Towards precision oncology: a multi-level cancer classification system integrating liquid biopsy and machine learning

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BACKGROUND: Millions of people die from cancer every year. Early cancer detection is crucial for ensuring higher survival rates, as it provides an opportunity for timely medical interventions. This paper proposes a multi-level cancer classification system that uses plasma cfDNA/ctDNA mutations and protein biomarkers to identify seven distinct cancer types: colorectal, breast, upper gastrointestinal, lung, pancreas, ovarian, and liver. RESULTS: The proposed system employs a multi-stage binary classification framework where each stage is customized for a specific cancer type. A majority vote feature selection process is employed by combining six feature selectors: Information Value, Chi-Square, Random Forest Feature Importance, Extra Tree Feature Importance, Recursive Feature Elimination, and L1 Regularization. Following the feature selection process, classifiers-including eXtreme Gradient Boosting, Random Forest, Extra Tree, and Quadratic Discriminant Analysis-are customized for each cancer type individually or in an ensemble soft voting setup to optimize predictive accuracy. The proposed system outperformed previously published results, achieving an AUC of 98.2% and an accuracy of 96.21%. To ensure reproducibility of the results, the trained models and the dataset used in this study are made publicly available via the GitHub repository ( https://github.com/SaraEl-Metwally/Towards-Precision-Oncology ). CONCLUSION: The identified biomarkers enhance the interpretability of the diagnosis, facilitating more informed decision-making. The system's performance underscores its effectiveness in tissue localization, contributing to improved patient outcomes through timely medical interventions.

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