2019 October JAMIA Journal Club Webinar

October 10, 2019
Free for AMIA members; $50 for non-members.
Kirk Roberts, PhD

Enhancing clinical concept extraction with contextual embeddings

Co-author Kirk Roberts, PhD will discuss this month's JAMIA Journal Club selection:

Si Y, Wang J, Xu H, Roberts K. Enhancing clinical concept extraction with contextual embeddings. J Am Med Inform Assoc. 2019 Jul 2. pii: ocz096. doi: 10.1093/jamia/ocz096. [Epub ahead of print] [Abstract]


Kirk Roberts, PhD, MS
Assistant Professor
University of Texas Health Science Center at Houston
UTHealth School of Biomedical Informatics
Houston, TX

Kirk Roberts is an assistant professor at the UTHealth School of Biomedical Informatics. Prior to joining SBMI, he obtained a PhD in Computer Science from UT Dallas and was a postdoctoral researcher at the U.S. National Library of Medicine. His research interests are in the application of natural language processing, information retrieval, and machine learning to biomedical problems. This includes applications such as question answering and information extraction from both electronic health records and the biomedical literature. He is a recipient of an NLM Career Development Award and is the organizer of the Clinical NLP Workshop series and the TREC Precision Medicine track.


  • 35-minute discussion between the authors and the JAMIA Student Editorial Board moderators including salient features of the published study and its potential impact on practice.
  • 25-minute discussion of questions submitted by listeners via the webinar tools and moderated by JAMIA Student Editorial Board members
JAMIA Journal Club managers and monthly moderators are JAMIA Student Editorial Board members:


Maryam Zolnoori, PhD, Postdoctoral Research Fellow, Department of Digital Health Sciences and Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN


Tiffany J. Callahan, MPH, PhD Candidate, Computational Bioscience Program at the University of Colorado Denver Anschutz Medical Campus, Aurora, CO


The PubMed citation for the paper under discussion is:

Si Y, Wang J, Xu H, Roberts K. Enhancing clinical concept extraction with contextual embeddings. J Am Med Inform Assoc. 2019 Jul 2. pii: ocz096. doi: 10.1093/jamia/ocz096. [Epub ahead of print] [Abstract]

Student Access

Students who are not AMIA members, but whose academic institutions are members of the Academic Forum, are eligible for a complimentary JAMIA Journal Club registration. Please contact Susanne Arnold at susanne@amia.org for the discount code. In the email, please include: full name, Academic Department, and the primary Academic Forum representative of that Academic Department. Note that AMIA Student memberships are $50, which allow access to JAMIA, all JAMIA Journal Clubs, and other webinars of interest to the biomedical informatics community. 

Statement of Purpose

Neural network–based representations (or “embeddings”) have dramatically advanced natural language processing (NLP) tasks, including clinical NLP tasks such as concept extraction. Recently, however, more advanced embedding methods and representations (such as ELMo and BERT) have further pushed the state of the art in NLP, yet there are no common best practices for how to integrate these representations into clinical tasks. The purpose of this study, then, is to explore the space of possible options in utilizing these new models for clinical concept extraction, including comparing these to traditional word embedding methods (including word2vec, GloVe, and fastText).

Target Audience

The target audience for this activity is professionals and students interested in biomedical and health informatics.

Learning Objectives

The general learning objective for all of the JAMIA Journal Club webinars is that participants will

  • Use a critical appraisal process to assess article validity and to gauge article findings' relevance to practice

After this live activity, the participant should be better able to:

  • Explain how neural network-based embedding techniques are utilized in natural language processing (NLP)
  • Discuss how recent (“contextual”) embedding techniques have advanced NLP, including their potential impact on NLP for electronic health records
  • Identify key considerations for maximizing the impact of contextual embedding techniques for clinical NLP

This JAMIA Journal Club does not offer continuing education credit.

In our dedication to providing unbiased education even when no CE credit is associated with it, we provide planners’ and presenters’ disclosure of relevant financial relationships with commercial interests that has the potential to introduce bias in the presentation: 

Disclosures for this Activity

These faculty, planners, and staff who are in a position to control the content of this activity disclose that they and their life partners have no relevant financial relationships with commercial interests: 

JAMIA Journal Club presenter: Kirk Roberts
JAMIA Journal Club planners: Michael Chiang, Tiffany J. Callahan, Maryam Zolnoori
AMIA staff: Susanne Arnold, Pesha Rubinstein

Contact Info

For questions about webinar access, email Susanne@amia.org.