[[SIGBIOMED]] | [[BioNLP 2025]]

===WORKSHOP TOPIC AND CONTEXT===

The interest in biomedical and clinical language continues to broaden due to unprecedented advances supported by success stories in improving health through supporting patients and clinicians. Access to biomedical information became easier, and more people generate and access health-related text. Only language technologies can enable and support adequate use of the biomedical and clinical text in most use cases. The advances in pre-trained language models and foundation models make all parties involved in healthcare turn to language technologies in the hope of getting tangible support in satisfying information needs, facilitating research and improving clinical documentation and healthcare. In addition to exposing BioNLP researchers to the mainstream ACL research, the workshop is a venue for informing the mainstream ACL researchers about the fast growing and important domain of biomedical / clinical language processing.

BioNLP 2026 will focus on evaluation frameworks and metrics that reflect the needs of health-related use cases and provide a good estimate of
reliability of the proposed solutions. BioNLP 2026 will continue focusing on transparency of the generative approaches and factuality of the generated
text. Language processing that supports DEIA (Diversity, Equity, Inclusion and Accessibility) continues to be of utmost importance. The work on detection and mitigation of bias and misinformation continues to be paramount. Research in languages other than English, particularly, under-represented languages, and health disparities are always of interest to BioNLP. Other areas of interest include, but are not limited to:
<ul>
<li> Extraction of complex relations and events; </li>
<li> Discourse analysis; Anaphora \& coreference resolution; </li>
<li> Question Answering; Summarization; Text simplification; </li>
<li> Resources and strategies for system testing and evaluation;</li>
<li> Synthetic data generation \& data augmentation; </li>
<li> Translating NLP research into practice: tangible explainable results of biomedical language processing applications;</li>
<li> Reproducibility of the published findings. </li>
</ul>

===SHARED TASKS===

BioNLP has a long-standing tradition of sponsoring Shared Tasks. This year, we invited SIGBioMed members to submit a description of a shared task to be included with the BioNLP proposal. We received four strong detailed descriptions of the tasks, which were reviewed by the workshop organizers. These well-defined and timely tasks are briefly described below.

==== MedExACT====
This task involves detection and labeling of medical decisions in ICU discharge summaries, with evaluation metrics emphasizing both accuracy and fairness across demographic and disease subgroups at the span and token levels, as well as through stratified analyses to measure robustness against biases in sex, race, English proficiency, and disease type. Baseline models such as RoBERTa indicated the complexity of the task, and participants will be supported with expedited access to MedDec through PhysioNet, a public leaderboard, and a starter kit in Python. The training and validation splits of MedDec are currently available on PhysioNet, while the test split has not been released and will remain withheld until the evaluation phase.

====Detecting Psychological Defense Mechanisms in Conversations====
This task is the first benchmark to capture psychologically grounded constructs (defense mechanisms) in real conversational data. It focuses on fine-grained coping strategies in dialogue, supporting research at the intersection of clinical psychology, counseling, and NLP. Given the dialogue history and a target seeker utterance, participants will (Task A) predict whether any defense is present and (Task B) classify the specific type (e.g., Disavowal, Obsessional, Highly Adaptive). The organizers provide an expert-annotated dataset, train/dev/test splits, baselines, and a starter kit. Submissions will be evaluated on a held-out test set using F1 for Task A and Macro-F1 for Task B.

====BioGen====
The task focuses on grounding answers with reference attribution to mitigate generation of false statements by LLMs when answering biomedical questions. BioGen 2026 introduces generation of multimodal answers from textual and visual sources with citations, leveraging PubMed and HealthVidQA as multimodal sources. The test set is based on the information requests submitted by self-identified non-clinicians to the MedlinePlus service provided by the National Library of Medicine. The evaluation will leverage BioACE, an automated metric that strongly correlates with human evaluation on the BioGen 2024 textual dataset.

==== Clinical Skill QA====
This task extends evaluation to a multimodal setting. Given an image of a medical student’s procedure, a question, and four answer options, the goal is for participants to train a model to generate the correct response. The dataset will be constructed from ~80 video clips of medical student clinical procedures, collected from a partner medical school. This task provides a unified framework for benchmarking, diagnosing, and advancing LLM capabilities for both clinical decision support and medical training. Evaluation will follow a multiple-choice QA setup with accuracy as the primary metric, with additional stratified analyses by skill type and modality.

BioNLP Workshop

2025-09-24T18:31:26Z

Dina: /* SHARED TASKS */

[[SIGBIOMED]] | [[BioNLP 2025]]

===WORKSHOP TOPIC AND CONTEXT===

The interest in biomedical and clinical language continues to broaden due to unprecedented advances supported by success stories in improving health through supporting patients and clinicians. Access to biomedical information became easier, and more people generate and access health-related text. Only language technologies can enable and support adequate use of the biomedical and clinical text in most use cases. The advances in pre-trained language models and foundation models make all parties involved in healthcare turn to language technologies in the hope of getting tangible support in satisfying information needs, facilitating research and improving clinical documentation and healthcare. In addition to exposing BioNLP researchers to the mainstream ACL research, the workshop is a venue for informing the mainstream ACL researchers about the fast growing and important domain of biomedical / clinical language processing.

BioNLP 2026 will focus on evaluation frameworks and metrics that reflect the needs of health-related use cases and provide a good estimate of
reliability of the proposed solutions. BioNLP 2026 will continue focusing on transparency of the generative approaches and factuality of the generated
text. Language processing that supports DEIA (Diversity, Equity, Inclusion and Accessibility) continues to be of utmost importance. The work on detection and mitigation of bias and misinformation continues to be paramount. Research in languages other than English, particularly, under-represented languages, and health disparities are always of interest to BioNLP. Other areas of interest include, but are not limited to:
<ul>
<li> Extraction of complex relations and events; </li>
<li> Discourse analysis; Anaphora \& coreference resolution; </li>
<li> Question Answering; Summarization; Text simplification; </li>
<li> Resources and strategies for system testing and evaluation;</li>
<li> Synthetic data generation \& data augmentation; </li>
<li> Translating NLP research into practice: tangible explainable results of biomedical language processing applications;</li>
<li> Reproducibility of the published findings. </li>
</ul>

===SHARED TASKS===

BioNLP has a long-standing tradition of sponsoring Shared Tasks. This year, we invited SIGBioMed members to submit a description of a shared task to be included with the BioNLP proposal. We received three strong detailed descriptions of the tasks, which were reviewed by the workshop organizers. These well-defined and timely tasks are briefly described below.

