Evaluation of four machine learning models for signal detection

Abstract

Background: Logistic regression-based signal detection algorithms have benefits over disproportionality analysis due to their ability to handle potential confounders and masking factors. Feature exploration and developing alternative machine learning algorithms can further strengthen signal detection. Objectives: Our objective was to compare the signal detection performance of logistic regression, gradient-boosted trees, random forest and support vector machine models utilizing Food and Drug Administration adverse event reporting system data. Design: Cross-sectional study. Methods: The quarterly data extract files from 1 October 2017 through 31 December 2020 were downloaded. Due to an imbalanced outcome, two training sets were used: one stratified on the outcome variable and another using Synthetic Minority Oversampling Technique (SMOTE). A crude model and a model with tuned hyperparameters were developed for each algorithm. Model performance was compared against a reference set using accuracy, precision, F1 score, recall, the receiver operating characteristic area under the curve (ROCAUC), and the precision-recall curve area under the curve (PRCAUC). Results: Models trained on the balanced training set had higher accuracy, F1 score and recall compared to models trained on the SMOTE training set. When using the balanced training set, logistic regression, gradient-boosted trees, random forest and support vector machine models obtained similar performance evaluation metrics. The gradient-boosted trees hyperparameter tuned model had the highest ROCAUC (0.646) and the random forest crude model had the highest PRCAUC (0.839) when using the balanced training set. Conclusion: All models trained on the balanced training set performed similarly. Logistic regression models had higher accuracy, precision and recall. Logistic regression, random forest and gradient-boosted trees hyperparameter tuned models had a PRCAUC ⩾ 0.8. All models had an ROCAUC ⩾ 0.5. Including both disproportionality analysis results and additional case report information in models resulted in higher performance evaluation metrics than disproportionality analysis alone.