Kidney Cancer Diagnosis and Surgery Selection by Machine Learning from CT Scans Combined with Clinical Metadata

SIMPLE SUMMARY: Diagnosis is the most important step in treating and managing kidney cancer, requiring accurate identification, localization, and classification of tumor regions. The selection of appropriate surgical procedures for malignant cases is further based on tumor volume and relative severity. In recent years, machine-learning-based approaches have been proposed to localize, quantify, and stratify kidney tumors using contrast-enhanced computed tomography (CT) images. However, previous studies have largely neglected the integration of patient metadata with clinical images to better diagnose and guide surgical interventions. In the current study, we developed a combined clinical and image-based approach to classify kidney cancers using a publicly available dataset. We show that the inclusion of clinical features alongside medical images improves the performance of kidney tumor classification. We further used clinical data together with a machine-learning approach to predict the expected surgical procedure employed in individual kidney cancer patients. In addition to cancer stage and tumor volume, some surprisingly common demographic features were revealed to be key determinants of the surgical procedure later selected for nephrectomy. ABSTRACT: Kidney cancers are one of the most common malignancies worldwide. Accurate diagnosis is a critical step in the management of kidney cancer patients and is influenced by multiple factors including tumor size or volume, cancer types and stages, etc. For malignant tumors, partial or radical surgery of the kidney might be required, but for clinicians, the basis for making this decision is often unclear. Partial nephrectomy could result in patient death due to cancer if kidney removal was necessary, whereas radical nephrectomy in less severe cases could resign patients to lifelong dialysis or need for future transplantation without sufficient cause. Using machine learning to consider clinical data alongside computed tomography images could potentially help resolve some of these surgical ambiguities, by enabling a more robust classification of kidney cancers and selection of optimal surgical approaches. In this study, we used the publicly available KiTS dataset of contrast-enhanced CT images and corresponding patient metadata to differentiate four major classes of kidney cancer: clear cell (ccRCC), chromophobe (chRCC), papillary (pRCC) renal cell carcinoma, and oncocytoma (ONC). We rationalized these data to overcome the high field of view (FoV), extract tumor regions of interest (ROIs), classify patients using deep machine-learning models, and extract/post-process CT image features for combination with clinical data. Regardless of marked data imbalance, our combined approach achieved a high level of performance (85.66% accuracy, 84.18% precision, 85.66% recall, and 84.92% F1-score). When selecting surgical procedures for malignant tumors (RCC), our method proved even more reliable (90.63% accuracy, 90.83% precision, 90.61% recall, and 90.50% F1-score). Using feature ranking, we confirmed that tumor volume and cancer stage are the most relevant clinical features for predicting surgical procedures. Once fully mature, the approach we propose could be used to assist surgeons in performing nephrectomies by guiding the choices of optimal procedures in individual patients with kidney cancer.