Gastric Cancer Detection with Ensemble Learning on Digital Pathology: Use Case of Gastric Cancer on GasHisSDB Dataset
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Literature Reviews
2.2. Dataset Description
2.3. Methodology Overview
2.4. Empty Patch Removal Process
2.5. Pretrained Networks as Base Models
2.5.1. ResNet34 Architecture
2.5.2. ResNet50 Architecture
2.5.3. VGGNet16 Architecture
2.5.4. EfficientNet Architecture
2.5.5. VitNet Architecture
2.5.6. Ensemble Architecture
2.6. Interpretability of the Ensemble Model
2.7. Experimental Setting
3. Results
4. Discussion
Experimental Setting
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Model | Fold | Train Accuracy | Train Loss | Val Accuracy | Val Loss | Jaccard Index | AUC | Specificity | Sensitivity |
---|---|---|---|---|---|---|---|---|---|
Resnet34 | 1 | 98.7508 | 0.0331 | 93.6131 | 0.2175 | 0.7447 | 0.9719 | 0.9604 | 0.8494 |
2 | 97.8192 | 0.0604 | 93.7206 | 0.2092 | 0.7472 | 0.9717 | 0.9638 | 0.8427 | |
3 | 98.8546 | 0.0329 | 93.8111 | 0.2210 | 0.7384 | 0.9760 | 0.9699 | 0.8204 | |
4 | 97.7773 | 0.0596 | 93.8226 | 0.1724 | 0.7466 | 0.9777 | 0.9625 | 0.8491 | |
5 | 98.1767 | 0.0487 | 93.7910 | 0.2399 | 0.7640 | 0.9754 | 0.9518 | 0.8900 | |
ResNet50 | 1 | 98.4818 | 0.0409 | 93.7408 | 0.1936 | 0.8763 | 0.8979 | 0.9682 | 0.8277 |
2 | 96.2419 | 0.0958 | 94.2439 | 0.1880 | 0.8860 | 0.9069 | 0.9703 | 0.8435 | |
3 | 98.4410 | 0.0413 | 93.4971 | 0.2024 | 0.8742 | 0.9042 | 0.9577 | 0.8508 | |
4 | 97.0654 | 0.0769 | 92.7688 | 0.2016 | 0.8601 | 0.9071 | 0.9431 | 0.8711 | |
5 | 93.5411 | 0.1673 | 93.8459 | 0.1869 | 0.8772 | 0.9064 | 0.9648 | 0.8480 | |
VitNet | 1 | 83.6243 | 0.3631 | 83.7591 | 0.3555 | 0.6945 | 0.7132 | 0.9347 | 0.4916 |
2 | 82.9835 | 0.3816 | 84.2836 | 0.3490 | 0.6969 | 0.7076 | 0.9493 | 0.4660 | |
3 | 78.4974 | 0.4755 | 78.8656 | 0.4560 | 0.5946 | 0.5054 | 0.9988 | 0.0121 | |
4 | 82.5612 | 0.3898 | 84.2841 | 0.3505 | 0.6986 | 0.7015 | 0.9488 | 0.4542 | |
5 | 78.3217 | 0.5231 | 77.4105 | 0.5353 | 0.5674 | 0.5 | 1 | 0 | |
VggNet | 1 | 98.7371 | 0.0366 | 93.7591 | 0.2579 | 0.8763 | 0.9746 | 0.9747 | 0.8053 |
2 | 96.2693 | 0.0969 | 94.3341 | 0.1785 | 0.8868 | 0.9757 | 0.9738 | 0.8353 | |
3 | 98.5683 | 0.0417 | 93.9220 | 0.2120 | 0.8763 | 0.9751 | 0.9720 | 0.8178 | |
4 | 94.3224 | 0.1519 | 93.7681 | 0.1621 | 0.8756 | 0.9733 | 0.9685 | 0.8245 | |
5 | 98.3636 | 0.0487 | 93.7910 | 0.2329 | 0.8768 | 0.9724 | 0.9693 | 0.8302 | |
