https://github.com/animesh/embeddings

Code for AMIA CRI 2016 paper "Learning Low-Dimensional Representations of Medical Concepts"

https://github.com/animesh/embeddings

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Code for AMIA CRI 2016 paper "Learning Low-Dimensional Representations of Medical Concepts"

https://github.com/animesh/embeddings/blob/master/

# embeddings
This repository contains code accompanying publication of the paper: 
> Y. Choi, Y. Chiu, D. Sontag. [Learning Low-Dimensional Representations of Medical Concepts](http://cs.nyu.edu/~dsontag/papers/ChoiChiuSontag_AMIA_CRI16.pdf). 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:
* `claims_codes_hs_300.txt.gz`: Embeddings of ICD-9 diagnosis and procedure codes, NDC medication codes, and LOINC laboratory codes, derived from a large claims dataset from 2005 to 2013 for roughly 4 million people.
* `stanford_cuis_svd_300.txt.gz`: Embeddings of [UMLS](https://www.nlm.nih.gov/research/umls/) concept unique identifiers (CUIs), derived from 20 million clinical notes spanning 19 years of data from Stanford Hospital and Clinics, using a  [data set](http://datadryad.org/resource/doi:10.5061/dryad.jp917) released in a [paper](http://www.nature.com/articles/sdata201432) by Finlayson, LePendu & Shah.
* `DeVine_etal_200.txt.gz`: Embeddings of UMLS CUIs learned by [De Vine et al. CIKM '14](http://dl.acm.org/citation.cfm?id=2661974), derived from 348,566 medical journal abstracts (courtesy of the authors).

In the `eval` directory there are three files of interest:
* [`eval/Embedding_Evaluation.ipynb`](https://github.com/clinicalml/embeddings/blob/master/eval/Embedding_Evaluation.ipynb), an iPython notebook which reproduces the main results of the paper. If you come up with your own embeddings, you can use this benchmark to quantitatively compare them to our embeddings.
* `eval/visualize_claims_embeddings.py` a Python program you can run which will allow you to look at nearest neighbors for the `claims_codes_hs_300.txt` embeddings (after decompressing the file using `gunzip`).
* `eval/visualize_stanford_embeddings.py`, same as above but for the `stanford_cuis_svd_300.txt` embeddings.

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](https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html) into the `eval` directory (we do not distribute this).

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