==== MedExACT====
This task involves detection and labeling of medical decisions in ICU discharge summaries, with evaluation metrics emphasizing both accuracy and fairness across demographic and disease subgroups at the span and token levels, as well as through stratified analyses to measure robustness against biases in sex, race, English proficiency, and disease type. Baseline models such as RoBERTa indicated the complexity of the task, and participants will be supported with expedited access to MedDec through PhysioNet, a public leaderboard, and a starter kit in Python. The training and validation splits of MedDec are currently available on PhysioNet, while the test split has not been released and will remain withheld until the evaluation phase.

====Detecting Psychological Defense Mechanisms in Conversations====
This task is the first benchmark to capture psychologically grounded constructs (defense mechanisms) in real conversational data. It focuses on fine-grained coping strategies in dialogue, supporting research at the intersection of clinical psychology, counseling, and NLP. Given the dialogue history and a target seeker utterance, participants will (Task A) predict whether any defense is present and (Task B) classify the specific type (e.g., Disavowal, Obsessional, Highly Adaptive). The organizers provide an expert-annotated dataset, train/dev/test splits, baselines, and a starter kit. Submissions will be evaluated on a held-out test set using F1 for Task A and Macro-F1 for Task B.

====BioGen====
The task focuses on grounding answers with reference attribution to mitigate generation of false statements by LLMs when answering biomedical questions. BioGen 2026 introduces generation of multimodal answers from textual and visual sources with citations, leveraging PubMed and HealthVidQA as multimodal sources. The test set is based on the information requests submitted by self-identified non-clinicians to the MedlinePlus service provided by the National Library of Medicine. The evaluation will leverage BioACE, an automated metric that strongly correlates with human evaluation on the BioGen 2024 textual dataset.

==== Clinical Skill QA====
This task extends evaluation to a multimodal setting. Given an image of a medical student’s procedure, a question, and four answer options, the goal is for participants to train a model to generate the correct response. The dataset will be constructed from ~80 video clips of medical student clinical procedures, collected from a partner medical school. This task provides a unified framework for benchmarking, diagnosing, and advancing LLM capabilities for both clinical decision support and medical training. Evaluation will follow a multiple-choice QA setup with accuracy as the primary metric, with additional stratified analyses by skill type and modality.

BioNLP Workshop

2025-09-24T18:10:02Z

Dina:

File:BioNLP2025.jpg

2025-08-08T04:09:52Z

Dina:

2025-06-18T00:12:17Z

Dina:

[[SIGBIOMED]] | [[BioNLP 2024]] | [[BioNLP 2023]]

<font size="4"><b>BIONLP 2025 and Shared Tasks @ ACL 2025</b></font>

The 24th BioNLP workshop associated with the ACL SIGBIOMED special interest group is co-located with [https://2025.aclweb.org/ ACL 2025]

===IMPORTANT DATES (Tentative) ===

* Paper submission deadline: March 20, 2025
* Notification of acceptance: April 28, 2025
* Camera-ready paper due: May 25, 2025 -- <b>No extensions due to ACL publication deadline</b>.
* Pre-recorded video due (hard deadline): July 7, 2025
* Workshop: August 1st 2025

=== Keynote ===
Speaker: Wojciech Kusa

Incorporating Changes in Review Outcomes in the Evaluation of Systematic Review Automation

Current evaluations of automation methods in systematic literature reviews often treat all included studies as equally important, ignoring their varying influence on review outcomes. This can misrepresent the effectiveness of search strategies, as not all relevant studies contribute equally to the conclusions of the review. To address this limitation, we propose a new evaluation framework that incorporates the differential impact of individual studies on review outcomes. Using data from the CLEF 2019 TAR task, we applied this framework to assess 74 automation models, leveraging meta-analysis effect estimates to weigh the influence of each study. Compared to conventional binary relevance metrics, our approach provided a more nuanced assessment, emphasizing the importance of retrieving high-impact studies. Results showed significant differences in model rankings, underscoring the value of outcome-based evaluation. This framework offers researchers a more precise method for evaluating systematic review automation tools, ultimately supporting higher-quality evidence synthesis and better-informed clinical decisions.

Wojciech is a Senior Researcher at the NASK National Research Institute in Poland, where he leads the Linguistic Engineering and Text Analysis Department. He holds a PhD in NLP from TU Wien, with a focus on applying and evaluating neural methods for domain-specific data. His research interests include the safety and evaluation of large language models, clinical and biomedical NLP, and AI-driven scientific discovery. Wojciech was a Marie Skłodowska-Curie Fellow in the EU Horizon 2020 project DoSSIER, specialising in biomedical information retrieval and NLP. He has industry experience from roles at Samsung and Allegro, and has completed research internships at Sony, UNINOVA, and the Polish Academy of Sciences.

