bioword2vec

Bioword2vec embeddings

The Bioword2vec pre-trained word embeddings can be obtained from the GitHub repository BioWordVec: Improving Biomedical Word Embeddings with Subowrd Information and MeSH. Execute the following command to download the file:

wget -O bio_embedding_extrinsic https://figshare.com/ndownloader/files/12551780

Once the binary file bio_embedding_extrinsic has been downloaded, it is necessary to transform it into .txt. In order to do so, execute the following Python code:

from gensim.models.keyedvectors import KeyedVectors

model = KeyedVectors.load_word2vec_format('path/to/bio_embedding_extrinsic', binary=True)
model.save_word2vec_format('path/to/bio_embedding_extrinsic.txt', binary=False)

The bio_embedding_extrinsic.txt file should be stored in this directory.