Shape representations are critical for visual analysis of cultural heritage materials. This article studies two types of shape representations in a bag-of-words-based pipeline to recognize Maya glyphs. The first is a knowledge-driven Histogram of Orientation Shape Context (HOOSC) representation, and the second is a data-driven representation obtained by applying an unsupervised Sparse Autoencoder (SA). In addition to the glyph data, the generalization ability of the descriptors is investigated on a larger-scale sketch dataset. The contributions of this article are four-fold: (1) the evaluation of the performance of a data-driven auto-encoder approach for shape representation; (2) a comparative study of hand-designed HOOSC and data-driven SA; (3) an experimental protocol to assess the effect of the different parameters of both representations; and (4) bridging humanities and computer vision/machine learning for Maya studies, specifically for visual analysis of glyphs. From our experiments, the data-driven representation performs overall in par with the hand-designed representation for similar locality sizes on which the descriptor is computed. We also observe that a larger number of hidden units, the use of average pooling, and a larger training data size in the SA representation all improved the descriptor performance. Additionally, the characteristics of the data and stroke size play an important role in the learned representation.