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 ¼ 0.62 for similarity and 0.58 for relatedness) are on par with measures computed from clinical reports (rho ¼ 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. We found that, with some limitations, biomedical articles may be used in lieu of clinical reports to represent the semantics of clinical terms and that distributional semantic methods are useful for clinical and biomedical natural language processing applications.

A medical scribe is a clinical professional who charts patient-physician encounters in real time, relieving physicians of most of their administrative burden and substantially increasing productivity and job satisfaction. We present a complete implementation of an automated medical scribe. Our system can serve either as a scalable, standardized, and economical alternative to human scribes; or as an assistive tool for them, providing a first draft of a report along with a convenient means to modify it. This solution is, to our knowledge, the first automated scribe ever presented and relies upon multiple speech and language technologies, including speaker diarization, medical speech recognition, knowledge extraction, and natural language generation.

Analogy completion via vector arithmetic has become a common means of demonstrating the compositionality of word embeddings. Previous work have shown that this strategy works more reliably for certain types of analogical word relationships than for others, but these studies have not offered a convincing account for why this is the case. We arrive at such an account through an experiment that targets a wide variety of analogy questions and defines a baseline condition to more accurately measure the efficacy of our system. We find that the most reliably solvable analogy categories involve either 1) the application of a morpheme with clear syntactic effects, 2) male-female alternations, or 3) named entities. These broader types do not pattern cleanly along a syntacticsemantic divide. We suggest instead that their commonality is distributional, in that the difference between the distributions of two words in any given pair encompasses a relatively small number of word types. Our study offers a needed explanation for why analogy tests succeed and fail where they do and provides nuanced insight into the relationship between word distributions and the theoretical linguistic domains of syntax and semantics.

A typical workflow to document clinical encounters entails dictating a summary, running speech recognition, and post-processing the resulting text into a formatted letter. Post-processing entails a host of transformations including punctuation restoration, truecasing, marking sections and headers, converting dates and numerical expressions, parsing lists, etc. In conventional implementations, most of these tasks are accomplished by individual modules. We introduce a novel holistic approach to post-processing that relies on machine callytranslation. We show how this technique outperforms an alternative conventional system-even learning to correct speech recognition errors during post-processingwhile being much simpler to maintain.