===Program Committee===
* Daniel Andrade, Hiroshima University, Japan
* Emilia Apostolova, Anthem, Inc., USA
* Eiji Aramaki, University of Tokyo, Japan
* Tanmay Basu, Indian Institute of Science Education and Research Bhopal, India
* Leandra Budau, Toronto Metropolitan University, Canada
* Leonardo Campillos-Llanos, Centro Superior de Investigaciones Científicas - CSIC, Spain
* Liuliu Chen, University of Melbourne, Australia
* Yingjian Chen, Henan University, China
* Brian Connolly, Cincinnati Children's Hospital Hospital Medical Center, Ohio, USA
* Mike Conway, University of Melbourne, Australia
* An Dao, University of Tokyo, Japan
* Berry de Bruijn, National Research Council, Canada
* Jean-Benoit Delbrouck, Stanford University, California, USA
* Dina Demner-Fushman, US National Library of Medicine
* Simona Doneva, University of Zurich, Switzerland
* Pietro Ferrazzi, University of Padua, Italy
* Kathleen C. Fraser, National Research Council Canada
* Natalia Grabar, CNRS, U Lille, France
* Cyril Grouin, Université Paris-Saclay, CNRS
* Tudor Groza, EMBL-EBI
* Yingjun Guan, University of Illinois Urbana-Champaign, USA
* Deepak Gupta, US National Library of Medicine
* Thierry Hamon, LIMSI-CNRS, France
* Ben Holgate, King's College London, UK
* Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
* Hidetaka Kamigaito, Nara Institute of Science and Technology, Japan
* Vani Kanjirangat, Dalle Molle Institute for Artificial Intelligence (IDSIA), Switzerland
* Sarvnaz Karimi, CSIRO, Australia
* Nazmul Kazi, University of North Florida, USA
* Siun Kim, Seoul National University, Korea
* Gaurav Kumar, University of California, San Diego, USA
* Andre Lamurias, NOVA School of Science and Technology, Lisbon, Portugal
* Majid Latifi, Department of Computer Science, University of York, York, UK
* Alberto Lavelli, FBK-ICT, Italy
* Robert Leaman, US National Library of Medicine
* Lung-Hao Lee, National Central University, Taiwan
* Ulf Leser, Humboldt-Universität zu Berlin, Germany
* Yuan Liang, Queen Mary University of London, UK
* Siting Liang, German Research Center for Artificial Intelligence, Germany
* Livia Lilli, Fondazione Policlinico Universitario Agostino Gemelli, Italy
* Abdine Maiga, University College London, UK
* Makoto Miwa, Toyota Technological Institute, Japan
* Claire Nedellec, National Research Institute for Agriculture, Food and Environment (INRAE), Paris-Saclay University, France
* Guenter Neumann, DFKI, Germany
* Aurélie Névéol, LISN - CNRS, France
* Mariana Neves, Hasso-Plattner-Institute at the University of Potsdam, Germany
* Andrei Niculae, Carol Davila University of Medicine and Pharmacy, Romania
* Brian Ondov, Yale University, USA
* Noon Pokaratsiri Goldstein, Deutsches Forschungszentrum für Künstliche Intelligenz (DFKI)
* François Remy, Ghent University, Belgium
* Francisco J. Ribadas-Pena, University of Vigo, Spain
* Fabio Rinaldi, Dalle Molle Institute for Artificial Intelligence Research (IDSIA), Switzerland
* Roland Roller, DFKI, Germany
* Mourad Sarrouti, CLARA Analytics, USA
* Efstathia Soufleri, Archimedes - Athena Research Center, Greece
* Peng Su, University of Delaware, USA
* Madhumita Sushil, University of California, San Francisco, USA
* Mario Sänger, Humboldt Universität zu Berlin, Germany
* Karin Verspoor, RMIT University, Australia
* Davy Weissenbacher, Cedars-Sinai, Los Angeles, California, USA
* Nathan M. White, James Cook University, Australia
* Dongfang Xu, Cedars-Sinai, USA
* Shweta Yadav, University of Illinois Chicago, USA
* Ken Yano, National Institute of Advanced Industrial Science and Technology, Japan
* Hyunwoo Yoo, Drexel University, USA
* Kai Zhang, Worcester Polytechnic Institute, MA, USA
* Xinyue Zhang, King's College London, UK
* Xiao Yu Cindy Zhang, University of British Columbia, Canada
* Jingqing Zhang, Imperial College London, UK
* Angelo Ziletti, Bayer, Germany
* Ayah Zirikly, Johns Hopkins, USA
* Pierre Zweigenbaum, LIMSI - CNRS, France

===Secondary Reviewers===
* Joseph Akinyemi, University of York, UK
* Robert Bossy, National Research Institute for Agriculture, Food and Environment (INRAE), France
* Marco Naguib, Interdisciplinary Laboratory on Numerical Sciences (LISN), France

===Sponsor===
We are pleased to announce that the Chen Institute is co-organizing the BioNLP 2025 Workshop. Founded in 2016 by Tianqiao Chen and Chrissy Luo, the Chen Institute is driven by a bold vision to improve the human experience by understanding how our brains perceive, learn, and interact with the world. Their global platform includes the Tianqiao and Chrissy Chen Institute for Neuroscience at Caltech, the Tianqiao Chen Institute for Translational Research in Shanghai, the Chen Frontier Lab for Applied Neurotechnology, and the Chen Frontier Lab for AI and Mental Health. The Chen Scholars program supports early- to mid-career scientists, and the recently launched Chen Institute and Science Prize for AI Accelerated Research highlights their deep commitment to innovation.

At this year’s BioNLP Workshop, the Chen Institute is interested in exploring how artificial intelligence can accelerate the pace of scientific discovery. We believe there are vast, untapped opportunities to make groundbreaking advances by leveraging the power of AI. The hope is that this meeting will serve as the beginning of an ongoing dialogue—focused on new developments, transformative successes, and emerging thinking at the intersection of AI and science. Through this collaboration, the Chen Institute aims to identify and support promising approaches with the potential to meaningfully change the world.

===Workshop Program===

Friday, August 1, 2025

*08:40 - 08:50 <b>Opening remarks</b>

*08:50 - 10:30 <b>Session 1: Foundational tasks</b>

*08:50 - 09:10 Accelerating Cross-Encoders in Biomedical Entity Linking, Javier Sanz-Cruzado and Jake Lever, University of Glasgow
*09:10 - 09:30 Beyond Citations: Integrating Finding-Based Relations for Improved Biomedical Article Representations, Yuan Liang, Massimo Poesio, Roonak Rezvani, Queen Mary University of London, University of Utrecht, Recursion
*09:30 - 09:50 MedSummRAG: Domain-Specific Retrieval for Medical Summarization, Guanting Luo and Yuki Arase, The University of Osaka, Institute of Science Tokyo
*09:50 - 10:10 Advancing Biomedical Claim Verification by Using Large Language Models with Better Structured Prompting Strategies, Siting Liang and Daniel Sonntag, German Research Center for Artificial Intelligence
*10:10 - 10:30 Questioning Our Questions: How Well Do Medical QA Benchmarks Evaluate Clinical Capabilities of Language Models? Siun Kim and Hyung-Jin Yoon, Seoul Natoinal University Hospital, Biomedical Engineering, Seoul National University College of Medicine

*10:30 - 11:00 <b>Coffee Break</b>

*11:00 - 12:30 <b>Session 2: Clinical NLP</b>

*11:00 - 11:20 A Retrieval-Based Approach to Medical Procedure Matching in Romanian, Andrei Niculae, Adrian Cosma, Emilian Radoi, National University of Science and Technology Politehnica Bucharest
*11:20 - 11:40 Error Detection in Medical Note through Multi Agent Debate, Abdine L Maiga, Anoop Shah, Emine Yilmaz, University College London, Amazon
*11:40 - 12:00 Converting Annotated Clinical Cases into Structured Case Report Forms, Pietro Ferrazzi, Alberto Lavelli, Bernardo Magnini, University of Padova, FBK

*12:00 - 12:30 <b>Invited Talk</b> -- Wojciech Kusa: Incorporating Changes in Review Outcomes in the Evaluation of Systematic Review Automation

