package cui2vec implements utilities for dealing with cui2vec embeddings and mapping cuis to text.
Paper (author not affiliated with this code): https://arxiv.org/pdf/1804.01486.pdf
Documentation: https://godoc.org/github.com/hscells/cui2vec
Example: See cmd/cui2vec/main.go
Pre-trained embeddings (model) can be downloaded from https://figshare.com/s/00d69861786cd0156d81.
A pre-computed distances version of these pre-trained embeddings is included in the testdata folder.
Example file structure of mapping file:
ICUI,title
5,(131)i-maa
39,dipalmitoylphosphatidylcholine
96,1-methyl-3-isobutylxanthine
107,"1-(n-methylglycine)-8-l-isoleucine-angiotensin ii"
139,"16,16-dimethyl-pge2"
151,"17 beta hydroxy 5 beta androstan 3 one"
167,17-ketosteroids
172,18-hydroxycorticosterone
173,"18 hydroxydesoxycorticosterone"
One way this can be constructed is detailed in:
Jimmy, Zuccon G., Koopman B. (2018) Choices in Knowledge-Base Retrieval for Consumer Health Search.
In: Pasi G., Piwowarski B., Azzopardi L., Hanbury A. (eds) Advances in Information Retrieval. ECIR 2018.
Lecture Notes in Computer Science, vol 10772. Springer, Cham
Command-line utility can be installed with:
go install github.com/hscells/cui2vec/cmd/cui2vecUsage: cui2vec [--cui CUI] [--model MODEL] [--type TYPE] [--skipfirst] [--numcuis NUMCUIS] [--mapping MAPPING] [--verbose]
Options:
--cui CUI
--model MODEL
--type TYPE
--skipfirst
--numcuis NUMCUIS, -n NUMCUIS
--mapping MAPPING
--verbose, -v
--help, -h display this help and exit
--version display version and exitA tool that can be used to compress and increase the speed of computing similar CUIs is included in the form of pcdvec.
Install the tool with
go get github.com/hscells/cui2vec/cmd/pcdvecUsage: pcdvec --cui CUI [--output OUTPUT] [--skipfirst]
Options:
--cui CUI
--output OUTPUT, -o OUTPUT
--skipfirst
--help, -h display this help and exit
--version display version and exit