Efficiency, accuracy and robustness of probability generating function based parameter inference method for stochastic biochemical reactions

Biochemical reactions are inherently stochastic, with their kinetics commonly described by chemical master equations (CMEs). However, the discrete nature of molecular states renders likelihood-based parameter inference from CMEs computationally intensive. Here, we introduce an inference method that leverages analytical solutions in the probability generating function (PGF) space and systematically evaluate its efficiency, accuracy, and robustness. Across both steady-state and time-resolved count data, our numerical experiments demonstrate that the PGF-based method consistently outperforms existing approaches in terms of both computational efficiency and inference accuracy, even under data contamination. These favorable properties further enable the extension of the PGF-based framework to model selection—a task typically considered computationally prohibitive. Using time-resolved data, we show that the method can correctly identify complex gene expression models with more than three gene states, a task that cannot be reliably achieved using steady-state data alone.