Corpus domain effects on distributional semantic modeling of medical terms

Motivation: Automatically quantifying semantic similarity and relatedness between clinical terms is an important aspect of text mining from electronic health records, which are increasingly recognized as valuable sources of phenotypic information for clinical genomics and bioinformatics research. A key obstacle to development of semantic relatedness measures is the limited availability of large quantities of clinical text to researchers and developers outside of major medical centers. Text from general English and biomedical literature are freely available; however, their validity as a substitute for clinical domain to represent semantics of clinical terms remains to be demonstrated. Results: We constructed neural network representations of clinical terms found in a publicly available benchmark dataset manually labeled for semantic similarity and relatedness. Similarity and relatedness measures computed from text corpora in three domains (Clinical Notes, PubMed Central articles and Wikipedia) were compared using the benchmark as reference. We found that measures computed from full text of biomedical articles in PubMed Central repository (rho = 0.62 for similarity and 0.58 for relatedness) are on par with measures computed from clinical reports (rho = 0.60 for similarity and 0.57 for relatedness). We also evaluated the use of neural network based relatedness measures for query expansion in a clinical document retrieval task and a biomedical term word sense disambiguation task....
Source: Bioinformatics - Category: Bioinformatics Authors: Tags: DATA AND TEXT MINING Source Type: research