*12:30 - 14:00 <b>Lunch</b>

*14:00 - 15:30 <b>Session 3: Shared Tasks</b>

*14:00 - 14:15 Overview of the BioLaySumm 2025 Shared Task on Lay Summarization of Biomedical Research Articles and Radiology Reports, Chenghao Xiao, Kun Zhao, Xiao Wang, Siwei Wu, Sixing Yan, Tomas Goldsack, Sophia Ananiadou, Noura Al Moubayed, Liang Zhan, William K. Cheung, Chenghua Lin, Durham University, University of Pittsburgh, University of Manchester, Hong Kong Baptist University, University of Sheffield
*14:15 - 14:20 Poster boaster: AEHRC at BioLaySumm 2025: Leveraging T5 for Lay Summarisation of Radiology Reports. Wenjun Zhang, Shekhar S. Chandra, Bevan Koopman, Jason Dowling and Aaron Nicolson
*14:20 - 14:25 Poster boaster: Team SXZ at BioLaySumm2025: Combining Section‐Wise Summarization, K‐Shot LLM Prompting, BioBART, and RL Fine‐Tuning for Biomedical Lay Summaries. Pengcheng Xu, Sicheng Shen, Jieli Zhou and Hongyi Xin
* 14:25 - 14:40 SMAFIRA Shared Task at the BioNLP'2025 Workshop: Assessing the Similarity of the Research Goal, Mariana Neves, Iva Sovadinova, Susanne Fieberg, Celine Heinl, diana Rubel, Gilbert Schönfelder, Bettina Bert, German Federal Institute for Risk Assessment, Masaryk University
*14:40 - 14:55 Overview of the ClinIQLink 2025 Shared Task on Medical Question-Answering, Brandon C Colelough, Davis Bartels, Dina Demner-Fushman, National Library of Medicine
*14:55 - 15:00 Poster boaster: VeReaFine: Iterative Verification Reasoning Refinement RAG for Hallucination-Resistant on Open-Ended Clinical QA. Pakawat Phasook, Rapepong Pitijaroonpong, Jiramet Kinchagawat, Amrest Chinkamol, Tossaporn Saengja, Kiartnarin Udomlapsakul, Jitkapat Sawatphol and Piyalitt Ittichaiwong
*15:00 - 15:15 Overview of the ArchEHR-QA 2025 Shared Task on Grounded Question Answering from Electronic Health Records, Sarvesh Soni, SOUMYA GAYEN, Dina Demner-Fushman, National Library of Medicine
*15:15 - 15:20 Poster boaster: ArgHiTZ at ArchEHR-QA 2025: A Two-Step Divide and Conquer Approach to Patient Question Answering for Top Factuality. Adrian Cuadron Cortes, Aimar Sagasti, Maitane Urruela, Iker De la Iglesia, Ane García Domingo-Aldama, Aitziber Atutxa Salazar, Josu Goikoetxea and Ander Barrena
*15:20 - 15:25 Poster boaster: Neural at ArchEHR-QA 2025: Agentic Prompt Optimization for Evidence-Grounded Clinical Question Answering. Sai Prasanna Teja Reddy Bogireddy, Abrar Majeedi, Viswanath Reddy Gajjala, Zhuoyan Xu, Siddhant Rai and Vaishnav Potlapalli

*15:30 - 16:00 <b>Coffee Break</b>

*16:00 - 18:00 <b>Poster Sessions</b> (online, onsite, workshop and shared tasks. Note: Shared Task papers listed in Volume 2)

* Improving Barrett's Oesophagus Surveillance Scheduling with Large Language Models: A Structured Extraction Approach, Xinyue Zhang, Agathe Zecevic, Sebastian Zeki, Angus Roberts, King's College London, Guy's and St Thomas' NHS Foundation Trust
* Effective Multi-Task Learning for Biomedical Named Entity Recognition, João Ruano, Gonçalo M Correia, Leonor Maria Machado Barreiros, Afonso Mendes, Priberam
* PetEVAL: A veterinary free text electronic health records benchmark, Sean Farrell, Alan Radford, Noura Al Moubayed, Peter-John Mäntylä Noble, Durham University, University of Liverpool
* Can Large Language Models Classify and Generate Antimicrobial Resistance Genes? Hyunwoo Yoo, Haebin Shin, Gail Rosen, Drexel University, KAIST AI
* Overcoming Data Scarcity in Named Entity Recognition: Synthetic Data Generation with Large Language Models. An Dao, Hiroki Teranishi, Yuji Matsumoto, Florian Boudin, Akiko Aizawa, The University of Tokyo, RIKEN Center for Advanced Intelligence Project, Nantes University, National Institute of Informatics
* Fine-tuning LLMs to Extract Epilepsy Seizure Frequency Data from Health Records, Ben Holgate, Joe Davies, Shichao Fang, Joel S. Winston, James T. Teo, Mark P. Richardson, King's College London
* Transformer-Based Medical Statement Classification in Doctor-Patient Dialogues, Farnod Bahrololloomi, Johannes Luderschmidt, Biying Fu, RheinMain University of Applied Sciences
* PreClinIE: An Annotated Corpus for Information Extraction in Preclinical Studies, Simona Emilova Doneva, Hanna Hubarava, Pia Andrea Härvelid, Wolfgang Emanuel Zürrer, Julia V Bugajska, Bernard Friedrich Hild, David Brüschweiler, Gerold Schneider, Tilia Ellendorff, Benjamin Victor Ineichen, University of Zurich
* QoLAS: A Reddit Corpus of Health-Related Quality of Life Aspects of Mental Disorders, Lynn Greschner, Amelie Wührl, Roman Klinger, University of Bamberg, University of Stuttgart
* Gender-Neutral Large Language Models for Medical Applications: Reducing Bias in PubMed Abstracts, Elizabeth Schaefer and Kirk Roberts, Yale University, University of Texas Health Science Center at Houston
* LLMs as Medical Safety Judges: Evaluating Alignment with Human Annotation in Patient-Facing QA, Yella Leonie Diekmann, Chase M Fensore, Rodrigo M Carrillo-Larco, Eduard R Castejon Rosales, Sakshi Shiromani, Rima Pai, Megha Shah, Joyce C Ho, Emory University
* AdaBioBERT: Adaptive Token Sequence Learning for Biomedical Named Entity Recognition, Sumit Kumar and Tanmay Basu, Indian Institute of Science Education and Research Bhopal
* Enhancing Stress Detection on Social Media Through Multi-Modal Fusion of Text and Synthesized Visuals, Efstathia Soufleri and Sophia Ananiadou, Athena RC, University of Manchester
* MuCoS: Efficient Drug–Target Discovery via Multi-Context-Aware Sampling in Knowledge Graphs, Haji Gul, Abdul Ghani Naim, Ajaz Ahmad Bhat, UBD
* Enhancing Antimicrobial Drug Resistance Classification by Integrating Sequence-Based and Text-Based Representations, Hyunwoo Yoo, Bahrad Sokhansanj, James R Brown, Drexel University
* Effect of Multilingual and Domain-adapted Continual Pre-training on Few-shot Promptability, Ken Yano and Makoto Miwa, The National Institute of Advanced Industrial Science and Technology, Toyota Technological Institute
* Understanding the Impact of Confidence in Retrieval Augmented Generation: A Case Study in the Medical Domain, Shintaro Ozaki, Yuta Kato, Siyuan Feng, Masayo Tomita, Kazuki Hayashi, Wataru Hashimoto, Ryoma Obara, Masafumi Oyamada, Katsuhiko Hayashi, Hidetaka Kamigaito, Taro Watanabe, Nara Institute of Science and Technology, The University of Tokyo, NEC
* Prompting Large Language Models for Italian Clinical Reports: A Benchmark Study, Livia Lilli, Carlotta Masciocchi, Antonio Marchetti, Giovanni Arcuri, Stefano Patarnello, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Catholic University of the Sacred Heart, Rome, Italy
* CaseReportCollective: A Large-Scale LLM-Extracted Dataset for Structured Medical Case Reports, Xiao Yu Cindy Zhang, Melissa Fong, Wyeth Wasserman, Jian Zhu, University of British Columbia
* RadQA-DPO: A Radiology Question Answering System with Encoder-Decoder Models Enhanced by Direct Preference Optimization, Md Sultan Al Nahian and Ramakanth Kavuluru, University of Kentucky
* Benchmarking zero-shot biomedical relation triplet extraction across language model architectures, Frederik Steensgaard Gade, Ole Lund, Marie Lisandra Zepeda Mendoza, Technical University of Denmark, Novo Nordisk Research Centre Oxford
* Virtual CRISPR: Can LLMs Predict CRISPR Screen Results? Steven Song, Abdalla Abdrabou, Asmita Dabholkar, Kastan Day, Pavan Dharmoju, Jason Perera, Volodymyr Kindratenko, Aly A Khan, University of Chicago, Chan Zuckerberg Biohub Chicago, University of Illinois Urbana-Champaign, Northwestern University

