We consider unsupervised learning methods for characterizing the disordered microscopic structure of super-cooled liquids and glasses. Specifically, we perform dimensionality reduction of smooth structural descriptors that describe radial and bond-orientational correlations, and assess the ability of the method to grasp the essential structural features of glassy binary mixtures. In several cases, a few collective variables account for the bulk of the structural fluctuations within the first coordination shell and also display a clear connection with the fluctuations of particle mobility. Fine-grained descriptors that characterize the radial dependence of bond-orientational order better capture the structural fluctuations relevant for particle mobility, but are also more difficult to parametrize and to interpret. We also find that principal component analysis of bond-orientational order parameters provides identical results to neural network autoencoders, while having the advantage of being easily interpretable. Overall, our results indicate that glassy binary mixtures have a broad spectrum of structural features. In the temperature range we investigate, some mixtures display well-defined locally favored structures, which are reflected in bimodal distributions of the structural variables identified by dimensionality reduction.