Ontology-Based and Weakly Supervised Rare Disease Phenotyping from Clinical Notes. (arXiv:2205.05656v2 [cs.CL] UPDATED)

Computational text phenotyping is the practice of identifying patients with
certain disorders and traits from clinical notes. Rare diseases are challenging
to be identified due to few cases available for machine learning and the need
for data annotation from domain experts. We propose a method using ontologies
and weak supervision, with recent pre-trained contextual representations from
Bi-directional Transformers (e.g. BERT). The ontology-based framework includes
two steps: (i) Text-to-UMLS, extracting phenotypes by contextually linking
mentions to concepts in Unified Medical Language …

arxiv disease notes ontology