BioNLP 2023

SIGBIOMED

BIONLP 2015 Call for Papers

Date of workshop: July 30, 2015

Venue: BioNLP 2015 will be held in conjunction with ACL 2015 in Beijing, People’s Republic of China.

IMPORTANT DATES

• 14 May 2015: Submission due date
• 4 June 2015: Notification of acceptance
• 21 June 2015: Camera-ready papers due
• 30 July 2015: Workshop, Beijing, PRC

Over the course of the past thirteen years, the ACL BioNLP workshop associated with the SIGBIOMED special interest group has established itself as the primary venue for presenting foundational research in language processing for the biological and medical domains. The workshop serves as both a venue for bringing together researchers in bio- and clinical NLP and exposing these researchers to the mainstream ACL research, and a venue for informing the mainstream ACL researchers about this fast-growing and important domain. The workshop will continue presenting work on a broad and interesting range of topics in NLP. Submissions are particularly solicited in the areas of:

• Wide-scale entity identification and normalization
• Extraction of complex relations and events
• Discourse analysis
• Coreference resolution
• Text mining
• Literature based discovery
• Summarization
• Question-answering
• Lexical and terminological resources for BioNLP
• Annotation (corpora), standards
• Resources and strategies for system testing and evaluation
• Processing and annotation platforms
• Interoperable platforms for biomedical text mining
• Domain adaptation
• Translating NLP research to practice

Submission instructions:

Long papers may consist of up to eight (8) pages of content, plus two pages for references; final versions of long papers will be given one additional page (up to 9 pages with 2 pages for references) so that reviewers’comments can be taken into account.

Poster submissions may consist of up to four (4) pages of content, plus 2 pages for references. Upon acceptance, short papers will be given five (5) pages in the proceedings and 2 pages for references. Authors are encouraged to use this additional page to address reviewers comments in their final versions.

https://www.softconf.com/acl2015/BioNLP/ Authors who cannot submit a PDF file electronically should contact the workshop organizers well in advance of the submission deadline. Dual submission policy: note that papers may NOT be submitted to the BioNLP 2014 workshop if they are or will be concurrently submitted to another meeting or publication. Submissions should be anonymous.

Program committee:

• Emilia Apostolova, DePaul University, Chicago, USA
• Eiji Aramaki, University of Tokyo
• Alan Aronson, National Library of Medicine
• Sabine Bergler, Concordia University, Canada
• Olivier Bodenreider, National Library of Medicine
• Aaron Cohen, Oregon Health and Science University
• Nigel Collier, EBI, the National Institute of Informatics
• Noémie Elhadad, Columbia University
• Marcelo Fiszman, National Library of Medicine
• Filip Ginter, University of Turku
• Cyril Grouin, LIMSI - CNRS, France
• Antonio Jimeno Yepes, IBM, Melbourne Area, Australia
• Halil Kilicoglu, National Library of Medicine
• Jin-Dong Kim, Database Center for Life Science, Japan
• Robert Leaman, National Library of Medicine
• Zhiyong Lu, National Library of Medicine
• Timothy Miller, Children's Hospital Boston
• Makoto Miwa, Toyota Technological Institute, Japan
• Aurelie Neveol, LIMSI - CNRS, France
• Naoaki Okazaki, Tohoku University
• Jong Park, KAIST
• Sampo Pyysalo, University of Turku
• Bastien Rance, Hopital Europeen Georges Pompidou
• Thomas Rindflesch, National Library of Medicine
• Kirk Roberts, National Library of Medicine
• Andrey Rzhetsky, University of Chicago
• Yoshimasa Tsuruoka, University of Tokyo, Japan
• Karin Verspoor, The University of Melbourne, Australia
• John Wilbur, National Library of Medicine
• Pierre Zweigenbaum, LIMSI - CNRS, France

Organizers

 * Kevin Bretonnel Cohen, University of Colorado School of Medicine
 * Dina Demner-Fushman, US National Library of Medicine
 * Sophia Ananiadou, National Centre for Text Mining and University of Manchester, UK
 * Jun-ichi Tsujii, Microsoft Research Asia