EfficientNet | 1 | 74.9474 | 0.5035 | 75.4057 | 0.5142 | 0.6094 | 0.7478 | 0.7172 | 0.7784 |
2 | 82.4435 | 0.3866 | 83.0474 | 0.3685 | 0.6829 | 0.6726 | 0.9421 | 0.4030 | |
3 | 81.0359 | 0.4139 | 82.3709 | 0.3855 | 0.6704 | 0.6346 | 0.9463 | 0.3229 | |
4 | 82.3379 | 0.3879 | 84.2231 | 0.3531 | 0.6975 | 0.6725 | 0.9419 | 0.4030 | |
5 | 82.6571 | 0.3805 | 83.5210 | 0.3651 | 0.6944 | 0.6816 | 0.9401 | 0.4232 | |
Ensemble | 1 | 98.3587 | 0.0436 | 99.3430 | 0.0252 | 0.9867 | 0.9904 | 0.9957 | 0.9850 |
2 | 98.5187 | 0.0410 | 99.2421 | 0.0211 | 0.9839 | 0.9875 | 0.9962 | 0.9787 | |
3 | 98.6001 | 0.0384 | 99.2056 | 0.0237 | 0.9836 | 0.9898 | 0.9936 | 0.9861 | |
4 | 97.9234 | 0.0627 | 97.8197 | 0.0651 | 0.9562 | 0.9642 | 0.9886 | 0.9398 | |
5 | 98.5642 | 0.0390 | 99.0869 | 0.0221 | 0.9823 | 0.9866 | 0.9943 | 0.9789 |
Model | Fold | Train Accuracy | Train Loss | Val Accuracy | Val Loss | Jaccard Index | AUC | Specificity | Sensitivity |
---|---|---|---|---|---|---|---|---|---|
Resnet34 | 1 | 98.8627 | 0.0327 | 96.8167 | 0.1097 | 0.8347 | 0.9879 | 0.9812 | 0.9075 |
2 | 99.2847 | 0.0187 | 97.0297 | 0.1327 | 0.8444 | 0.9815 | 0.9884 | 0.8884 | |
3 | 98.9145 | 0.0336 | 96.9364 | 0.1025 | 0.8392 | 0.9907 | 0.9901 | 0.8762 | |
4 | 99.1640 | 0.0234 | 96.4475 | 0.1208 | 0.8175 | 0.9879 | 0.9836 | 0.8778 | |
5 | 99.2957 | 0.0214 | 96.6893 | 0.1074 | 0.8149 | 0.9897 | 0.9877 | 0.8642 | |
ResNet50 | 1 | 99.5552 | 0.0125 | 96.7257 | 0.1120 | 0.9316 | 0.9518 | 0.9756 | 0.9281 |
2 | 99.2449 | 0.0213 | 96.9856 | 0.1156 | 0.9372 | 0.9254 | 0.9951 | 0.8557 | |
3 | 99.7229 | 0.0089 | 97.0930 | 0.1198 | 0.9388 | 0.9493 | 0.9833 | 0.9154 | |
4 | 99.5007 | 0.0142 | 96.8166 | 0.1253 | 0.9339 | 0.9379 | 0.9853 | 0.8905 | |
5 | 99.5042 | 0.0147 | 97.0748 | 0.0995 | 0.9379 | 0.9406 | 0.9860 | 0.8951 | |
VitNet | 1 | 86.6963 | 0.3109 | 87.4715 | 0.2875 | 0.7518 | 0.7395 | 0.9488 | 0.5301 |
2 | 84.6948 | 0.3495 | 86.1826 | 0.3185 | 0.7254 | 0.7123 | 0.9470 | 0.4775 | |
3 | 82.2817 | 0.4486 | 81.7531 | 0.4287 | 0.6310 | 0.5 | 1 | 0 | |
4 | 85.7447 | 0.3298 | 87.9123 | 0.2929 | 0.7581 | 0.7607 | 0.9464 | 0.5750 | |
5 | 84.2084 | 0.3465 | 86.3265 | 0.3085 | 0.7231 | 0.6767 | 0.9582 | 0.3951 | |
VggNet | 1 | 76.6185 | 0.4764 | 75.6162 | 0.5053 | 0.6152 | 0.7657 | 0.7776 | 0.7538 |
2 | 88.3740 | 0.2758 | 89.1768 | 0.2611 | 0.7889 | 0.7476 | 0.9592 | 0.5361 | |
3 | 88.1351 | 0.2822 | 88.3388 | 0.2732 | 0.7756 | 0.7372 | 0.9605 | 0.5139 | |
