Identifying dynamical system (DS) is a vital task in science and engineering. Traditional methods require numerous calls to the DS solver, rendering likelihood-based or least-squares inference frameworks impractical. For efficient parameter inference, two state-of-the-art techniques are the kernel method for modeling and the "one-step framework" for jointly inferring unknown parameters and hyperparameters. The kernel method is a quick and straightforward technique, but it cannot estimate solutions and their derivatives, which must strictly adhere to physical laws. We propose a model-embedded "one-step" Bayesian framework for joint inference of unknown parameters and hyperparameters by maximizing the marginal likelihood. This approach models the solution and its derivatives using Gaussian process regression (GPR), taking into account smoothness and continuity properties, and treats differential equations as constraints that can be naturally integrated into the Bayesian framework in the linear case. Additionally, we prove the convergence of the model-embedded Gaussian process regression (ME-GPR) for theoretical development. Motivated by Taylor expansion, we introduce a piecewise first-order linearization strategy to handle nonlinear dynamic systems. We derive estimates and confidence intervals, demonstrating that they exhibit low bias and good coverage properties for both simulated models and real data.
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