With the development of medical imaging technology and machine learning, computer-assisted diagnosis which can provide impressive reference to pathologists, attracts extensive research interests. The exponential growth of medical images and uninterpretability of traditional classification models have hindered the applications of computer-assisted diagnosis. To address these issues, we propose a novel method for Learning Binary Semantic Embedding (LBSE). Based on the efficient and effective embedding, classification and retrieval are performed to provide interpretable computer-assisted diagnosis for histology images. Furthermore, double supervision, bit uncorrelation and balance constraint, asymmetric strategy and discrete optimization are seamlessly integrated in the proposed method for learning binary embedding. Experiments conducted on three benchmark datasets validate the superiority of LBSE under various scenarios.