<p dir="ltr">Deep neural networks (DNNs) have demonstrated outstanding performance in numerous tasks such as image recognition and natural language processing. However, in dynamic systems modeling, the tasks of estimating and uncovering the potentially nonlinear structure of systems represented by ordinary differential equations (ODEs) pose a significant challenge. In this dissertation, we employ DNNs to enable precise and efficient parameter estimation of dynamic systems. In addition, we introduce a highly flexible neural ODE model to capture both nonlinear and sparse dependent relations among multiple functional processes. Nonetheless, DNNs are susceptible to overfitting and often struggle to accurately assess predictive uncertainty despite their widespread success across various AI domains. The challenge of defining meaningful priors for DNN weights and characterizing predictive uncertainty persists. In this dissertation, we present a novel neural adaptive empirical Bayes framework with a new class of prior distributions to address weight uncertainty.</p><p dir="ltr">In the first part, we propose a precise and efficient approach utilizing DNNs for estimation and inference of ODEs given noisy data. The DNNs are employed directly as a nonparametric proxy for the true solution of the ODEs, eliminating the need for numerical integration and resulting in significant computational time savings. We develop a gradient descent algorithm to estimate both the DNNs solution and the parameters of the ODEs by optimizing a fidelity-penalized likelihood loss function. This ensures that the derivatives of the DNNs estimator conform to the system of ODEs. Our method is particularly effective in scenarios where only a set of variables transformed from the system components by a given function are observed. We establish the convergence rate of the DNNs estimator and demonstrate that the derivatives of the DNNs solution asymptotically satisfy the ODEs determined by the inferred parameters. Simulations and real data analysis of COVID-19 daily cases are conducted to show the superior performance of our method in terms of accuracy of parameter estimates and system recovery, and computational speed.</p><p dir="ltr">In the second part, we present a novel sparse neural ODE model to characterize flexible relations among multiple functional processes. This model represents the latent states of the functions using a set of ODEs and models the dynamic changes of these states utilizing a DNN with a specially designed architecture and sparsity-inducing regularization. Our new model is able to capture both nonlinear and sparse dependent relations among multivariate functions. We develop an efficient optimization algorithm to estimate the unknown weights for the DNN under the sparsity constraint. Furthermore, we establish both algorithmic convergence and selection consistency, providing theoretical guarantees for the proposed method. We illustrate the efficacy of the method through simulation studies and a gene regulatory network example.</p><p dir="ltr">In the third part, we introduce a class of implicit generative priors to facilitate Bayesian modeling and inference. These priors are derived through a nonlinear transformation of a known low-dimensional distribution, allowing us to handle complex data distributions and capture the underlying manifold structure effectively. Our framework combines variational inference with a gradient ascent algorithm, which serves to select the hyperparameters and approximate the posterior distribution. Theoretical justification is established through both the posterior and classification consistency. We demonstrate the practical applications of our framework through extensive simulation examples and real-world datasets. Our experimental results highlight the superiority of our proposed framework over existing methods, such as sparse variational Bayesian and generative models, in terms of prediction accuracy and uncertainty quantification.</p>