Phenotype identification and precise intervention for multimorbidity of rheumatoid arthritis and diabetes mellitus using interpretable machine learning

Objective Rheumatoid arthritis (RA) and diabetes mellitus (DM) frequently coexist, yet the heterogeneity of RA-DM multimorbidity remains unclear. This study aims to develop an interpretable machine learning framework to reveal the phenotypic subgroups of RA-DM multimorbidity, providing a potential direction for precision public health interventions. Methods Utilizing data from the National Health and Nutrition Examination Survey (1999–2018), we developed a Bayesian-optimized eXtreme Gradient Boosting (XGBoost) model to classify RA-DM multimorbidity status and compared with other machine learning models. Shapley Additive Explanations (SHAP) was applied to interpret the optimal model and quantify the contributions of different features. A dual-clustering approach combining Self-Organizing Maps and K-means was used to identify RA-DM phenotypic subgroups with different feature contribution patterns based on SHAP profiles. Results The optimized XGBoost model achieved the best classification performance, outperforming other models such as K-nearest neighbors, support vector machine and logistic regression. SHAP analysis identified nine key contributing features (homocysteine, age, glucose, etc), and revealed non-linear interactions among the features. The dual-clustering based on SHAP values identified four distinct RA-DM phenotypes—inflammatory, metabolically protective, age-related and non-obese protective—each exhibiting unique clinical and biochemical patterns. Conclusion This study established an interpretable machine learning framework for identifying distinct phenotypes of RA-DM multimorbidity. These findings provide a data-driven basis for targeted interventions in precision public health, while offering a transferable paradigm for phenotype discovery in other multimorbid conditions.