Title: Active Learning based Structural Inference. Abstract: In this paper, we propose an active-learning based framework, Active Learning based Structural Inference (ALaSI), to infer the existence of directed connections from observed agents' states over a time period in a dynamical system. With the help of deep active learning, ALaSI is competent in learning the representation of connections with relatively small pool of prior knowledge. Moreover, based on information theory, we propose inter- and out-of-scope message learning pipelines, which are remarkably beneficial to the structural inference for large dynamical systems. We evaluate ALaSI on various large datasets including simulated systems and real-world networks, to demonstrate that ALaSI is able to precisely infer the existence of connections in these systems under either supervised learning or unsupervised learning, with better performance than baseline methods.