# Unsupervised Annotation of Phenotypic Abnormalities via Semantic Latent Representations on Electronic Health Records

arXiv: https://arxiv.org/abs/1911.03862 · HTML: https://mlsanity.com/paper/1911.03862/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 10 Nov 2019.

## Built on by (most cited first, 2 of 2)

- [Neural Natural Language Processing for Unstructured Data in Electronic Health Records: a Review](https://mlsanity.com/paper/2107.02975/) (2021)
- [Self-Supervised Detection of Contextual Synonyms in a Multi-Class Setting: Phenotype Annotation Use Case](https://mlsanity.com/paper/2109.01935/) (2021)

## Abstract (arXiv)

The extraction of phenotype information which is naturally contained in electronic health records (EHRs) has been found to be useful in various clinical informatics applications such as disease diagnosis. However, due to imprecise descriptions, lack of gold standards and the demand for efficiency, annotating phenotypic abnormalities on millions of EHR narratives is still challenging. In this work, we propose a novel unsupervised deep learning framework to annotate the phenotypic abnormalities from EHRs via semantic latent representations. The proposed framework takes the advantage of Human Phenotype Ontology (HPO), which is a knowledge base of phenotypic abnormalities, to standardize the annotation results. Experiments have been conducted on 52,722 EHRs from MIMIC-III dataset. Quantitative and qualitative analysis have shown the proposed framework achieves state-of-the-art annotation performance and computational efficiency compared with other methods.