snap-umls-clusters

Project Google Site

clusterize the SNAP-IV ADHD questions based on Unified Medical Language System (UMLS) terms and expanded UMLS terms present in them.

Thesis Supervisors:

• Dr. Mohammad Maree
• Dr. Mohammad Herzallah
• Dr. Joman Natsheh

Clustering

• Feature matrix
• Sillhouete determines the best number of clusters, after evaluating multiple values, where 2 <= N < 12

Visualization

• NetworkX graphs depicting CUI terms that usually appear on the same sentences.
• Distance matrices: reordered to match clusters.
• Feature matrices: reordered to match clusters.

Usage

Setup

• Install requirements: pip install -r requirements.txt

• Install scispacy model:

pip install https://s3-us-west-2.amazonaws.com/ai2-s2-scispacy/releases/v0.4.0/en_core_sci_md-0.4.0.tar.gz

• Download the UMLS Metathesaurus (login required). Place it on the base directory.

https://download.nlm.nih.gov/umls/kss/2021AA/umls-2021AA-metathesaurus.zip

Execute

python main.py SNAP_IV_Long_with_Scoring.pdf