Radiomics-Based Classification of Clear Cell Renal Cell Carcinoma ISUP Grade: A Machine Learning Approach with SHAP-Enhanced Explainability
Abstract
:1. Introduction
2. Material and Methods
2.1. Demographics
2.2. Image Acquisition
2.3. Image Analysis
2.4. Feature Selection
2.5. Model Elaboration and SHAP Values
3. Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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High ISUP Grade (n = 67) | Low ISUP Grade (n = 42) | ||
---|---|---|---|
Sex | Male (n = 84) | 32 (85.1%) | 52 (64.3%) |
Female (n = 25) | 10 (14.9%) | 15 (35.7%) | |
Mean age (years) | 62.07 11.91 | 63.35 11.11 | |
Laterality | Right (n = 59) | 40 (59.7%) | 19 (45.2%) |
Left (n = 50) | 27 (20.3%) | 23 (54.8%) |
Excellent (≥0.9) | Good (0.9–0.75) | Moderate (0.75–0.5) | Poor (≤0.5) | |
---|---|---|---|---|
Shape (15) | 9 (64.3%) | 2 (14.3%) | 2 (14.3%) | 1 (7.1%) |
First Order (18) | 15 (83.3%) | 2 (11.1%) | 1 (5.6%) | 0 (0%) |
GLCM (22) | 16 (72.7%) | 5 (22.7%) | 1 (4.6%) | 0 (0%) |
GLRLM (16) | 8 (50.0%) | 4 (25.0%) | 4 (25.0%) | 0 (0%) |
GLSZM (16) | 5 (31.3%) | 5 (31.3) | 3 (18.7%) | 3 (18.7%) |
GLDM (14) | 8 (57.1%) | 2 (14.3%) | 4 (28.6%) | 0 (0%) |
NGTDM (5) | 4 (80.0%) | 1 (20.0%) | 0 (0%) | 0 (0%) |
Features After Applying Correlation (Threshold ≥ 0.9) | |
---|---|
Shape | Major axis length (ICC = 0.989) |
First order | 10 th percentile (ICC = 0.985) Entropy (ICC = 0.911) Maximum (ICC = 0.971) Minimum (ICC = 0.938) Uniformity (ICC = 0.921) |
GLCM | Prominence (ICC = 0.964) Shade (ICC = 0.916) Contrast (ICC = 0.977) Inverse difference moment (ICC = 0.976) Inverse variance (ICC = 0.967) |
GLRLM | Run length emphasis (ICC = 0.986) Gray-level non-uniformity (ICC = 0.990) |
GLZSM | Large area emphasis (ICC = 0.983) Percentage (ICC = 0.963) |
GLDM | Low dependence high gray level emphasis (ICC = 0.915) |
NGTDM | Busyness (ICC = 0.984) Complexity (ICC = 0.961) Contrast (ICC = 0.945) Strength (ICC = 0.919) |
Classification Metrics for the Test Subset | |||||
---|---|---|---|---|---|
Model | Accuracy | F1-Score | Precision | Recall | AUC (Confidence Interval) |
Support Vector Machine (SVM) | 0.73 | 0.69 | 0.71 | 0.71 | 0.76 (0.56–0.92) |
Random Forest (RF) | 0.64 | 0.61 | 0.61 | 0.61 | 0.67 (0.48–0.87) |
Logistic Regression (LR) | 0.82 | 0.80 | 0.80 | 0.80 | 0.86 (0.71–1.00) |
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Aymerich, M.; García-Baizán, A.; Franco, P.N.; González, M.; San Miguel Fraile, P.; Ortiz-Rey, J.A.; Otero-García, M. Radiomics-Based Classification of Clear Cell Renal Cell Carcinoma ISUP Grade: A Machine Learning Approach with SHAP-Enhanced Explainability. Diagnostics 2025, 15, 1337. https://doi.org/10.3390/diagnostics15111337
Aymerich M, García-Baizán A, Franco PN, González M, San Miguel Fraile P, Ortiz-Rey JA, Otero-García M. Radiomics-Based Classification of Clear Cell Renal Cell Carcinoma ISUP Grade: A Machine Learning Approach with SHAP-Enhanced Explainability. Diagnostics. 2025; 15(11):1337. https://doi.org/10.3390/diagnostics15111337
Chicago/Turabian StyleAymerich, María, Alejandra García-Baizán, Paolo Niccolò Franco, Mariña González, Pilar San Miguel Fraile, José Antonio Ortiz-Rey, and Milagros Otero-García. 2025. "Radiomics-Based Classification of Clear Cell Renal Cell Carcinoma ISUP Grade: A Machine Learning Approach with SHAP-Enhanced Explainability" Diagnostics 15, no. 11: 1337. https://doi.org/10.3390/diagnostics15111337
APA StyleAymerich, M., García-Baizán, A., Franco, P. N., González, M., San Miguel Fraile, P., Ortiz-Rey, J. A., & Otero-García, M. (2025). Radiomics-Based Classification of Clear Cell Renal Cell Carcinoma ISUP Grade: A Machine Learning Approach with SHAP-Enhanced Explainability. Diagnostics, 15(11), 1337. https://doi.org/10.3390/diagnostics15111337