We introduce Deep Reasoning Networks (DRNets), an end-to-end framework that combines deep learning with constraint reasoning for solving pattern de-mixing problems, typically in an unsupervised or very-weakly-supervised setting. DRNets exploit problem structure and prior knowledge by tightly combining constraint reasoning with stochastic-gradient-based neural network optimization. Our motivating task is from materials discovery and concerns inferring crystal structures of materials from X-ray diffraction data (Crystal-Structure-Phase-Mapping). Given the complexity of its underlying scientific domain, we start by introducing DRNets on an analogous but much simpler task: de-mixing overlapping hand-written Sudokus (Multi-MNIST-Sudoku). DRNets significantly outperform the state of the art and experts' capabilities on Crystal-Structure-Phase-Mapping, recovering more precise and physically meaningful crystal structures. On Multi-MNIST-Sudoku, DRNets almost perfectly recovered the mixed Sudokus' digits, with 100% digit accuracy, outperforming the supervised state-of-the-art MNIST de-mixing models.