An Unsupervised Approach to Structuring and Analyzing Repetitive Semantic Structures in Free Text of Electronic Medical Records

Abstract

Electronic medical records (EMRs) include many valuable data about patients, which is, however, unstructured. Therefore, there is a lack of both labeled medical text data in Russian and tools for automatic annotation. As a result, today, it is hardly feasible for researchers to utilize text data of EMRs in training machine learning models in the biomedical domain. We present an unsupervised approach to medical data annotation. Syntactic trees are produced from initial sentences using morphological and syntactical analyses. In retrieved trees, similar subtrees are grouped using Node2Vec and Word2Vec and labeled using domain vocabularies and Wikidata categories. The usage of Wikidata categories increased the fraction of labeled sentences 5.5 times compared to labeling with domain vocabularies only. We show on a validation dataset that the proposed labeling method generates meaningful labels correctly for 92.7% of groups. Annotation with domain vocabularies and Wikidata categories covered more than 82% of sentences of the corpus, extended with timestamp and event labels 97% of sentences got covered. The obtained method can be used to label EMRs in Russian automatically. Additionally, the proposed methodology can be applied to other languages, which lack resources for automatic labeling and domain vocabulary.