AMIA NLP WG 2025

Introduction

The application of Natural Language Processing (NLP) in everyday life has rapidly progressed over the past decades. This progress has been enabled by the availability of tools, large language models, and resources that could be shared, reused, and fine-tuned to support users’ projects and collaborations. Today, recently evolved large generative language models are being integrated into general search and workplace productivity tools. Applying NLP to the textual content of patient electronic health records (i.e., clinical text) is constrained by strict patient privacy and confidentiality laws and regulations. These domain-specific peculiarities for access and sharing of resources (e.g., annotated text corpora) and tools (e.g., trained machine learning algorithms) require creative solutions. Despite these privacy restrictions, many research teams have succeeded in developing novel biomedical and clinical NLP methods, creating and then sharing resources based on clinical text in a thoughtful and sustainable manner. Despite the legal specifics surrounding patient data, NLP-based technologies have permeated clinical and translational research. Our general objective with this pre-symposium is to (1) provide a platform for the next generation of biomedical NLP scientists to get focused feedback on their in-progress graduate work from a panel of senior academicians, (2) provide a forum for people to present their state-of-the-art NLP and LLM work, providing awareness and opportunities for networking and collaboration within the AMIA NLP community, and (3) to discuss promises and challenges related to the emerging generative AI technologies, especially in health systems (and adjunct industries).

Program

Time	Title	Speaker
8:30 – 8:35 am	Welcome to AMIA 2025 NLP Working Group Pre-symposium	Rui Zhang AMIA NLP WG Chair University of Minnesota
Session 1 – Graduate Student Consortium Session Chair: Sunyang Fu, Yonghui Wu Faculty Mentors: Hua Xu, Suzanne Tamang, Ramakanth Kavuluru, and Timothy Miller Hua Xu Professor and Vice Chair for Research and Development, Assistant Dean for Biomedical Informatics, Yale School of Medicine Suzanne Tamang Assistant Professor in the Department of Medicine, Division of Immunology and Rheumatology, Faculty Fellow at the Stanford Center for Population Health Sciences Ramakanth Kavuluru Professor of Internal Medicine, University of Kentucky Timothy Miller Associate Professor of Pediatrics, Harvard Medical School
8:35 - 8:50 am	Context Matching is not Reasoning: Assessing MCQA-Based Evaluation of Generative Language Models in Clinical Settings	Andrew Wen University of Texas Health Science Center at Houston
8:50 - 9:05 am	Identifying Federal Pain Research Priorities in NIH Funded Research Grant Abstracts Using Seed-Guided NLP Algorithms	Zhe Zhao University of Michigan
9:05 - 9:20 am	Expanding Suicide-SDoH Coverage from Death Investigation Narratives	Geoffrey Martin Weill Cornell Medicine
9:20 - 9:35 am	Context-Aware Clinical Natural Language Processing	Kurt Miller University of Texas Health Science Center at Houston
9:35 - 9:50 am	Advancing Personalized Oncology Treatment Planning with Large Language Models	Mengxian Lyu University of Florida
9:50 - 10:05 am	Embedding Privacy Controls and Testing to Prevent Personal Health Information (PHI) Leakage in Clinical Foundation Model Workflows	Dalton Simancek University of Michigan
10:05 – 10:20 am	Coffee Break
Session 2 – State-of-the-art Biomedical and Clinical NLP Session Chair: Xinsong Du, Jiyeong Kim
10:20 – 10:30 am	Clinical Decision Support for Dementia: Large Language Models Enhance ADRD Risk Prediction from Electronic Health Records	Jiankun Wang University of Michigan
10:30 – 10:40 am	Identifying and Characterizing Gallstone Disease from Clinical Narratives with Zero-shot Learning and Automated Prompt Optimization	Sy Hwang University of Pennsylvania
10:40 – 10:50 am	Automating Expert-Level Medical Reasoning Evaluation of LLMs	Shuang Zhou University of Minnesota
10:50 – 11:00 am	GENIE: Generative Note Information Extraction model for structuring EHR data	Huaiyuan Ying Tsinghua University
11:00 – 11:10 am	Efficient and Scalable Retrieval in Knowledge Graphs: From Single-Graph to Partitioned Multi-Graph Approaches	He Cheng University of Colorado
11:10 – 11:20 am	Overview of the ArchEHR-QA 2025 Shared Task on Grounded Question Answering from Electronic Health Records at the BioNLP Workshop at ACL	Sarvesh Soni National Library of Medicine, National Institutes of Health
Session 3 – Generative AI in Health Systems Session Chair: Rui Zhang Time: 11:20 - 11:50 am
Adam Wright Professor of Biomedical Informatics and Medicine at Vanderbilt University Medical Center, Director of the Vanderbilt Clinical Informatics Center (VCLIC) Hongfang Liu Professor at McWilliams School of Biomedical Informatics, Vice President of Learning Health System UTHealth Houston Yiye Zhang Associate Professor of health informatics at Weill Cornell Medicine, Informatics Director of Clinical Decision Support at NewYork-Presbyterian Hospital, editor-in-chief, npj Health Systems Yonghui Wu Chief Data Scientist & Associate Professor, Department of Health Outcomes & Biomedical Informatics College of Medicine at University of Florida Suzanne Tamang Assistant Professor in the Department of Medicine, Division of Immunology and Rheumatology, Faculty Fellow at the Stanford Center for Population Health Sciences
11:50 - 12:00	Closing

