BioNLP Workshop

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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
9:10–9:30Natural 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
9:30–9:50Temporal Expression Recognition for Cell Cycle Phase Concepts in Biomedical Literature
Negacy Hailu, Natalya Panteleyeva and Kevin Cohen
9:50–10:10Classifying Negative Findings in Biomedical Publications
Bei Yu and Daniele Fanelli
10:10–10:30Automated Disease Normalization with Low Rank Approximations
Robert Leaman and Zhiyong Lu
10:30–11:00Coffee Break

Keynote by Junichi Tsujii: BioNLP as the Pioneering field of linking text, knowledge and data

 Session 2: Processing consumer language
11:50–12:10Decomposing Consumer Health Questions
Kirk Roberts, Halil Kilicoglu, Marcelo Fiszman and Dina Demner-Fushman
12:10–12:30Detecting Health Related Discussions in Everyday Telephone Conversations for Studying Medical Events in the Lives of Older Adults
Golnar Sheikhshab, Izhak Shafran and Jeffrey Kaye
 Session 3: Processing clinical text and gray literature
2:00–2:20Coreference Resolution for Structured Drug Product Labels
Halil Kilicoglu and Dina Demner-Fushman
2:20–2:40Generating 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
2:40–3:00A System for Predicting ICD-10-PCS Codes from Electronic Health Records
Michael Subotin and Anthony Davis
3:00–3:20Structuring Operative Notes using Active Learning
Kirk Roberts, Sanda Harabagiu and Michael Skinner
3:30-4:00Afternoon Break
4:00–4:20Chunking Clinical Text Containing Non-Canonical Language
Aleksandar Savkov, John Carroll and Jackie Cassell
4:20–4:40Decision Style in a Clinical Reasoning Corpus
Limor Hochberg, Cecilia Ovesdotter Alm, Esa M. Rantanen, Caroline M. DeLong and Anne Haake
4:40-5:30Poster 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
9:00–9:40Using 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
9:40-10:05BioCreative by Lynette Hirschman and John Wilbur
10:05-10:30BioNLP-ST by Sophia Ananiadou and Junichi Tsujii
10:30-11:00Coffee Break
11:00-11:20TREC Medical tracks by Ellen Voorhees
11:20-11:25Introduction to the TAC 2014 Biomedical Summarization Track by Lucy Vanderwende
11:25-11:50i2b2 by Ozlem Uzuner
11:50-12:10ShARe/CLEF/SemEval by Danielle Mowery, Sumithra Velupillai and Sameer Pradhan
2:00-3:30Tutorial by Olivier Bodenreider: UMLS in biomedical text processing
3:30-4:00Afternoon Break
4:00-5:30Tutorial 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


  • 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


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


Jun-ichi Tsujii




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

Submissions should follow the two-column format of ACL 2014 proceedings. Please see the style files and formatting instructions at

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