BIONLP 2014 Workshop Schedule

Registration is now open (scroll to 2-Day Workshops): ACL 2014 Registration

Thursday, June 26, 2014
9:00–9:10	Opening remarks
	Session 1: Processing biomedical publications
9:10–9:30	Natural Language Processing Methods for Enhancing Geographic Metadata for Phylogeography of Zoonotic Viruses Tasnia Tahsin, Robert Rivera, Rachel Beard, Rob Lauder, Davy Weissenbacher, Matthew Scotch, Garrick Wallstrom and Graciela Gonzalez
9:30–9:50	Temporal Expression Recognition for Cell Cycle Phase Concepts in Biomedical Literature Negacy Hailu, Natalya Panteleyeva and Kevin Cohen
9:50–10:10	Classifying Negative Findings in Biomedical Publications Bei Yu and Daniele Fanelli
10:10–10:30	Automated Disease Normalization with Low Rank Approximations Robert Leaman and Zhiyong Lu
10:30–11:00	Coffee Break
11:00–11:50	Keynote by Junichi Tsujii: BioNLP as the Pioneering field of linking text, knowledge and data
	Session 2: Processing consumer language
11:50–12:10	Decomposing Consumer Health Questions Kirk Roberts, Halil Kilicoglu, Marcelo Fiszman and Dina Demner-Fushman
12:10–12:30	Detecting Health Related Discussions in Everyday Telephone Conversations for Studying Medical Events in the Lives of Older Adults Golnar Sheikhshab, Izhak Shafran and Jeffrey Kaye
12:30–2:00	Lunch
	Session 3: Processing clinical text and gray literature
2:00–2:20	Coreference Resolution for Structured Drug Product Labels Halil Kilicoglu and Dina Demner-Fushman
2:20–2:40	Generating Patient Problem Lists from the ShARe Corpus using SNOMED CT/SNOMED CT CORE Problem List Danielle Mowery, Mindy Ross, Sumithra Velupillai, Stephane Meystre, Janyce Wiebe and Wendy Chapman
2:40–3:00	A System for Predicting ICD-10-PCS Codes from Electronic Health Records Michael Subotin and Anthony Davis
3:00–3:20	Structuring Operative Notes using Active Learning Kirk Roberts, Sanda Harabagiu and Michael Skinner
3:30-4:00	Afternoon Break
4:00–4:20	Chunking Clinical Text Containing Non-Canonical Language Aleksandar Savkov, John Carroll and Jackie Cassell
4:20–4:40	Decision Style in a Clinical Reasoning Corpus Limor Hochberg, Cecilia Ovesdotter Alm, Esa M. Rantanen, Caroline M. DeLong and Anne Haake
4:40-5:30	Poster session
	Temporal Expressions in Swedish Medical Text – A Pilot Study Sumithra Velupillai
	A repository of semantic types in the MIMIC II database clinical notes Richard Osborne, Alan Aronson and Kevin Cohen
	Extracting drug indications and adverse drug reactions from Spanish health social media Isabel Segura-Bedmar, Santiago de la Peña González and Paloma Martínez
	Symptom extraction issue Laure Martin, Delphine Battistelli and Thierry Charnois
	Seeking Informativeness in Literature Based Discovery Judita Preiss
	Towards Gene Recognition from Rare and Ambiguous Abbreviations using a Filtering Approach Matthias Hartung, Roman Klinger, Matthias Zwick and Philipp Cimiano
	FFTM: A Fuzzy Feature Transformation Method for Medical Documents Amir Karami and Aryya Gangopadhyay
Friday, June 27, 2014
	Session 1: NLP approaches for assessment of clinical conditions
9:00–9:40	Using statistical parsing to detect agrammatic aphasia Kathleen C. Fraser, Graeme Hirst, Jed A. Meltzer, Jennifer E. Mack and Cynthia K. Thompson Discussants: Thamar Solorio and Yang Liu
	Panel: Life cycles of BioCreative, BioNLP-ST, i2b2, TREC Medical tracks, and ShARe /CLEF/ SemEval
9:40-10:05	BioCreative by Lynette Hirschman and John Wilbur
10:05-10:30	BioNLP-ST by Sophia Ananiadou and Junichi Tsujii
10:30-11:00	Coffee Break
11:00-11:20	TREC Medical tracks by Ellen Voorhees
11:20-11:25	Introduction to the TAC 2014 Biomedical Summarization Track by Lucy Vanderwende
11:25-11:50	i2b2 by Ozlem Uzuner
11:50-12:10	ShARe/CLEF/SemEval by Danielle Mowery, Sumithra Velupillai and Sameer Pradhan
12:10-12:30	Discussion
12:30-2:00	Lunch
2:00-3:30	Tutorial by Olivier Bodenreider: UMLS in biomedical text processing
3:30-4:00	Afternoon Break
4:00-5:30	Tutorial by Alan R. Aronson: Using MetaMap

