Abstract Identification of module or community structures is important for characterizing and understanding complex systems. While designed with different objectives, i.e., stochastic models for regeneration and modularity maximization models for discrimination, both these two types of model look for low-rank embedding to best represent and reconstruct network topology. However, the mapping through such embedding is linear, whereas real networks have various nonlinear features, making these models less effective in practice. Inspired by the strong representation power of deep neural networks, we propose a novel nonlinear reconstruction method by adopting deep neural networks for representation. We then extend the method to a semi-supervised community detection algorithm by incorporating pairwise constraints among graph nodes. Extensive experimental results on synthetic and real networks show that the new methods are effective, outperforming most state-of-the-art methods for community detection.