The dynamics of networks enables the function of a variety of systems we rely on every day, from gene regulation and metabolism in the cell to the distribution of electric power and communication of information. Understanding, steering and predicting the function of interacting nonlinear dynamical systems, in particular if they are externally driven out of equilibrium, relies on obtaining and evaluating suitable models, posing at least two major challenges. First, how can we extract key structural system features of networks if only time series data provide information about the dynamics of (some) units? Second, how can we characterize nonlinear responses of nonlinear multi-dimensional systems externally driven by fluctuations, and consequently, predict tipping points at which normal operational states may be lost? Here we report recent progress on nonlinear response theory extended to predict tipping points and on model-free inference of network structural features from observed dynamics.