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Causal network inference using biochemical kinetics

Network models are widely used as structural summaries of biochemical systems. Statistical estimation of networks is usually based on linear or discrete models. However, the dynamics of these systems are generally nonlinear, suggesting that suitable nonlinear formulations may offer gains with respect to network inference and associated prediction problems. We present a general framework for both network inference and dynamical prediction that is rooted in nonlinear biochemical kinetics. This is done by considering a dynamical system based on a chemical reaction graph and associated kinetics parameters. Inference regarding both parameters and the reaction graph itself is carried out within a fully Bayesian framework. Prediction of dynamical behavior is achieved by averaging over both parameters and reaction graphs, allowing prediction even when the underlying reactions themselves are unknown or uncertain. Results, based on (i) data simulated from a mechanistic model of mitogen-activated protein kinase signaling and (ii) phosphoproteomic data from cancer cell lines, demonstrate that nonlinear formulations can yield gains in network inference and permit dynamical prediction in the challenging setting where the reaction graph is unknown.