clinical-nlp
Science Score: 44.0%
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○Scientific vocabulary similarity
Low similarity (5.4%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: mo-arvan
- Language: Python
- Default Branch: main
- Size: 5.22 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Clinical NLP
% Transfer Learning is not a Silver Bullet: A Case Study on Medical Relation Extraction
Datasets
i2b2 2010
This dataset provides a corpus of assertions in clinical discharge summaries. The task is split into six classes, namely present, possible, absent, hypothetical, conditional and associated with someone else. However, the distribution is highly skewed, such that only 6% of the assertions belong to the latter three classes. Hence we only use the present, possible, and absent assertions for our evaluation as they present the most important information for doctors.
From [1].
BioScope
This is a corpus of assertions in biomedical publications. It was specifically curated for the study of negation and speculation (or absent and possible in this paper) scope and does not contain present annotations. The BioScope dataset does not completely match the information need of health professionals and the i2b2 corpus lacks varied medical text types.
From [1].
MIMIC-III
provides texts from discharge summaries as well as other clinical notes (physician letters, nurse letters, and radiology reports) representing a promising source of varied medical text. Therefore, two annotators followed the annotation guidelines from the i2b2 challenge, and labelled 5,000 assertions, i.e. word spans of entities and their corresponding present / possible / absent class.
From [1].
*sem2012 - Sherlock
Taken from stories by Sir Author Conan Doyle (literary work)
SFU Review Corpus
A collection of product reviews (free text by human users)
References
Owner
- Name: Mo Arvan
- Login: mo-arvan
- Kind: user
- Location: Chicago
- Company: University of Illinois at Chicago
- Website: https://mo-arvan.github.io/
- Repositories: 42
- Profile: https://github.com/mo-arvan
Computer Scientist
Citation (CITATION.cff)
# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!
cff-version: 1.2.0
title: clinical-nlp
message: >-
If you use this software, please cite it using the
metadata from this file.
type: software
authors:
- given-names: Mohammad
family-names: Arvan
email: marvan3@uic.edu
affiliation: University of Illinois at Chicago
orcid: 'https://orcid.org/0000-0001-9155-4559'
- given-names: Hunter
family-names: Holt
email: hholt2@uic.edu
affiliation: University of Illinois at Chicago
orcid: 'https://orcid.org/0000-0001-6833-8372'
- given-names: Natalie
family-names: Parde
email: parde@uic.edu
affiliation: University of Illinois at Chicago
orcid: 'https://orcid.org/0000-0003-0072-7499'
repository-code: 'https://github.com/mo-arvan/clinical-nlp'
license: CC-BY-NC-4.0
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