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We propose Segment Convolutional Neural Networks (Seg-CNNs) for classifying relations from clinical notes. Seg-CNNs use only word-embedding features without manual feature engineering. Unlike typical CNN models, relations between 2 concepts are identified by simultaneously learning separate representations for text segments in a sentence: preceding, concept1, middle, concept2, and succeeding. We evaluate Seg-CNN on the i2b2/VA relation classification challenge dataset. We show that Seg-CNN achieves a state-of-the-art micro-average F-measure of 0.742 [...]

The gap between domain experts and natural language processing expertise is a barrier to extracting understanding from clinical text. We describe a prototype tool for interactive review and revision of natural language processing models of binary concepts extracted from clinical notes. We evaluated our prototype in a user study involving 9 physicians, who used our tool to build and revise models for 2 colonoscopy quality variables. We report changes in [...]

Understanding how to identify the social determinants of health from electronic health records (EHRs) could provide important insights to understand health or disease outcomes. We developed a methodology to capture 2 rare and severe social determinants of health, homelessness and adverse childhood experiences (ACEs), from a large EHR repository.

The traditional concept of personalized nutrition is based on adapting diets according to individual needs and preferences. Discussions about personalized nutrition have been on since the Human Genome Project, which has sequenced the human genome. Thenceforth, topics such as nutrigenomics have been assessed to help in better understanding the genetic variation influence on the dietary response and association between nutrients and gene expression. Hence, some challenges impaired the understanding about [...]

Secure clinical messaging and document exchange utilizing the Direct Protocol (Direct interoperability) has been widely implemented in health information technology (HIT) applications including electronic health records (EHRs) and by health care providers and organizations in the United States. While Direct interoperability has allowed clinicians and institutions to satisfy regulatory requirements and has facilitated communication and electronic data exchange as patients transition across care environments, feature and function enhancements to HIT [...]

Simple measures of electronic health record (EHR) adoption may be inadequate to evaluate EHR use; and positive outcomes associated with EHRs may be better gauged when varying degrees of EHR use are taken into account. In this article, we aim to assess the current state of the literature regarding measuring EHR use.

While evidence generally supports the use of medication management technology, systems are typically implemented and evaluated piecemeal rather than as part of a comprehensive model for medication management. Systems to support drug therapy optimization, increasingly a key role of pharmacists in our healthcare system, have not yet been reported.

The DAta Tag Suite (DATS) is a model supporting dataset description, indexing, and discovery. It is available as an annotated serialization with schema.org, a vocabulary used by major search engines, thus making the datasets discoverable on the web. DATS underlies DataMed, the National Institutes of Health Big Data to Knowledge Data Discovery Index prototype, which aims to provide a "PubMed for datasets." The experience gained while indexing a heterogeneous range [...]

To provide an open source, interoperable, and scalable data quality assessment tool for evaluation and visualization of completeness and conformance in electronic health record (EHR) data repositories.

Various tasks within health care processes are repetitive and time-consuming, requiring personnel who could be better utilized elsewhere. The task of assigning clinical urgency categories to internal patient referrals is one such case of a time-consuming process, which may be amenable to automation through the application of text mining and natural language processing (NLP) techniques.