https://github.com/c-martinez/sarrlek
Semantic Analysis of Radiology Reports with Lexicon as Embedded Knowledge
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 4 committers (25.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (5.1%) to scientific vocabulary
Repository
Semantic Analysis of Radiology Reports with Lexicon as Embedded Knowledge
Basic Info
- Host: GitHub
- Owner: c-martinez
- Language: Jupyter Notebook
- Default Branch: master
- Size: 14.8 MB
Statistics
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
SARRLEK
Semantic Analysis of Radiology Reports with Lexicon as Embedded Knowledge
Installing required packages
Python requirements are listed on the requirements.txt file. To install all
requirements, make sure your run:
pip install -r requirements.txt
Running pipeline
Currently there are 3 steps to run in the pipeline: data preparation, training word2vec model and training topic model (LDA). This can be done with the following python scripts:
data preparation:
python cleaning.py --in=Data/ct_report_dmg_thoracic_only.csv --out=Data/ct_report_dmg_thoracic_only_CLEAN.csv --augment-data
data preparation (with additional structurize step):
python cleaning.py --in=Data/ct_report_dmg_thoracic_only.csv --out=Data/ct_report_dmg_thoracic_only_CLEAN_STRUCT.csv --augment-data --structurize
training word2vec model:
python buildw2v.py --in Data/ct_report_dmg_thoracic_only_CLEAN.csv --out Data/ct_report_model.w2v --vectors Data/ct_report_vectors.csv
training topic model:
python buildlda.py --in Data/ct_report_dmg_thoracic_only_CLEAN.csv --out-dict Data/ct_report_topics.dict --out-model Data/ct_report_topics.lda --out-topics Data/ct_report_topics.csv
training flair model:
python buildflair.py --in-reports=Data/ct_report_dmg_thoracic_only_CLEAN.csv --in-classes=Data/classes.csv --cancer-classifier=out/classifier_cancer --prog-classifier=out/classifier_prog
Owner
- Name: Carlos Martinez
- Login: c-martinez
- Kind: user
- Company: @NLeSC
- Website: https://fosstodon.org/@neocarlitos
- Repositories: 108
- Profile: https://github.com/c-martinez
GitHub Events
Total
Last Year
Committers
Last synced: almost 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Carlos Martinez | c****z@e****l | 25 |
| Chaitanya Kulkarni | c****6@g****m | 19 |
| Chaitanya Kulkarni | c****i@r****u | 6 |
| Leonard Wee | l****e@m****l | 6 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: over 1 year ago
All Time
- Total issues: 1
- Total pull requests: 0
- Average time to close issues: about 4 hours
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- c-martinez (1)