Improving appendix cancer prediction with SHAP-based feature engineering for machine learning models: a prediction study.

PURPOSE: This study aimed to leverage Shapley additive explanation (SHAP)-based feature engineering to predict appendix cancer. Traditional models often lack transparency, hindering clinical adoption. We propose a framework that integrates SHAP for feature selection, construction, and weighting to enhance accuracy and clinical relevance.

METHODS

Data from the Kaggle Appendix Cancer Prediction dataset (260,000 samples, 21 features) were used in this prediction study conducted from January through March 2025, in accordance with TRIPOD-AI guidelines. Preprocessing involved label encoding, SMOTE (synthetic minority over-sampling technique) to address class imbalance, and an 80:20 train-test split. Baseline models (random forest, XGBoost, LightGBM) were compared; LightGBM was selected for its superior performance (accuracy=0.8794). SHAP analysis identified key features and guided 3 engineering steps: selection of the top 15 features, construction of interaction-based features (e.g., chronic severity), and feature weighting based on SHAP values. Performance was evaluated using accuracy, precision, recall, and F1-score.

RESULTS

Four LightGBM model configurations were evaluated: baseline (accuracy=0.8794, F1-score=0.8691), feature selection (accuracy=0.8968, F1-score=0.8860), feature construction (accuracy=0.8980, F1-score=0.8872), and feature weighting (accuracy=0.8986, F1-score=0.8877). SHAP-based engineering yielded performance improvements, with feature weighting achieving the highest precision (0.9940). Key features (e.g., red blood cell count and chronic severity) contributed to predictions while maintaining interpretability.

CONCLUSION

The SHAP-based framework substantially improved the accuracy and transparency of appendix cancer predictions using LightGBM (F1-score=0.8877). This approach bridges the gap between predictive power and clinical interpretability, offering a scalable model for rare disease prediction. Future validation with real-world data is recommended to ensure generalizability.