Infectious disease epidemics such as influenza and Ebola pose a serious threat to global public health. It is crucial to characterize the disease and the evolution of the ongoing epidemic efficiently and accurately. Computational epidemiology can model the disease progress and underlying contact network, but suffers from the lack of real-time and fine-grained surveillance data. Social media, on the other hand, provides timely and detailed disease surveillance, but is insensible to the underlying contact network and disease model. This paper proposes a novel semi-supervised deep learning framework that integrates the strengths of computational epidemiology and social media mining techniques. Specifically, this framework learns the social media users' health states and intervention actions in real time, which are regularized by the underlying disease model and contact network. Conversely, the learned knowledge from social media can be fed into computational epidemic model to improve the efficiency and accuracy of disease diffusion modeling. We propose an online optimization algorithm to substantialize the above interactive learning process iteratively to achieve a consistent stage of the integration. The extensive experimental results demonstrated that our approach can effectively characterize the spatio-temporal disease diffusion, outperforming competing methods by a substantial margin on multiple metrics.