Challenges in Natural Language Processing in Clinical Text

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Challenges in Natural Language Processing for Clinical Narratives Abstract: Narratives of electronic health records (EHRs) contain useful information that is difficult to automatically extract, index, search, or interpret. Clinical natural language processing (NLP) technologies for automatic extraction, indexing, searching, and interpretation of EHRs are in development; however, due to privacy concerns related to EHRs, such technologies are usually developed by teams that have privileged access to EHRs in a specific institution. Technologies that are tailored to a specific set of data from a given institution generate inspiring results on that data; however, they can fail to generalize to similar data from other institutions and even other departments from the same institution. Therefore, learning from these technologies and building on them becomes difficult. In order to improve NLP in EHRs, there is need for head-to-head comparison of approaches that can address a given task on the same data set. Shared-tasks provide one way of conducting systematic head-to- head comparisons. This proposal describes a series of shared-task challenges and conferences, spread over a five year period, that promote the development and evaluation of cutting edge clinical NLP systems by distributing de-identified EHRs to the broad research community, under data use agreements, so that:  the state-of-the-art in clinical NLP technologies can be identified and advanced,  a set of technologies that enable the use of the information contained in EHR narratives becomes available, and  the information from EHR narratives can be made more accessible, for example, for clinical and medical research. The scientific activities supporting the organization of the shared-task challenges are sponsored in part by Informatics for Integrating Biology and the Bedside (i2b2), grant number U54-LM008748, PI: Kohane. CEGS NGRID, NIH P50 MH106933, PI: Isaac Kohane also supported these shared tasks. This proposal aims to organize a series of workshops, conference proceedings, and journal special issues that will accompany the shared-task challenges in order to disseminate the knowledge generated by the challenges.