Welcome to the AMIA 2017

NLP working group pre-symposium

Graduate Student Consortium, Highlight, and Codeathon

Nov 4, 2017, Georgetown East, Washington Hilton Hotel

Download final program >here<



The application of Natural Language Processing (NLP) in the general English domain has seen enormous progress over the past decades, progress that was largely enabled by availability of tools and resources that could be shared, reused, and improved in multiple projects and collaborations. Applying NLP to the textual content of patient electronic health records (i.e., clinical text) is limited by strict patient privacy and confidentiality laws and regulations. These limitations render access and sharing of resources (e.g., annotated text corpora) and tools based on this clinical text (e.g., trained machine learning algorithms) very difficult. As a consequence, the impact of NLP on clinical and translational research is limited. Despite these difficulties, several research teams have succeeded in creating and then sharing resources based on clinical text. Our general objective with this pre-symposium is to enhance the awareness of these resources and tools within the biomedical and clinical NLP communities and improve the reusability, portability, and interoperability of these tools and resources.

Goals of the Pre-symposium

After participating in this event, attendees should be better able to:

  1. Implement constructive feedback on their graduate research efforts
  2. Discover and understand existing and available clinical and biomedical NLP tools and resources as well as the latest advancement in the field
  3. Users will gain hands on experience using tools they have been trained on during the pre-symposium
  4. Providers (tool developers) will have acquired better understanding of the usability and robustness of their tools and areas for improvement.

Final Program

The pre-symposium includes the graduate student consortium session (i.e., ‘doctoral’ consortium also open to Masters students), where students will present their work and get feedback from experienced researchers in the field, followed by highlight and poster session, where significant articles will be highlighted and discussed, and then practical implementation and testing of NLP tools for practical NLP tasks in a ‘hackathon’.

Session 1 – Graduate students consortium (8:35am-12:30pm):

This session is chaired by Dr. Stephane Meystre. The expert panel includes Hongfang Liu, Pierre Zweigenbaum, Dina Demner-Fushman, Ozlem Uzuner, Hua Xu, and Stephane Meystre. Each presenter will prepare a 15min presentation followed by questions and constructive feedback from the expert panel about the following:

  1. Presentation (slides, speech clarity and rhythm)
  2. Significance (real problem, real people, and potential impact)
  3. Innovation (new or improved, in one field or broader)
  4. Approach (appropriate research design, methods used, and feasibility)
  5. Environment (adequate resources, supervisors/collaborators, guidance)

Session 2 – NLP highlights and posters (1:30-2:45pm):

This session is chaired by Hongfang Liu. For highlight, each presenter will prepare a 15min presentation followed by 5min for questions. For poster, each presenter will prepare a 5min presentation with posters posted for discussion.

Session 3 – NLP tooling “hackathon” (3:00-4:30pm):

This session is chaired by Sivaram Arabandi and Kavishwar Wagholiar. Each provider provides a 15min overview of the tool and tasks. Then the participants will choose one of the two teams to gain hands-on experience of using the tools to solve specific tasks and explore areas of improvement in usability.


  • Hongfang Liu, PhD, Section of Medical Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
  • Rong Xu, PhD, Case Western Reserve University, Cleveland, OH
  • Stephane Meystre, MD, PhD, Medical University of South Carolina, Charleston, SC
  • Sivaram Arabandi, MD, MS, Ontopro, Houston, TX
  • Kavishwar Wagholikar, MBBS, PhD, Massachusetts General Hospital, Boston, MA
  • Dina Demner-Fushman, MD, PhD, National Library of Medicine, Bethesda, MD
  • Jon Patrick, PhD, Product Development Director, Health Language Analytics, Sydney, Australia
  • Guergana Savova, PhD, Boston Children’s Hospital, Harvard Medical School, Boston, MA
  • Ozlem Uzuner, PhD, Department of Computer Science, University at Albany, SUNY, Albany, NY
  • Chunhua Weng, PhD, Columbia University, New York, NY
  • Hua Xu, PhD, The University of Texas Health Science Center at Houston, TX
  • Pierre Zweigenbaum, PhD, LIMSI-CNRS, Université Paris-Saclay, Orsay, France

Submission and Review

Submission deadline:    July 31, 2017

Submission format:       All submissions have a page limit of 2 pages using AMIA template

Submission guideline:

Poster: All researchers in the biomedical and clinical NLP fields are invited to submit applications for a poster of their research. Please follow AMIA poster format.

Graduate Student Consortium: Graduate students are invited to submit applications for a podium presentation of their graduate research work (in the biomedical and clinical NLP fields). The submission is suggested to include the following sections:

  • Aims and Objectives - State the main objective(s) of your project.
  • Justification for the Research Topic - Explain the motivations for your project.
  • Research Questions - Stating your research question is essential. This might be done in a list.
  • Research Methodology - If you already have plans for your research methodology, explain them here. If you have not found an appropriate methodology yet, or wonder which one to choose, this is also the place to mention it. In this case, list the requirements your methodology should fulfill.
  • Research Results to Date - You are not required to have results. But if you already have some, present them here.
  • References – Any citation.

Highlight: All researchers in the biomedical and clinical NLP are invited to submit their significant paper or research projects. The submission is suggested to include the following sections:

  • Overview of the paper or project – It can be an abstract or project overview.
  • Justification of Highlight – Explain the relevance, interest, and value of the topic to NLP-WG and the impact of the paper(s) or efforts on informatics/medicine/biology.

Codeathon: For participating as a Provider, please provide a two-page document, detailing thetargeted NLP tasks and directions to accomplish each task. The following sections are suggested:

  • Aims and Objectives - State the main objective(s) of your participation in the Hackathon.
  • Description of your NLP Application - Describe your tool briefly including its features, its advantages, disadvantages, etc.
  • Proposed Tasks - List of tasks to be accomplished by your users to best showcase your tool.
  • Projects/Products using your tool - List projects or products that are using the NLP application. Mention if this is in a production setting.
  • References - List bibliographic references in Vancouver format.

Submission method: