Linear Noise Approximation Assisted Bayesian Inference on Mechanistic Model of Partially Observed Stochastic Reaction Network

Partially observed stochastic reaction network (SRN) modeling the dynamics of a population of interacting species, such as chemical molecules participating in multiple reactions, is the fundamental building block of multi-scale bioprocess mechanistic model characterizing the causal interdependences from molecular-to macro-kinetics. It plays a critical role to: (1) facilitate digital twin development and support mechanism learning for biomanufacturing processes; (2) allow us to probe critical latent state based on partially observed information; and (3) serve as a fundamental model for a biofoundry platform [1] that can integrate heterogeneous online and offline measures collected from different manufacturing processes and speed up the bioprocess development with much less experiments. Model inference on the SRN mechanistic model based on heterogeneous data also helps to strengthen the theoretical foundations of federated learning on bioprocess mechanisms, through which we can train and advance knowledge. The SRN mechanistic model has three key features that make the model inference challenging. First, the continuoustime state transition model, representing the evolution of concentration or number of molecules, is highly nonlinear.