BIONLP 2014 Call for Papers

An ACL 2014 2-day Workshop associated with the SIGBIOMED special interest group Featuring a special track on NLP approaches for assessment of clinical conditions and a panel on shared tasks. Baltimore, MD, June 26-27, 2014

IMPORTANT DATES

• Submission deadline: Tuesday March 25, 2014, 11:59 PM Eastern US
• Notification of acceptance: Tuesday April 15, 2014
• Camera-ready copy due from authors: Friday April 25, 2014
• Workshop: Th - Fr June 26 - 27, 2014

WORKSHOP OVERVIEW AND SCOPE

Over the course of the past twelve years, the ACL BioNLP workshop associated with the SIGBIOMED special interest group has established itself as the primary venue for presenting foundational research in language processing for the biological and medical domains. The workshop serves as both a venue for bringing together researchers in bio- and clinical NLP and exposing these researchers to the mainstream ACL research, and a venue for informing the mainstream ACL researchers about the fast growing and important domain.

The workshop will continue presenting work on a broad and interesting range of topics in NLP.

We especially encourage submissions on:

- Entity identification and normalization
  for a broad range of semantic categories
- Species-independent gene normalization
- Extraction of complex relations
- Discourse analysis
- Anaphora resolution
- Coreference resolution
- Text mining
- Summarization
	-- Summarization/translation of clinical data for patients
- Question Answering

The special track invites contributions from researchers working in NLP approaches for the analysis of language samples to help in the assessment of clinical conditions. Topics of relevance to the special track:

• Development of linguistic resources in support of clinical applications research
• Identification of clinical markers using NLP techniques
• NLP techniques for assisting the development of intervention practices
• Opinion papers related to pursuing this cross-disciplinary research
• Automated approaches for the identification of clinical conditions from language samples

KEYNOTE SPEAKER

Jun-ichi Tsujii

PANEL ON SHARED TASKS

TBD

SUBMISSION INSTRUCTIONS

Two types of submissions are invited: full papers and short papers. Submissions are due by 11:59 PM EST on Tuesday March 25, 2014.

Full papers should not exceed eight (8) pages of text and one page of references. These are intended to be reports of original research. BioNLP aims to be the forum for interesting, innovative, and promising work involving biomedicine and language technology, whether or not yielding high performance at the moment. We particularly welcome reports on mature results, strong performance, and thorough evaluation. Both types of research and combinations thereof are encouraged.

Short papers should not exceed four (4) pages plus at most 2 pages for references. Accepted short papers will be published in a separate section of the workshop proceedings. Appropriate short paper topics include preliminary results, application notes, descriptions of work in progress, etc.

Electronic Submission: Submission must be electronic and in PDF format, using the Softconf submission software at

https://www.softconf.com/acl2014/BioNLP

Submissions should follow the two-column format of ACL 2014 proceedings. Please see the style files and formatting instructions at http://www.cs.jhu.edu/ACL2014/CallforPapers.htm

Submissions need to be anonymous. Authors who cannot submit a PDF file electronically should contact the workshop organizers well in advance of the submission deadline.

Dual submission policy: note that papers may NOT be submitted to the BioNLP 2014 workshop if they are or will be concurrently submitted to another meeting or publication.

 * Kevin Bretonnel Cohen, University of Colorado School of Medicine
 * Dina Demner-Fushman, US National Library of Medicine
 * Sophia Ananiadou, National Centre for Text Mining and University of Manchester, UK
 * John Pestian, Cincinnati Children's Hospital and Medical Center
 * Jun-ichi Tsujii, Microsoft Research Asia

Special track organizers:

 * Thamar Solorio, The University of Alabama at Birmingham 
 * Yang Liu, The University of Texas at Dallas