Finding Safety Signals in Sparse Data: Zero-Inflated Models for Pharmacovigilance studies

Signal detection is a core task in pharmacovigilance, and disproportionality analysis (DA) remains the dominant approach for spontaneous reporting systems (SRS). However, SRS data are sparse and heavily zero-inflated, reflecting rare adverse drug reactions (ADRs) and substantial under-reporting, which can distort standard count-model assumptions. Using Medicines and Healthcare products Regulatory Agency (MHRA) interactive Drug Analysis Profiles (iDAPs) for selective serotonin reuptake inhibitors (SSRIs), we derived system organ class (SOC) level adverse event counts. Goodness-of-fit testing indicated that SOC counts were variably consistent with Poisson or negative binomial (NB) distributions, motivating the use of zero-inflated Poisson and zero-inflated NB models. Model adequacy was assessed using Pearson-residual dispersion (absolute fit) and Akaikes Information Criterion (relative fit). Zero-inflated models provided improved fit for 10 out of all 27 SOCs (Endocrine disorders, Immune system disorders, Metabolism and nutrition disorders, Infections and infestations, Renal and urinary disorders, Hepatobiliary disorders, Ear and labyrinth disorders, Pregnancy, puerperium and perinatal conditions, Congenital, familial and genetic disorders, Neoplasms benign, malignant and unspecified (including cysts and polyps)) and yielded signals broadly concordant with DA, including for metabolism-related events. These results support zero-inflated modelling as a complementary signal detection method for iDAPs-derived count data, particularly where internal model-based validation and explicit handling of excess zeros are desired.