===SUBMISSION INSTRUCTIONS===

Two types of submissions are invited: full (long) papers (8 pages) and short papers (4 pages).

<font size="4"> Submission site for the workshop https://softconf.com/acl2025/BioNLP2025 </font>
<font size="4"> Submission site for Shared Tasks https://softconf.com/acl2025/BioNLP2025-ST </font>

Please follow these formatting guidelines: https://github.com/acl-org/acl-style-files
Please note that the review process is double-blind.

Final versions of accepted papers will be given one additional page of content (up to 9 pages for long papers, up to 5 pages for short papers) to address reviewers’ comments.

==== Submissions from ACL rolling review ====
We will consider ACL rolling review submissions with all reviews and scores.
If you are interested in submitting your work for consideration, please contact ddemner at gmail.

===WORKSHOP OVERVIEW AND SCOPE===

The BioNLP workshop, associated with the ACL SIGBIOMED special interest group, is an established primary venue for presenting research in language processing and language understanding for the biological and medical domains. The workshop has been running every year since 2002 and continues getting stronger. Many other emerging biomedical and clinical language processing workshops can afford to be more specialized because BioNLP truly encompasses the breadth of the domain and brings together researchers in biomedical and clinical NLP from all over the world.

BioNLP 2025 will be particularly interested in evaluation frameworks and metrics that reflect the needs of health-related use cases and provide a good estimate of reliability of the proposed solutions. BioNLP 2025 continues to focus on transparency of tgenerative approaches and factuality of the generated text. Language processing that supports DEIA (Diversity, Equity, Inclusion
and Accessibility) continues to be of utmost importance. The work on detection and mitigation of bias and misinformation continues to be of interest. Research in languages other than English, particularly, under-represented languages, and health disparities
are always of interest to BioNLP. Other active areas of research include, but are not limited to:
<ul>
<li> Extraction of complex relations and events; </li>
<li> Discourse analysis; Anaphora \& coreference resolution; </li>
<li> Text mining \& Literature based discovery; </li>
<li> Question Answering; Summarization; Text simplification; </li>
<li> Resources and strategies for system testing and evaluation;</li>
<li> Synthetic data generation \& data augmentation; </li>
<li> Translating NLP research into practice: tangible explainable results of biomedical language
processing applications.</li>
</ul>

===SHARED TASKS===

====SMAFIRA====
The SMAFIRA project supports finding alternative methods to animal experiments. The organizers have released SMAFIRA Web tool that allows researchers to perform searches for methods alternative to animal experiments. The input to the tool is a PubMed identifier (PMID) of a publication that represents the animal experiment for which one wants to find an alternative method. The tool retrieves up to 200 similar articles available in PubMed, and presents these as a list of results. The task is to validate and annotate the top 10 similar articles, either automatically, with any system of the participants choice, or manually using the SMAFIRA tool. See details at https://smafira-bf3r.github.io/smafira-st/

====ClinIQLink 2025 - LLM Lie Detector Test====
The LLM Lie Detector Test aims to evaluate the effectiveness of generative models in producing factually accurate information, with a benchmark dataset specifically curated to align with the knowledge level of a General Practitioner (GP) Medical Doctor. Participants will submit model ouptputs to be assessed using a structured set of atomic question-answer pairs (factoid, true/false and list questions), which focus on retrieving precise, factually correct information. The test will evaluate internal model knowledge retrieval. See details at https://brandonio-c.github.io/ClinIQLink-2025/

====ArchEHR-QA 2025: Grounded Electronic Health Record Question Answering====

The participants will automatically generate answers to patients’ health-related questions that are grounded in the evidence from patients’ clinical notes. The dataset will consist of hand-curated realistic patient questions (submitted through a patient portal) and their corresponding clinician-rewritten versions (crafted to assist in formulating their responses). The task is to construct coherent answers or responses to input questions that must use and be grounded in the provided clinical note excerpts. See details at https://archehr-qa.github.io/

