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This repository contains code accompanying publication of the paper:

Y. Choi, Y. Chiu, D. Sontag. Learning Low-Dimensional Representations of Medical Concepts. To appear in Proceedings of the AMIA Summit on Clinical Research Informatics (CRI), 2016.

In the base directory there are three files containing the two best 300-dimensional embeddings learned in the paper, and the embeddings used in the previous work which we compared to:

In the eval directory there are three files of interest:

Note that you may need to decompress, using gunzip, files in the eval directory prior to being able to run some of the programs. Additionally, to run the iPython notebook, you need to place the file MRCONSO.RRF from the UMLS Metathesaurus into the eval directory (we do not distribute this).