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Health Services Research & Development

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2019 HSR&D/QUERI National Conference Abstract

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3006 — An introduction to Natural Language Processing methods in clinical research

Lead/Presenter: Olga Patterson,  Resource Center - VINCI
All Authors: Patterson OV, VA Informatics and Computing Infrastructure (VINCI); DuVall SL, VA Informatics and Computing Infrastructure (VINCI);

Workshop Objectives:
As the use of natural language processing (NLP) methods in preparing data for research and operations projects continues to increase, users should understand the benefits and limitations of text processing approaches. This workshop will provide attendees with a general overview of NLP tools and methods used with clinical text. Synthetic clinical notes will be provided along with open-source tools that will allow participants to implement a working NLP pipeline. Attendees will experience the process of completing an NLP task and leave the tutorial with concrete examples of how NLP can be used at their institutions to benefit research studies or patient care.

1. NLP Overview - The workshop will present an overview of what NLP is and how it is used in healthcare. It will provide a description of current challenges in NLP, which problems can be addressed with NLP, and how to conceptually frame an NLP project. 2 Creation of NLP Modules - Participants will be walked through the creation of NLP modules. Each step in the implementation process will be explained from defining annotation types to programming the actual modules to reviewing the module output. Participants will be assisted in the actual implementation of the modules. 3 Evaluation of System Performance - Sample clinical notes will be processed through the completed NLP pipeline. Participants will be shown how to set up the pipeline output for scoring against the manually annotated reference standard and the NLP system will be evaluated. Result interpretation and how to translate those results into practice will be addressed. The workshop is designed to be interactive from beginning to the end as the participants walk through the steps of creating an NLP pipeline.

Target Audience:
This workshop is intended for informaticians, application programmers in clinical settings, and clinicians with an interest in implementing NLP tools. Code samples, step-by-step instructions for creating NLP modules, and assistance with building pipelines will be provided. This workshop will involve a hands-on demonstration. In order to fully participate in all activities, the participants need a laptop and internet access.

Assumed Audience Familiarity with Topic:
The workshop content is basic and does not assume any prior technical knowledge. Familiarity with healthcare data will be helpful.