Pre-trained word embeddings using the text of published biomedical manuscripts. These embeddings use 300 dimensions and were trained using the word2vec algorithm on all available manuscripts found in the PMC Open Access Subset. See the paper here: https://pubmed.ncbi.nlm.nih.gov/34920127/
Citation:
@article{flamholz2022word,
title={Word embeddings trained on published case reports are lightweight, effective for clinical tasks, and free of protected health information},
author={Flamholz, Zachary N and Crane-Droesch, Andrew and Ungar, Lyle H and Weissman, Gary E},
journal={Journal of Biomedical Informatics},
volume={125},
pages={103971},
year={2022},
publisher={Elsevier}
}
First download the files from this archive. Then load the embeddings into Python.
python
12from gensim.models import FastText, Word2Vec, KeyedVectors # KeyedVectors are used to load the GloVe models34# Load the model5model = Word2Vec.load('w2v_oa_all_300d.bin')67# Return 100-dimensional vector representations of each word8model.wv.word_vec('diabetes')9model.wv.word_vec('cardiac_arrest')10model.wv.word_vec('lymphangioleiomyomatosis')1112# Try out cosine similarity13model.wv.similarity('copd','chronic_obstructive_pulmonary_disease')14model.wv.similarity('myocardial_infarction','heart_attack')15model.wv.similarity('lymphangioleiomyomatosis','lam')16
