Machine Learning Framework for Ovarian Cancer Diagnostics Using Plasma Lipidomics and Metabolomics

Ovarian cancer (OC), the third most common gynecologic malignancy, exhibits distinct metabolic alterations that could enable early detection via liquid biopsy. We developed an advanced machine learning pipeline integrating lipidomics (HPLC-MS, positive/negative ion modes) and NMR-based metabolomics to analyze plasma samples from 229 subjects, including 103 serous OC patients, 107 benign cases, and 19 healthy controls. By systematically evaluating feature selection methods and machine learning architectures, we identified optimal biomarker combinations for OC detection. Convolutional Neural Network (CNN) model based on Mann-Whitney-selected features demonstrated strong discriminatory power (81% accuracy) in distinguishing malignant from benign cases, while Extreme Gradient Boosting (XGBoost) combined with Support Vector Machine-Recursive Feature Elimination (SVM-RFE) achieved exceptional performance (96% accuracy) in differentiating benign from control samples. For multiclass classification, XGBoost with Kruskal-Wallis-selected features achieved 77% accuracy, while one-versus-one CNN models utilizing Mann-Whitney-selected features attained 78% accuracy, demonstrating optimal performance among tested approaches. The complementary strengths of deep learning and ensemble methods underscore their potential for tailored diagnostic applications. While clinical implementation requires further standardization, these findings provide both a methodological framework for metabolic biomarker discovery and biological insights into OC pathophysiology, paving the way for integrated multi-omics approaches in gynecologic oncology.