Applying machine learning to pharmacovigilance data: A proof-of-concept study

Machine learning (ML) applications in pharmacovigilance remain limited and underexplored. Using data from the French National pharmacovigilance database (FNPV), this proof-of-concept study aimed to assess the feasibility of using a ML algorithm-eXtreme Gradient Boosting (XGBoost)-combined with SHapley Additive exPlanations (SHAP) analysis, to classify a well-defined drug-adverse reaction pair (warfarin-associated gastrointestinal bleeding) and identify risk factors for reporting this adverse reaction.

We extracted individual case safety reports (ICSRs) involving warfarin from the FNPV. Following data preprocessing, the dataset was randomly split into a training set (75%) and an independent test set (25%). The XGBoost algorithm was trained to classify reports as either gastrointestinal bleeding or non-gastrointestinal bleeding adverse reactions. Model performance was assessed on the test set using multiple metrics: accuracy, recall, precision, F1-score and the area under the receiver operating characteristic curve (AUC-ROC). Feature importance and directional effects were interpreted using SHAP values.

A total of 2025 ICSRs involving warfarin were extracted from the FNPV. After preprocessing, 1045 ICSRs were retained. On the test set, the XGBoost model demonstrated an accuracy of 0.68, recall of 0.80, precision of 0.68, F1-score of 0.74 and an AUC-ROC of 0.716. SHAP analysis revealed the four most influential features in predicting gastrointestinal bleeding reporting: age, gastrointestinal bleeding risk, antiplatelet and history of renal dysfunction.

We demonstrated the feasibility of using an XGBoost algorithm combined with SHAP analysis to pharmacovigilance data for the classification of adverse drug reactions and identify predictive features of reporting, following post hoc model interpretation by pharmacologists.