4 | 86.6576 | 0.3140 | 88.2826 | 0.2813 | 0.7673 | 0.6979 | 0.9591 | 0.4368 | |
5 | 88.3702 | 0.2745 | 88.4198 | 0.2781 | 0.7779 | 0.7460 | 0.9594 | 0.5325 | |
EfficientNet | 1 | 99.1949 | 0.0265 | 96.8167 | 0.1372 | 0.9340 | 0.9878 | 0.9867 | 0.8818 |
2 | 99.8978 | 0.0054 | 96.9416 | 0.1716 | 0.9363 | 0.9886 | 0.9873 | 0.8884 | |
3 | 98.4339 | 0.0464 | 97.1824 | 0.1130 | 0.9403 | 0.9883 | 0.9901 | 0.8897 | |
4 | 96.4544 | 0.1011 | 96.0322 | 0.1098 | 0.9176 | 0.9860 | 0.9757 | 0.8905 | |
5 | 99.8366 | 0.0061 | 96.9614 | 0.1410 | 0.9338 | 0.9902 | 0.98363 | 0.9005 | |
Ensemble | 1 | 97.2581 | 0.0728 | 97.6125 | 0.0646 | 0.9501 | 0.9593 | 0.9853 | 0.9332 |
2 | 97.7973 | 0.0622 | 98.1738 | 0.0533 | 0.9627 | 0.9647 | 0.9913 | 0.9381 | |
3 | 97.7894 | 0.0603 | 97.8756 | 0.0618 | 0.9531 | 0.9636 | 0.9874 | 0.9399 | |
4 | 97.8457 | 0.0625 | 97.5778 | 0.0685 | 0.9486 | 0.9549 | 0.9876 | 0.9223 | |
5 | 98.9735 | 0.0316 | 99.4250 | 0.0226 | 0.9872 | 0.9895 | 0.9965 | 0.9826 |
Model | Fold | Train Accuracy | Train Loss | Val Accuracy | Val Loss | Jaccard Index | AUC | Specificity | Sensitivity |
---|---|---|---|---|---|---|---|---|---|
Resnet34 | 1 | 99.6311 | 0.0132 | 97.9807 | 0.0648 | 0.8949 | 0.9961 | 0.9887 | 0.9398 |
2 | 99.5496 | 0.0148 | 98.1776 | 0.0656 | 0.9022 | 0.9913 | 0.9922 | 0.9341 | |
3 | 99.7337 | 0.0083 | 98.1038 | 0.0535 | 0.8928 | 0.9976 | 0.9912 | 0.9308 | |
4 | 97.1184 | 0.0896 | 97.2005 | 0.0821 | 0.8665 | 0.9931 | 0.9806 | 0.9361 | |
5 | 99.5437 | 0.0213 | 98.4187 | 0.0738 | 0.9105 | 0.9929 | 0.9862 | 0.9739 | |
ResNet50 | 1 | 99.3660 | 0.0288 | 98.4396 | 0.0579 | 0.9678 | 0.9739 | 0.9904 | 0.9573 |
2 | 99.5842 | 0.0170 | 98.3143 | 0.0592 | 0.9628 | 0.9719 | 0.9894 | 0.9544 | |
3 | 99.8263 | 0.0066 | 98.1038 | 0.0776 | 0.9599 | 0.9684 | 0.9874 | 0.9494 | |
4 | 99.9538 | 0.0018 | 97.9348 | 0.0743 | 0.9574 | 0.9620 | 0.9903 | 0.9338 | |
5 | 99.7718 | 0.0112 | 98.3708 | 0.0625 | 0.9648 | 0.9832 | 0.9839 | 0.9826 | |
VitNet | 1 | 82.2614 | 0.4526 | 81.6888 | 0.4532 | 0.6295 | 0.5 | 1 | 0 |
2 | 84.4919 | 0.3426 | 86.2870 | 0.3141 | 0.7307 | 0.6980 | 0.9555 | 0.4405 | |
3 | 81.9212 | 0.4638 | 83.0248 | 0.4527 | 0.6543 | 0.5 | 1 | 0 | |
4 | 84.3706 | 0.3502 | 84.6718 | 0.3393 | 0.6977 | 0.6841 | 0.9498 | 0.4184 | |
5 | 82.0483 | 0.3951 | 86.3919 | 0.3069 | 0.7274 | 0.6337 | 0.9776 | 0.2898 | |
VggNet | 1 | 77.3246 | 0.4784 | 76.5826 | 0.4820 | 0.6291 | 0.7732 | 0.7643 | 0.7822 |
2 | 90.0875 | 0.2296 | 93.0702 | 0.1838 | 0.8607 | 0.7924 | 0.9604 | 0.6244 | |
