An Interpretable Machine Learning Approach to Predict Survival Outcomes in Spinal and Sacropelvic Chordomas

Retrospective, population-based cohort study.

This study aimed to develop machine learning (ML) models to predict five-year and 10-year mortality in spinal and sacropelvic chordoma patients and integrate them into a web application for enhanced prognostication.

Past research has uncovered factors influencing survival in spinal chordoma patients. While identifying individual predictors is important, personalized survival predictions are equally vital. Though prior efforts have resulted in nomograms aiming to serve this purpose, they cannot capture complex interactions within data and rely on statistical assumptions that may not fit real-world data.

Adult spinal and sacropelvic chordoma patients were identified from the National Cancer Database. Sociodemographic, clinicopathologic, diagnostic, and treatment-related variables were utilized as predictive features. Five supervised ML algorithms (TabPFN, CatBoost, XGBoost, LightGBM, and Random Forest) were implemented to predict mortality at five and 10 years postdiagnosis. Model performance was primarily evaluated using the area under the receiver operating characteristic (AUROC). SHapley Additive exPlanations (SHAP) values and partial dependence plots provided feature importance and interpretability. The top models were integrated into a web application.

From the NCDB, 1206 adult patients diagnosed with histologically confirmed spinal and sacropelvic chordomas were retrieved for the five-year mortality outcome [423 (35.1%) with five-year mortality] and 801 patients for the 10-year mortality outcome [588 (73.4%) with 10-year mortality]. Top-performing models for both of the outcomes were the models created with the CatBoost algorithm. The CatBoost model for five-year mortality predictions displayed a mean AUROC of 0.801, and the CatBoost model predicting 10-year mortality yielded a mean AUROC of 0.814.

This study developed ML models that can accurately predict five-year to 10-year survival probabilities in spinal chordoma patients. Integrating these interpretable, personalized prognostic models into a web application provides quantitative survival estimates for a given patient. The local interpretability enables transparency into how predictions are influenced. Further external validation is warranted to support generalizability and clinical utility.