, Yuta Nambu, Mai Nagata, Toshihiro Horimai, Shintaro Sugita, Takayuki Kanaseki, Yuka Takenaka, Shota Shinkai, Motoki Matsuura, and et al. 2024. "Prediction of Mismatch Repair Status in Endometrial Cancer from Histological Slide Images Using Various Deep Learning-Based Algorithms" Cancers 16, no. 10: 1810. https://doi.org/10.3390/cancers16101810
APA StyleUmemoto, M., Mariya, T., Nambu, Y., Nagata, M., Horimai, T., Sugita, S., Kanaseki, T., Takenaka, Y., Shinkai, S., Matsuura, M., Iwasaki, M., Hirohashi, Y., Hasegawa, T., Torigoe, T., Fujino, Y., & Saito, T. (2024). Prediction of Mismatch Repair Status in Endometrial Cancer from Histological Slide Images Using Various Deep Learning-Based Algorithms. Cancers, 16(10), 1810. https://doi.org/10.3390/cancers16101810