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Have you ever wanted to extract medical information from clinical notes, biomedical textbooks, tweets or other unstructured text data? Have you tried to extract it yourself and hit roadblocks? Or, perhaps you were successful and but want to raise the bar and meet people doing similar work at UCSF.

On May 18, the Research Data Community Organizing team hosted an event dedicated to using natural language processing (NLP) to enable research.

This was a two-part event:

  • The first part of the morning featured current work by researchers on campus who have successfully used NLP to enable their research. Learn what's possible with text analysis and information retrieval, and the support available to conduct medical research using NLP at UCSF. 
    View Presentations - Part 1
  • The second part of the morning was a deep dive into the code and techniques used by analysts and programmers, with the goal of enabling participants to get started with NLP. It highlighted tools, examples, challenges and technical particulars in the use of NLP.
    View Presentations - Part 2

Couldn't attend in person? Watch it now!



AGENDA

9:00

Visionary Key Note
Atul Butte, MD, PhD, Priscilla Chan and Mark Zuckerberg Distinguished Professor, Director, UCSF Institute for Computational Health Sciences

*Light breakfast will be served starting 8:30

9:20

Examples of NLP-enabled research from UCSF community

  • Using NLP to Identify Predictors of Mortality in ICU Text: Methodological Options
    Adams Dudley, MD, MBA, Professor of Medicine and Health Policy and Associate Director for Research, Philip R. Lee UCSF Institute for Health Policy Studies
  • Large-Scale Analysis of Clinical Records at UCSF with state of the art Natural language Processing Platforms
    Maryam Panahiazar, PhD, Postdoctoral Scholar, Butte Lab, UCSF Institute for Computational Health Sciences

  • Using Text Mining Methods to Detect a Clinical Infection
    Milena Gianfrancesco, PhD, MPH, Postdoctoral Scholar, UCSF and
    Suzanne Tamang, PhD, Assistant Faculty Director, Data Science, Stanford Center for Population Health Sciences, Instructor, Biomedical Data Science
  • Employing NLP to Measure Patient Health Literacy and Clinician Linguistic Complexity: The UCSF/Kaiser ECLIPSSE Study
    Dean Schillinger, MD, UCSF Professor of Medicine in Residence, Chief of the UCSF Division of General Internal Medicine at Zuckerberg San Francisco General Hospital


10:35Community & information resources
10:40Break; morning snack provided
10:55

General purpose NLP tools and infrastructure available at UCSF

  • An Absolute Beginner's Guide to NLP
    Robert Thombley, Data Scientist, UCSF Institute for Health Policy Studies
  • Tools and Approaches to NLP in Clinical Notes
    Madison Myers, Data Scientist, IBM
  • cTAKES - What Does it Take?
    Gundolf Schenk, Sr. Biomedical Data Scientist, UCSF Institute for Computational Health Sciences
  • Building Custom, Scalable, and Generalizable NLP Tools
    Beau Norgeot, Butte Lab, UCSF Institute for Computational Health Sciences
  • Infrastructure for NLP
    Rick Larsen, UCSF Director, Research Informatics, Enterprise Information and Analytics
12:25Wrap up




Friday, May 18

9:00am to 12:30pm

Byers Auditorium
600 16th Street, San Francisco, California 94158

Organized by:

UCSF Clinical Data Community Organizing Team

Beth Berrean, Deputy Director, Design and Discovery, SOM Tech
Ariel Deardorff, Data Services Librarian, UCSF Library
Oksana Gologorskaya, Sr. Product Manager, Research Technology, UCSF Clinical and Translational Science Institute
Sharat Israni, Executive Director, UCSF Institute for Computational Health Sciences
Rick Larsen, UCSF Director of Research Informatics, Enterprise Information and Analytics
Karla Lindquist, Scientific Lead, Data Science Initiative, UCSF Library
Georgina Lopez, Director of Finance and Administration, UCSF Department of Epidemiology and Biostatistics
Ed Martin, Director of Technology, UCSF Center for Digital Health Innovation
Angela Rizk-Jackson, Director of Operations, UCSF Institute for Computational Health Sciences
Eugenia Rutenberg, Director of Research Computing, UCSF Institute for Computational Health Sciences
Robert Thombley, Data Scientist, UCSF Institute for Health Policy Studies
Leslie Yuan, Chief Information Officer, UCSF Clinical and Translational Science Institute

Sponsored by:

UCSF Institute for Computational Health Sciences

UCSF Information Technology Academic Research Systems

UCSF Clinical & Translational Science Institute (CTSI)

UCSF Library

Center for Digital Health Innovation at UCSF

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