Interpretable Deep Learning Models for Breast Cancer Diagnosis Using Medical Imaging
Organizations: Information Systems Department College of Computer Science and Information Technology King Faisal University, Alahsaa, Saudi Arabia · Department of Artificial Intelligence & Data Science National University of Computer and Emerging Sciences Islamabad, Pakistan · Department of Computer Science National University of Computer and Emerging Sciences Islamabad, Pakistan
Abstract
Deep learning shows promise for breast cancer diagnosis, but limited interpretability hinders clinical adoption. We benchmark ten ImageNet-pretrained models (ResNet50, VGG19, InceptionV3, DenseNet121, Xception, MobileNetV2, EfficientNet, ConvNeXt, ViT, and Swin Transformer) for benign-versus-malignant classification on the BreakHis histopathology dataset using a patient-level split, and explain their predictions with Grad-CAM, LIME, Integrated Gradients, and LRP. DenseNet121 performed best, with 99.4% test accuracy and an AUC-ROC of 0.999, and significantly outperformed all other models (p < 0.001). Transformer-based models trailed the CNNs. The explanations consistently highlighted nuclei-rich and glandular regions of diagnostic relevance. Combining transfer learning with explainable AI can thus yield accurate, interpretable tools for breast cancer diagnosis.
Figures & tables
| Dataset | Accuracy (%) | Precision (%) | Recall (%) | F1-score (%) | Specificity (%) | AUC |
|---|---|---|---|---|---|---|
| Validation (All Mag.) | 89.2 | 90.7 | 95.5 | 93.0 | 70.3 | 0.936 |
| Test (All Mag.) | 99.4 | 99.9 | 99.5 | 99.6 | 99.2 | 0.999 |
| Test (40 ) | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 1.000 |
| Test (100 ) | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 1.000 |
| Test (200 ) | 100.0 | 100.0 | 100.0 | 100.0 | 100.0 | 1.000 |
| Test (400 ) | 97.5 | 99.4 | 97.7 | 98.5 | 96.4 | 0.998 |
| Dataset | Accuracy (%) | Precision (%) | Recall (%) | F1-score (%) | Specificity (%) | AUC |
|---|---|---|---|---|---|---|
| Validation (All Mag.) | 93.1 | 96.1 | 94.3 | 95.2 | 89.7 | 0.979 |
| Test (All Mag.) | 86.2 | 83.6 | 86.0 | 84.8 | 86.3 | 0.940 |
| Test (40 ) | 85.9 | 87.8 | 80.4 | 83.9 | 90.6 | 0.946 |
| Test (100 ) | 86.3 | 86.4 | 84.3 | 85.4 | 88.1 | 0.941 |
| Test (200 ) | 85.5 | 83.2 | 83.2 | 83.2 | 87.3 | 0.959 |
| Test (400 ) | 84.3 | 78.7 | 86.7 | 82.5 | 82.4 | 0.915 |
| Dataset | Accuracy (%) | Precision (%) | Recall (%) | F1-score (%) | Specificity (%) | AUC |
|---|---|---|---|---|---|---|
| Validation (All Mag.) | 80.9 | 80.6 | 91.1 | 85.6 | 64.2 | 0.881 |
| Test (All Mag.) | 77.1 | 85.1 | 89.1 | 87.0 | 2.4 | 0.653 |
| Test (40 ) | 76.1 | 83.6 | 89.5 | 86.4 | 0.0 | 0.450 |
| Test (100 ) | 79.1 | 84.7 | 92.1 | 88.3 | 2.7 | 0.708 |
| Test (200 ) | 79.7 | 88.3 | 88.8 | 88.6 | 8.7 | 0.823 |
| Test (400 ) | 76.4 | 85.2 | 88.0 | 86.6 | 3.5 | 0.780 |
| Dataset | Accuracy (%) | Precision (%) | Recall (%) | F1-score (%) | Specificity (%) | AUC |
|---|---|---|---|---|---|---|
| Validation (All Mag.) | 94.3 | 96.2 | 95.9 | 96.1 | 89.9 | 0.980 |
| Test (All Mag.) | 84.6 | 79.5 | 88.4 | 83.7 | 81.5 | 0.933 |
| Test (40 ) | 87.2 | 86.0 | 86.0 | 86.0 | 88.2 | 0.937 |
| Test (100 ) | 81.2 | 77.0 | 85.9 | 81.3 | 76.9 | 0.924 |
| Test (200 ) | 85.1 | 80.4 | 86.3 | 83.3 | 84.1 | 0.938 |
| Test (400 ) | 86.9 | 78.3 | 95.9 | 86.2 | 80.2 | 0.943 |
| Dataset | Accuracy (%) | Precision (%) | Recall (%) | F1-score (%) | Specificity (%) | AUC |
|---|---|---|---|---|---|---|
| Validation (All Mag.) | 91.8 | 95.9 | 92.7 | 94.3 | 89.5 | 0.975 |
| Test (All Mag.) | 84.7 | 83.5 | 81.9 | 82.7 | 86.9 | 0.933 |
| Test (40 ) | 81.6 | 84.0 | 73.8 | 78.6 | 88.2 | 0.923 |