====BioLaySumm 2025====
This is the 3nd iteration of BioLaySumm, following the success of the 2nd edition of the task at BioNLP 2024 which attracted 200 plus submissions across 53 different teams and the 1st edition of the task at BioNLP 2023 which attracted 56 submissions across 20 different teams. This edition builds on last year’s task by introducing a new task: radiology report generation with layman’s terms, extending the shared task to a new domain and multi-modality. See detail at https://biolaysumm.org/

BioNLP 2025

2025-06-12T21:07:09Z

Dina: /* Sponsor */

BioNLP 2025

2025-06-12T18:57:52Z

Dina:

BioNLP 2025

2025-06-12T18:51:50Z

Dina:

SIGBIOMED

2025-06-01T21:17:52Z

Dina: /* Upcoming Events */

__NOTOC__

<h1>ACL Special Interest Group on Biomedical Natural Language Processing </h1>

<h4 style="width:85%;margin:0;background-color:#cedff2;font-size:120%;font-weight:bold;border:1px solid #a3b0bf;text-align:left;color:#000;padding:0.2em 0.4em;">Welcome to the home page for the Biomedical Natural Language Processing Special Interest Group of the Association for Computational Linguistics (ACL). This SIG is dedicated to language processing in the biological, biomedical, and clinical domain.

Biomedical language processing poses specific technical challenges that make it of interest to general NLP practitioners and make it of compelling importance to the larger field of biomedical informatics. The purpose of the BioMed SIG is to bring together researchers in NLP, bioinformatics, medical (clinical) informatics, and computational biology, providing a venue (both wiki and workshop) for the promotion and dissemination of original research in this area.</h4>



== Upcoming Events ==

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[BioNLP_Workshop|BioNLP 2025 Workshop and Shared Tasks]] at [https://2025.aclweb.org/ ACL], 1 August, 2025, Vienna, Austria </div>

The office terms for SIGBIOMED Chair, Secretary, and Vice Chair are expiring this year. <br>
These positions are elected by members, as described in the SIGBIOMED Constitution. <br>
Please send nominations (self-nominations are fine) by directly emailing any member of the nominating committee:

*Ben Holgate, King’s College London (benjamin.holgate kcl dot ac dot uk)
*Ayah Zirikly, Johns Hopkins University (ayah.zirikly gmail dot com)
*Steven Bethard, University of Arizona (bethard arizona dot edu)
*Steven Bedrick, Oregon Health & Science University (bedricks ohsu dot edu)
*Kirk Roberts, UTHealth Houston (kirk.roberts uth dot tmc dot edu)

Nominations are due June 6, 2025. Voting will begin the week after.

Note: Candidates must be ACL members in good standing. Also, both the candidate and nominator must be SIGBIOMED members in good standing. Functionally, this means simply being a member of the SIGBIOMED Google Group: https://groups.google.com/forum/#!forum/sigbiomed

== Past Events ==

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [https://bionlp.nlm.nih.gov/cl4health2025/ CL4Health 2025]. Patient-oriented language processing at [https://2025.naacl.org/ NAACL 2025], May Albuquerque, New Mexico </div>

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[BioNLP_2024|BioNLP 2024 Workshop and Shared Tasks]] at [https://2024.aclweb.org/ ACL], August 16, 2024, Bangkok, Thailand</div>

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [https://bionlp.nlm.nih.gov/cl4health2024/ CL4Health 2024]. Patient-oriented language processing at [https://lrec-coling-2024.org/ LREC-COLING], May 20, 2024, Turin, Italy </div>

[[File: CL4Health2024.jpg|150px|thumb|left|CL4Health 2024 in-person presentations]]

<p> Thanks to our special volunteer Ibai Guillén-Pacho, Universidad Politécnica de Madrid

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> PLAIN LANGUAGE ADAPTATION OF BIOMEDICAL ABSTRACTS [https://bionlp.nlm.nih.gov/plaba2023/ PLABA. @ TAC 2023] </div>

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> TRECVID Task on Medical Video Question Answering
[https://medvidqa.github.io/ MedVidQA 2023] </div>

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[BioNLP_2023|BioNLP 2023 Workshop and Shared Tasks]] at [https://2023.aclweb.org/ ACL], July 13, 2023, Toronto, Canada </div>









== Organization and Governance ==

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[SIGBioMed constitution|BioMed SIG Constitution ]]</div>
<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[SigBioMed_officers|Officers and Membership information]]</div>
<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[Sigbiomed_members|The SIGBioMed organizing committee and members]] </div>

== Workshop Proceedings ==
https://www.aclweb.org/anthology/venues/bionlp/
<ul>

<li style="text-align:left;margin-bottom:0.1em;">[https://aclanthology.org/volumes/2024.bionlp-1/ Proceedings of the 23rd Workshop on Biomedical Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://aclanthology.org/volumes/2023.bionlp-1/ Proceedings of the 22nd Workshop on Biomedical Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://aclanthology.org/volumes/2022.bionlp-1/ Proceedings of the 21st Workshop on Biomedical Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://aclanthology.org/volumes/2021.bionlp-1/ Proceedings of the 20th Workshop on Biomedical Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/2020.bionlp-1.pdf Proceedings of the 2020 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W19-50/ Proceedings of the 2019 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W18-23/ Proceedings of the 2018 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W17-23/ Proceedings of the 2017 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/W16-2900.pdf Proceedings of the 2016 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/W15-3800.pdf Proceedings of the 2015 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[http://acl2014.org/acl2014/W14-34/index.html Proceedings of the 2014 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W13-19/ Proceedings of the 2013 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W12-24/ Proceedings of the 2012 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/events/bionlp-2011/ Proceedings of the 2011 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W10-19/ Proceedings of the 2010 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/events/bionlp-2009/ Proceedings of the BioNLP 2009 Workshop]</li>
<li style="text-align:left;margin-bottom:0.1em;">[http://aclweb.org/anthology/W09-14 Proceedings of the BioNLP 2009 Workshop Companion Volume] BioNLP'09 shared task on Event Extraction</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://bmcbioinformatics.biomedcentral.com/articles/supplements/volume-9-supplement-11 Proceedings of the BioNLP 08 ACL Workshop: Themes in biomedical language processing.] BMC Bioinformatics supplement</li>
<li style="text-align:left;margin-bottom:0.1em;">[http://aclweb.org/anthology/W07-10 BioNLP 07.] Biological, translational, and clinical language processing</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W06-33/ HLT-NAACL BioNLP 06 Workshop on Linking Natural Language and Biology]</li>
<li style="text-align:left;margin-bottom:0.1em;">[http://aclweb.org/anthology/W05-13 ACL-ISMB 2005 Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W04-12/ International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA/BioNLP 04)]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W03-13/ ACL 2003 Workshop on Natural Language Processing in Biomedicine]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W02-03/ ACL-02 Workshop on Natural Language Processing in the Biomedical Domain]
</li></ul>

