https://github.com/hscells/cui2vec

Utility for cui2vec in Go
https://github.com/hscells/cui2vec

cui2vec embeddings

Last synced: about 2 months ago
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Utility for cui2vec in Go

• Host: GitHub
• URL: https://github.com/hscells/cui2vec
• Owner: hscells
• License: mit
• Created: 2018-07-19T02:20:28.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2023-02-25T00:38:38.000Z (almost 2 years ago)
• Last Synced: 2024-06-19T06:56:34.417Z (7 months ago)
• Topics: cui2vec, embeddings
• Language: Go
• Size: 4.09 MB
• Stars: 11
• Watchers: 3
• Forks: 1
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# cui2vec

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](cmd/cui2vec/main.go)

## Data

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](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

Command-line utility can be installed with:

```bash

go install github.com/hscells/cui2vec/cmd/cui2vec

```

```bash

Usage: 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 exit

```

### Pre-computing distances

A 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 

```bash

go get github.com/hscells/cui2vec/cmd/pcdvec

```

```bash

Usage: 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

```