| Test (100 ) | 84.7 | 82.0 | 86.8 | 84.3 | 82.8 | 0.928 |
| Test (200 ) | 86.4 | 85.0 | 83.2 | 84.0 | 88.9 | 0.956 |
| Test (400 ) | 84.3 | 81.6 | 81.6 | 81.6 | 86.3 | 0.927 |
| Dataset | Accuracy (%) | Precision (%) | Recall (%) | F1-score (%) | Specificity (%) | AUC |
|---|---|---|---|---|---|---|
| Validation (All Mag.) | 93.2 | 96.2 | 94.4 | 95.3 | 90.2 | 0.978 |
| Test (All Mag.) | 83.6 | 79.1 | 86.2 | 82.5 | 81.5 | 0.919 |
| Test (40 ) | 87.2 | 87.4 | 84.1 | 85.7 | 89.8 | 0.914 |
| Test (100 ) | 82.4 | 80.6 | 82.6 | 81.6 | 82.1 | 0.925 |
| Test (200 ) | 83.3 | 76.4 | 88.4 | 81.9 | 79.4 | 0.928 |
| Test (400 ) | 80.8 | 73.3 | 86.7 | 79.4 | 76.3 | 0.907 |
| Dataset | Accuracy (%) | Precision (%) | Recall (%) | F1-score (%) | Specificity (%) | AUC |
|---|---|---|---|---|---|---|
| Test (All Mag.) | 79.5 | 73.6 | 84.6 | 78.7 | 75.3 | 0.860 |
| Test (40 ) | 85.0 | 81.6 | 86.9 | 84.2 | 83.5 | 0.929 |
| Test (100 ) | 79.2 | 74.6 | 85.1 | 79.5 | 73.9 | 0.874 |
| Test (200 ) | 77.8 | 69.8 | 85.3 | 76.8 | 72.2 | 0.834 |
| Test (400 ) | 77.7 | 70.1 | 83.7 | 76.3 | 73.3 | 0.821 |
| Dataset | Accuracy (%) | Precision (%) | Recall (%) | F1-score (%) | Specificity (%) | AUC |
|---|---|---|---|---|---|---|
| Validation (All Mag.) | 93.1 | 95.9 | 94.6 | 95.2 | 89.3 | 0.975 |
| Test (All Mag.) | 81.3 | 76.5 | 84.1 | 80.1 | 79.0 | 0.905 |
| Test (40 ) | 80.3 | 75.6 | 84.1 | 79.6 | 77.2 | 0.899 |
| Test (100 ) | 78.8 | 74.5 | 84.3 | 79.1 | 73.9 | 0.914 |
| Test (200 ) | 84.2 | 76.8 | 90.5 | 83.1 | 79.4 | 0.938 |
| Test (400 ) | 80.4 | 74.8 | 81.6 | 78.1 | 79.4 | 0.892 |
| Dataset | Accuracy (%) | Precision (%) | Recall (%) | F1-score (%) | Specificity (%) | AUC |
|---|---|---|---|---|---|---|
| Validation (All Mag.) | 86.5 | 90.9 | 90.5 | 90.7 | 75.9 | 0.892 |
| Test (All Mag.) | 77.6 | 71.1 | 84.3 | 77.2 | 72.2 | 0.858 |
| Test (40 ) | 79.1 | 71.0 | 91.6 | 80.0 | 68.5 | 0.856 |
| Test (100 ) | 72.6 | 68.4 | 78.5 | 73.1 | 67.2 | 0.789 |
| Test (200 ) | 81.0 | 73.9 | 86.3 | 79.6 | 77.0 | 0.893 |
| Test (400 ) | 79.0 | 71.9 | 83.7 | 77.4 | 75.6 | 0.862 |
| Dataset | Accuracy (%) | Precision (%) | Recall (%) | F1-score (%) | Specificity (%) | AUC |
|---|---|---|---|---|---|---|
| Validation (All Mag.) | 94.5 | 95.7 | 96.9 | 96.3 | 88.3 | 0.985 |
| Test (All Mag.) | 85.8 | 80.0 | 91.2 | 85.2 | 81.5 | 0.939 |
| Test (40 ) | 87.2 | 82.9 | 90.7 | 86.6 | 84.3 | 0.945 |
| Test (100 ) | 84.3 | 80.9 | 87.6 | 84.1 | 81.3 | 0.935 |
| Test (200 ) | 87.3 | 80.2 | 93.7 | 86.4 | 82.5 | 0.961 |
| Test (400 ) | 83.8 | 74.0 | 95.9 | 83.6 | 74.8 | 0.928 |
| Model | Arch. | Acc. (%) | Prec. (%) | Recall (%) | Spec. (%) | F1 (%) | AUC | MCC | F-Rank | |
|---|---|---|---|---|---|---|---|---|---|---|
| DenseNet121 | CNN | 99.4 [98.6, 99.7] | 99.9 | 99.5 | 99.2 | 99.6 | 0.999 [0.9963, 1.0000] | 0.986 | 0.984 | 1.00 |
| EfficientNet | CNN | 86.2 [83.6, 88.4] | 83.6 | 86.0 | 86.3 | 84.8 | 0.940 [0.9192, 0.9608] | 0.685 | 0.700 | 3.62 |
| Xception | CNN | 85.8 [83.2, 88.1] | 80.0 | 91.2 | 81.5 | 85.2 | 0.939 [0.9180, 0.9600] | 0.676 | 0.689 | 3.50 |
| InceptionV3 | CNN | 84.6 [81.9, 86.9] | 79.5 | 88.4 | 81.5 | 83.7 | 0.933 [0.9111, 0.9549] | 0.648 | 0.665 | 4.00 |
| MobileNetV2 | CNN | 84.7 [82.0, 87.0] | 83.5 | 81.9 | 86.9 | 82.7 | 0.933 [0.9111, 0.9549] | 0.651 | 0.673 | 4.12 |
| ResNet50 | CNN | 83.6 [80.9, 86.0] | 79.1 | 86.2 | 81.5 | 82.5 | 0.919 [0.8950, 0.9430] | 0.625 | 0.645 | 5.25 |
Explainable Medical Image Analysis
Explainable Medical Image Analysis develops methods that make medical image predictions understandable, verifiable, and useful for clinical review.
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