== Related Workshop Proceedings ==
<ul><li style="text-align:left;margin-bottom:0.1em;">[http://www.nactem.ac.uk/biotxtm2014/programme.php Fourth Workshop on Building and Evaluating Resources for Health and Biomedical Text Processing (BioTxtM 2014)]
</li></ul>

SIGBIOMED

2025-05-28T23:00:36Z

Dina: /* Upcoming Events */

__NOTOC__

<h1>ACL Special Interest Group on Biomedical Natural Language Processing </h1>

<h4 style="width:85%;margin:0;background-color:#cedff2;font-size:120%;font-weight:bold;border:1px solid #a3b0bf;text-align:left;color:#000;padding:0.2em 0.4em;">Welcome to the home page for the Biomedical Natural Language Processing Special Interest Group of the Association for Computational Linguistics (ACL). This SIG is dedicated to language processing in the biological, biomedical, and clinical domain.

Biomedical language processing poses specific technical challenges that make it of interest to general NLP practitioners and make it of compelling importance to the larger field of biomedical informatics. The purpose of the BioMed SIG is to bring together researchers in NLP, bioinformatics, medical (clinical) informatics, and computational biology, providing a venue (both wiki and workshop) for the promotion and dissemination of original research in this area.</h4>



== Upcoming Events ==

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[BioNLP_Workshop|BioNLP 2025 Workshop and Shared Tasks]] at [https://2025.aclweb.org/ ACL], July-August, 2025, Vienna, Austria </div>

The office terms for SIGBIOMED Chair, Secretary, and Vice Chair are expiring this year. <br>
These positions are elected by members, as described in the SIGBIOMED Constitution. <br>
Please send nominations (self-nominations are fine) by directly emailing any member of the nominating committee:

*Ben Holgate, King’s College London (benjamin.holgate kcl dot ac dot uk)
*Ayah Zirikly, Johns Hopkins University (ayah.zirikly gmail dot com)
*Steven Bethard, University of Arizona (bethard arizona dot edu)
*Steven Bedrick, Oregon Health & Science University (bedricks ohsu dot edu)
*Kirk Roberts, UTHealth Houston (kirk.roberts uth dot tmc dot edu)

Nominations are due June 6, 2025. Voting will begin the week after.

Note: Candidates must be ACL members in good standing. Also, both the candidate and nominator must be SIGBIOMED members in good standing. Functionally, this means simply being a member of the SIGBIOMED Google Group: https://groups.google.com/forum/#!forum/sigbiomed

== Past Events ==

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [https://bionlp.nlm.nih.gov/cl4health2025/ CL4Health 2025]. Patient-oriented language processing at [https://2025.naacl.org/ NAACL 2025], May Albuquerque, New Mexico </div>

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[BioNLP_2024|BioNLP 2024 Workshop and Shared Tasks]] at [https://2024.aclweb.org/ ACL], August 16, 2024, Bangkok, Thailand</div>

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [https://bionlp.nlm.nih.gov/cl4health2024/ CL4Health 2024]. Patient-oriented language processing at [https://lrec-coling-2024.org/ LREC-COLING], May 20, 2024, Turin, Italy </div>

[[File: CL4Health2024.jpg|150px|thumb|left|CL4Health 2024 in-person presentations]]

<p> Thanks to our special volunteer Ibai Guillén-Pacho, Universidad Politécnica de Madrid

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> PLAIN LANGUAGE ADAPTATION OF BIOMEDICAL ABSTRACTS [https://bionlp.nlm.nih.gov/plaba2023/ PLABA. @ TAC 2023] </div>

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> TRECVID Task on Medical Video Question Answering
[https://medvidqa.github.io/ MedVidQA 2023] </div>

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[BioNLP_2023|BioNLP 2023 Workshop and Shared Tasks]] at [https://2023.aclweb.org/ ACL], July 13, 2023, Toronto, Canada </div>









== Organization and Governance ==

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[SIGBioMed constitution|BioMed SIG Constitution ]]</div>
<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[SigBioMed_officers|Officers and Membership information]]</div>
<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[Sigbiomed_members|The SIGBioMed organizing committee and members]] </div>

== Workshop Proceedings ==
https://www.aclweb.org/anthology/venues/bionlp/
<ul>

<li style="text-align:left;margin-bottom:0.1em;">[https://aclanthology.org/volumes/2024.bionlp-1/ Proceedings of the 23rd Workshop on Biomedical Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://aclanthology.org/volumes/2023.bionlp-1/ Proceedings of the 22nd Workshop on Biomedical Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://aclanthology.org/volumes/2022.bionlp-1/ Proceedings of the 21st Workshop on Biomedical Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://aclanthology.org/volumes/2021.bionlp-1/ Proceedings of the 20th Workshop on Biomedical Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/2020.bionlp-1.pdf Proceedings of the 2020 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W19-50/ Proceedings of the 2019 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W18-23/ Proceedings of the 2018 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W17-23/ Proceedings of the 2017 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/W16-2900.pdf Proceedings of the 2016 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/W15-3800.pdf Proceedings of the 2015 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[http://acl2014.org/acl2014/W14-34/index.html Proceedings of the 2014 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W13-19/ Proceedings of the 2013 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W12-24/ Proceedings of the 2012 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/events/bionlp-2011/ Proceedings of the 2011 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W10-19/ Proceedings of the 2010 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/events/bionlp-2009/ Proceedings of the BioNLP 2009 Workshop]</li>
<li style="text-align:left;margin-bottom:0.1em;">[http://aclweb.org/anthology/W09-14 Proceedings of the BioNLP 2009 Workshop Companion Volume] BioNLP'09 shared task on Event Extraction</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://bmcbioinformatics.biomedcentral.com/articles/supplements/volume-9-supplement-11 Proceedings of the BioNLP 08 ACL Workshop: Themes in biomedical language processing.] BMC Bioinformatics supplement</li>
<li style="text-align:left;margin-bottom:0.1em;">[http://aclweb.org/anthology/W07-10 BioNLP 07.] Biological, translational, and clinical language processing</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W06-33/ HLT-NAACL BioNLP 06 Workshop on Linking Natural Language and Biology]</li>
<li style="text-align:left;margin-bottom:0.1em;">[http://aclweb.org/anthology/W05-13 ACL-ISMB 2005 Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W04-12/ International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA/BioNLP 04)]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W03-13/ ACL 2003 Workshop on Natural Language Processing in Biomedicine]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W02-03/ ACL-02 Workshop on Natural Language Processing in the Biomedical Domain]
</li></ul>