3 | 91.0623 | 0.2155 | 92.8018 | 0.1911 | 0.8572 | 0.8139 | 0.9641 | 0.6636 | |
4 | 91.0069 | 0.2178 | 93.0925 | 0.1655 | 0.8589 | 0.8168 | 0.9628 | 0.6709 | |
5 | 91.4476 | 0.2077 | 92.0146 | 0.1945 | 0.8444 | 0.8186 | 0.9659 | 0.6712 | |
EfficientNet | 1 | 99.9769 | 0.0014 | 98.2101 | 0.1121 | 0.9623 | 0.9946 | 0.9915 | 0.9398 |
2 | 99.6882 | 0.0098 | 97.9498 | 0.0795 | 0.9584 | 0.9944 | 0.9952 | 0.9088 | |
3 | 98.8773 | 0.0347 | 97.9683 | 0.0896 | 0.9579 | 0.9921 | 0.9934 | 0.9122 | |
4 | 99.2738 | 0.0244 | 97.2005 | 0.0940 | 0.9464 | 0.9912 | 0.9834 | 0.9243 | |
5 | 99.6692 | 0.0091 | 98.1312 | 0.0814 | 0.9586 | 0.9948 | 0.9896 | 0.9391 | |
Ensemble | 1 | 98.4785 | 0.0412 | 98.8067 | 0.0313 | 0.9751 | 0.9829 | 0.9910 | 0.9749 |
2 | 99.0877 | 0.0268 | 98.9066 | 0.0325 | 0.9753 | 0.9775 | 0.9955 | 0.9594 | |
3 | 99.1203 | 0.0298 | 99.1873 | 0.0260 | 0.9830 | 0.9866 | 0.9945 | 0.9787 | |
4 | 99.4813 | 0.0150 | 99.7246 | 0.0079 | 0.9942 | 0.9964 | 0.9977 | 0.9952 | |
5 | 98.9165 | 0.0319 | 99.3291 | 0.0245 | 0.9836 | 0.9901 | 0.9948 | 0.9855 |
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Mudavadkar, G.R.; Deng, M.; Al-Heejawi, S.M.A.; Arora, I.H.; Breggia, A.; Ahmad, B.; Christman, R.; Ryan, S.T.; Amal, S. Gastric Cancer Detection with Ensemble Learning on Digital Pathology: Use Case of Gastric Cancer on GasHisSDB Dataset. Diagnostics 2024, 14, 1746. https://doi.org/10.3390/diagnostics14161746
Mudavadkar GR, Deng M, Al-Heejawi SMA, Arora IH, Breggia A, Ahmad B, Christman R, Ryan ST, Amal S. Gastric Cancer Detection with Ensemble Learning on Digital Pathology: Use Case of Gastric Cancer on GasHisSDB Dataset. Diagnostics. 2024; 14(16):1746. https://doi.org/10.3390/diagnostics14161746
Chicago/Turabian StyleMudavadkar, Govind Rajesh, Mo Deng, Salah Mohammed Awad Al-Heejawi, Isha Hemant Arora, Anne Breggia, Bilal Ahmad, Robert Christman, Stephen T. Ryan, and Saeed Amal. 2024. "Gastric Cancer Detection with Ensemble Learning on Digital Pathology: Use Case of Gastric Cancer on GasHisSDB Dataset" Diagnostics 14, no. 16: 1746. https://doi.org/10.3390/diagnostics14161746
APA StyleMudavadkar, G. R., Deng, M., Al-Heejawi, S. M. A., Arora, I. H., Breggia, A., Ahmad, B., Christman, R., Ryan, S. T., & Amal, S. (2024). Gastric Cancer Detection with Ensemble Learning on Digital Pathology: Use Case of Gastric Cancer on GasHisSDB Dataset. Diagnostics, 14(16), 1746. https://doi.org/10.3390/diagnostics14161746