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2014 Workshop on Biomedical Natural Language Processing

WORKSHOP PROGRAM

Thursday, June 26, 2014

9:00–9:10Opening 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
11:00–11:50BioNLP 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
12:30–14:00Lunch
 Session 3: Processing clinical text and gray literature
14:00–14:20Coreference Resolution for Structured Drug Product Labels
Halil Kilicoglu and Dina Demner-Fushman
14:20–14:40Generating 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
14:40–15:00A System for Predicting ICD-10-PCS Codes from Electronic Health Records
Michael Subotin and Anthony Davis
15:00–15:20Structuring Operative Notes using Active Learning
Kirk Roberts, Sanda Harabagiu and Michael Skinner
15:30–16:00Afternoon Break
16:00–16:20Chunking Clinical Text Containing Non-Canonical Language
Aleksandar Savkov, John Carroll and Jackie Cassell
16:20–16:40Decision Style in a Clinical Reasoning Corpus
Limor Hochberg, Cecilia Ovesdotter Alm, Esa M. Rantanen, Caroline M. DeLong and Anne Haake
 (16:40–17:30) 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
9:00–9:40Using statistical parsing to detect agrammatic aphasia
Kathleen C. Fraser, Graeme Hirst, Jed A. Meltzer, Jennifer E. Mack and Cynthia K. Thompson
 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
11:00–11:25TREC Medical tracks by Ellen Voorhees
11:25–11:50i2b2 by Ozlem Uzuner
11:50–12:10ShARe/CLEF/SemEval by Danielle Mowery, Sumithra Velupillai and Sameer Pradhan
12:10–12:30Discussion
12:30–14:00Lunch
 Tutorials
14:00–15:30UMLS in biomedical text processing by Olivier Bodenreider
15:30–16:00Afternoon Break
16:00–17:30Using MetaMap by Alan R. Aronson