Predicting anti-CCP positivity and early rheumatoid arthritis onset from routine laboratory parameters: a SHAP-explained machine learning pipeline - Summary - MDSpire

Predicting anti-CCP positivity and early rheumatoid arthritis onset from routine laboratory parameters: a SHAP-explained machine learning pipeline

  • By

  • Juan Wang

  • Jiaqing Chen

  • Kaiwen Wang

  • June 29, 2026

  • 0 min

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Objective:

To improve early prediction of rheumatoid arthritis (RA) by utilizing routine laboratory parameters and machine learning techniques, specifically targeting anti-CCP positivity and early RA onset.

Approach:
  • Study Design: 500 patients were enrolled, and 29 routine laboratory features were collected to predict anti-CCP positivity and early RA onset, defined as dual binary prediction targets.
Key Findings:
  • Logistic regression achieved the best overall performance with accuracy of 0.848, AUC of 0.857, F1 of 0.910, and MCC of 0.441.
  • The Transformer deep learning model performed well with an AUC of 0.812.
  • ESR and CRP were identified as the most important positive predictive drivers, while albumin was a key protective factor.
Interpretation:

The machine learning pipeline predicts early RA risk, and the SHAP analysis provides interpretable decision rationale.

Limitations:
  • Existing studies often evaluate only a single or few models, lacking systematic cross-comparison.
  • The 'black-box' nature of deep learning models limits clinical credibility.
  • RA datasets commonly exhibit class imbalance, which can affect model performance.
Conclusion:

The study demonstrates the potential of machine learning and SHAP analysis in enhancing early RA risk prediction using routine laboratory data.

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