== Related Workshop Proceedings ==
<ul><li style="text-align:left;margin-bottom:0.1em;">[http://www.nactem.ac.uk/biotxtm2014/programme.php Fourth Workshop on Building and Evaluating Resources for Health and Biomedical Text Processing (BioTxtM 2014)]
</li></ul>

SIGBIOMED

2025-05-18T11:47:53Z

Dina:

__NOTOC__

<h1>ACL Special Interest Group on Biomedical Natural Language Processing </h1>

<h4 style="width:85%;margin:0;background-color:#cedff2;font-size:120%;font-weight:bold;border:1px solid #a3b0bf;text-align:left;color:#000;padding:0.2em 0.4em;">Welcome to the home page for the Biomedical Natural Language Processing Special Interest Group of the Association for Computational Linguistics (ACL). This SIG is dedicated to language processing in the biological, biomedical, and clinical domain.

Biomedical language processing poses specific technical challenges that make it of interest to general NLP practitioners and make it of compelling importance to the larger field of biomedical informatics. The purpose of the BioMed SIG is to bring together researchers in NLP, bioinformatics, medical (clinical) informatics, and computational biology, providing a venue (both wiki and workshop) for the promotion and dissemination of original research in this area.</h4>



== Upcoming Events ==

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[BioNLP_Workshop|BioNLP 2025 Workshop and Shared Tasks]] at [https://2025.aclweb.org/ ACL], July-August, 2025, Vienna, Austria </div>

== Past Events ==

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [https://bionlp.nlm.nih.gov/cl4health2025/ CL4Health 2025]. Patient-oriented language processing at [https://2025.naacl.org/ NAACL 2025], May Albuquerque, New Mexico </div>

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[BioNLP_2024|BioNLP 2024 Workshop and Shared Tasks]] at [https://2024.aclweb.org/ ACL], August 16, 2024, Bangkok, Thailand</div>

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [https://bionlp.nlm.nih.gov/cl4health2024/ CL4Health 2024]. Patient-oriented language processing at [https://lrec-coling-2024.org/ LREC-COLING], May 20, 2024, Turin, Italy </div>

[[File: CL4Health2024.jpg|150px|thumb|left|CL4Health 2024 in-person presentations]]

<p> Thanks to our special volunteer Ibai Guillén-Pacho, Universidad Politécnica de Madrid

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> PLAIN LANGUAGE ADAPTATION OF BIOMEDICAL ABSTRACTS [https://bionlp.nlm.nih.gov/plaba2023/ PLABA. @ TAC 2023] </div>

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> TRECVID Task on Medical Video Question Answering
[https://medvidqa.github.io/ MedVidQA 2023] </div>

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[BioNLP_2023|BioNLP 2023 Workshop and Shared Tasks]] at [https://2023.aclweb.org/ ACL], July 13, 2023, Toronto, Canada </div>









== Organization and Governance ==

<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[SIGBioMed constitution|BioMed SIG Constitution ]]</div>
<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[SigBioMed_officers|Officers and Membership information]]</div>
<div style="width:85%;margin:0;font-size:120%;text-align:left;"> [[Sigbiomed_members|The SIGBioMed organizing committee and members]] </div>

== Workshop Proceedings ==
https://www.aclweb.org/anthology/venues/bionlp/
<ul>

<li style="text-align:left;margin-bottom:0.1em;">[https://aclanthology.org/volumes/2024.bionlp-1/ Proceedings of the 23rd Workshop on Biomedical Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://aclanthology.org/volumes/2023.bionlp-1/ Proceedings of the 22nd Workshop on Biomedical Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://aclanthology.org/volumes/2022.bionlp-1/ Proceedings of the 21st Workshop on Biomedical Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://aclanthology.org/volumes/2021.bionlp-1/ Proceedings of the 20th Workshop on Biomedical Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/2020.bionlp-1.pdf Proceedings of the 2020 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W19-50/ Proceedings of the 2019 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W18-23/ Proceedings of the 2018 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W17-23/ Proceedings of the 2017 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/W16-2900.pdf Proceedings of the 2016 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/W15-3800.pdf Proceedings of the 2015 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[http://acl2014.org/acl2014/W14-34/index.html Proceedings of the 2014 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W13-19/ Proceedings of the 2013 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W12-24/ Proceedings of the 2012 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/events/bionlp-2011/ Proceedings of the 2011 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W10-19/ Proceedings of the 2010 Workshop on Biomedical Natural Language Processing]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/events/bionlp-2009/ Proceedings of the BioNLP 2009 Workshop]</li>
<li style="text-align:left;margin-bottom:0.1em;">[http://aclweb.org/anthology/W09-14 Proceedings of the BioNLP 2009 Workshop Companion Volume] BioNLP'09 shared task on Event Extraction</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://bmcbioinformatics.biomedcentral.com/articles/supplements/volume-9-supplement-11 Proceedings of the BioNLP 08 ACL Workshop: Themes in biomedical language processing.] BMC Bioinformatics supplement</li>
<li style="text-align:left;margin-bottom:0.1em;">[http://aclweb.org/anthology/W07-10 BioNLP 07.] Biological, translational, and clinical language processing</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W06-33/ HLT-NAACL BioNLP 06 Workshop on Linking Natural Language and Biology]</li>
<li style="text-align:left;margin-bottom:0.1em;">[http://aclweb.org/anthology/W05-13 ACL-ISMB 2005 Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W04-12/ International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (NLPBA/BioNLP 04)]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W03-13/ ACL 2003 Workshop on Natural Language Processing in Biomedicine]</li>
<li style="text-align:left;margin-bottom:0.1em;">[https://www.aclweb.org/anthology/volumes/W02-03/ ACL-02 Workshop on Natural Language Processing in the Biomedical Domain]
</li></ul>

== Related Workshop Proceedings ==
<ul><li style="text-align:left;margin-bottom:0.1em;">[http://www.nactem.ac.uk/biotxtm2014/programme.php Fourth Workshop on Building and Evaluating Resources for Health and Biomedical Text Processing (BioTxtM 2014)]
</li></ul>

BioNLP 2025

2025-05-05T14:16:12Z

Dina: /* Program Committee */

BioNLP 2025

2025-04-28T02:35:33Z

Dina: /* Program Committee */