New adaptive lasso approaches for variable selection in automated pharmacovigilance signal detection

Background Adverse effects of drugs are often identified after market introduction. Post-marketing pharmacovigilance aims to detect them as early as possible and relies on spontaneous reporting systems collecting suspicious cases. Signal detection tools have been developed to mine these large databases and counts of reports are analysed with disproportionality methods. To address disproportionality method biases, recent methods apply to individual observations taking into account all exposures for the same patient. In particular, the logistic lasso provides an efficient variable selection framework, yet the choice of the regularization parameter is a challenging issue and the lasso variable selection may give inconsistent results. Methods We propose a new signal detection methodology based on the adaptive lasso. We derived two new adaptive weights from (i) a lasso regression using the Bayesian Information Criterion (BIC), and (ii) the class-imbalanced subsampling lasso (CISL), an extension of stability selection. The BIC is used in the adaptive lasso stage for variable selection. We performed an extensive simulation study and an application to real data, where we compared our methods to the existing adaptive lasso, and recent detection approaches based on lasso regression or propensity scores in high dimension. For both studies, we evaluate the methods in terms of false discoveries and sensitivity. Results In the simulations and the application, both proposed adaptive weights show equivalent or better performances than the other competitors, with an advantage for the CISL-based adaptive weights. CISL and lasso regression using BIC are solid alternatives. Conclusion Our proposed adaptive lasso is an appealing methodology for signal detection in pharmacovigilance. Although we cannot rely on test theory, our approaches show a low and stable False Discovery Rate in all simulation settings. All methods evaluated in this work are implemented in the adapt4pv R package.

Automated summary

This study proposes a new signal detection methodology based on the adaptive lasso, which shows equivalent or better performances compared to other competitors in simulations and real data applications. The CISL-based adaptive weights have an advantage over others, making the adaptive lasso a solid alternative for signal detection in pharmacovigilance.