Recent advances in machine learning offer new ways to represent and study scholarly works and the space of knowledge. Graph and text embeddings provide a convenient vector representation of scholarly works based on citations and text. Yet, it is unclear whether their representations are consistent or provide different views of the structure of science. Here, we compare graph and text embedding by testing their ability to capture the hierarchical structure of the Physics and Astronomy Classification Scheme (PACS) of papers published by the American Physical Society (APS). We also provide a qualitative comparison of the overall structure of the graph and text embeddings for reference. We find that neural network-based methods outperform traditional methods and graph embedding methods such as node2vec are better than other methods at capturing the PACS structure. Our results call for further investigations into how different contexts of scientific papers are captured by different methods, and how we can combine and leverage such information in an interpretable manner.