dermatologist / cui-embed

Gensim wrapper for the clinical (CUI) embeddings

cui-embed

Update 2/16/2023

• Added support for LOINC embedding from this repo. Please cite the paper in the above repo if you use LOINC embedding.

This is a gensim wrapper for the Concept Unique Identifier (CUI) embeddings from the model presented here. The paper describing the model creation is here. This can be used with pyomop for efficient electronic phenotyping from OHDSI CDM databases.

You can use cui-cdm for mapping CUI to OHDSI OMOP concepts and umlsjs for accessing UMLS REST APIs for CUI and other terminology management.

• This does not include data/model.
• Model is downloaded on first use

Install

pip install git+https://github.com/dermatologist/cui-embed.git

Use

# CUI embedding
from cui_embed import Cuimodel
cm = Cuimodel('cui')
m = cm.model()
print(m.most_similar_cosmul(['C0002268']))

# LOINC embedding
lm = Cuimodel('loinc')
lm = cm.model()
print(lm.most_similar_cosmul(['2324-2']))