Organization Commite

• Rui Zhang (Chair), PhD, FACMI, FAMIA, FIAHSI, University of Minnesota, Minneapolis, MN
• Sunyang Fu (Vice Chair), PhD, MHI, University of Texas Health Science Center at Houston, TX
• Yanshan Wang (Past Chair), PhD, University of Pittsburgh, PA
• Sujani Kakumanu (Member-at-Large), MD, University of Wisconsin, Madison, WI
• Jiyeong Kim (Member-at-Large), PhD, Stanford University, CA
• Xinsong Du (Secretary), PhD, Harvard Medical School, Boston, MA
• Kirk Roberts, PhD, University of Texas Health Science Center at Houston, Houston, TX
• Hua Xu, PhD, Yale University, New Haven, CT
• Özlem Uzuner, PhD, FACMI, George Mason University, Fairfax, VA
• Meliha Yetişgen, PhD, University of Washington, Seattle, WA
• Hongfang Liu, PhD, University of Texas Health Science Center at Houston, TX
• Stephane Meystre, MD, PhD, University of Applied Sciences and Arts of Southern Switzerland (SUPSI), Lugano, Switzerland
• Chunhua Weng, PhD, Columbia University, New York, NY
• Mesoud Rouhizadeh, PhD, University of Florida, Gainesville, FL
• Yifan Peng, PhD, Weill Cornell Medicine, New York City, NY
• Abeed Sarker, PhD, Emory University, Atlanta, GA
• Ramakanth Kavuluru, University of Kentucky, Lexington, KY
• Joseph M. Plasek, PhD, Mass General Brigham, Boston, MA

• Satya Sahoo, PhD, Case Western Reserve University, Cleveland, OH
• Steve Bedrick, PhD, Oregon Health & Science University, Portland, OR
• Dina Demner-Fushman, MD, PhD, National Library of Medicine, Bethesda, MD

Submission

Important Dates

Submission Deadline: August 31, 2025
Notification of Acceptance: September 12, 2025
Workshop: November 16, 2025

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 and significance 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 relevant citation.

State-of-the-Art Biomedical and Clinical NLP

Researchers are encouraged to submit the most recent research studies (published, in press, or under development projects), tools, resources, events, and community shared tasks. The following sections are suggested:

• Methods/Tools/Resources/Events/Shared Tasks Description
• Justification of the Inclusion – Explain the relevance, interest, and value of the submission to NLP WG and its impact on medical informatics
• Summary/Outcome – A summary of the outcomes, such as participants in the event, experimental outcomes of methods, etc.
• References

Submission Guidelines

All submissions have a page limit of 2 pages using AMIA Template

📝 Submit Your Paper Here

AMIA 2025 NLP Working Group Pre-Symposium Workshop

Nov 16, 2025, 8:30 AM – 12:00 PM

Atlanta Marriott Marquis, Atlanta, GA

Introduction

Program

Organization Commite

Submission

Important Dates

Graduate Student Consortium

State-of-the-Art Biomedical and Clinical NLP

Submission Guidelines

Sponsors

AMIA NLP Working Group Leadership

Past Events

2021

2022

2023

2024

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