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BioNLP 2007

Friday, June 29, whole day

  Welcome and opening remarks
8:30–8:40 BioNLP 2007: Biological, translational, and clinical language processing
  Syntax in BioNLP
8:40–9:00 Syntactic complexity measures for detecting Mild Cognitive Impairment
Brian Roark, Margaret Mitchell and Kristy Hollingshead
9:00–9:20 Determining the Syntactic Structure of Medical Terms in Clinical Notes
Bridget McInnes, Ted Pedersen and Serguei Pakhomov
9:20–9:40 The Role of Roles in Classifying Annotated Biomedical Text
Son Doan, Ai Kawazoe and Nigel Collier
9:40–10:00 On the unification of syntactic annotations under the Stanford dependency scheme: A case study on BioInfer and GENIA
Sampo Pyysalo, Filip Ginter, Veronika Laippala, Katri Haverinen, Juho Heimonen and Tapio Salakoski
  Terminology and computational lexical semantics in BioNLP, Part I
10:00–10:20 An Unsupervised Method for Extracting Domain-specific Affixes in Biological Literature
Haibin Liu, Christian Blouin and Vlado Keselj
10:20–10:40 Combining multiple evidence for gene symbol disambiguation
Hua Xu, Jung-Wei Fan and Carol Friedman
10:45–11:15 Coffee break
  Terminology and computational lexical semantics in BioNLP, Part II
11:15–11:35 Mining a Lexicon of Technical Terms and Lay Equivalents
Noemie Elhadad and Komal Sutaria
11:35–11:55 Annotation of Chemical Named Entities
Peter Corbett, Colin Batchelor and Simone Teufel
11:55–12:15 Recognising Nested Named Entities in Biomedical Text
Beatrice Alex, Barry Haddow and Claire Grover
12:30–14:30 Lunch
14:30–15:25 Keynote speech
  Interfaces and usability in BioNLP
15:25–15:45 Exploring the Efficacy of Caption Search for Bioscience Journal Search Interfaces
Marti Hearst, Anna Divoli, Ye Jerry and Michael Wooldridge
15:45–16:15 Coffee break
  Information extraction in BioNLP
16:15–16:35 ConText: An Algorithm for Identifying Contextual Features from Clinical Text
Wendy Chapman, John Dowling and David Chu
16:35–16:55 BioNoculars: Extracting Protein-Protein Interactions from Biomedical Text
Amgad Madkour, Kareem Darwish, Hany Hassan, Ahmed Hassan and Ossama Emam
  Shared tasks in BioNLP
16:55–17:15 A shared task involving multi-label classification of clinical free text
John P. Pestian, Chris Brew, Pawel Matykiewicz, DJ Hovermale, Neil Johnson, K. Bretonnel Cohen and Wlodzislaw Duch
17:15–17:35 From indexing the biomedical literature to coding clinical text: experience with MTI and machine learning approaches
Alan R. Aronson, Olivier Bodenreider, Dina Demner-Fushman, Kin Wah Fung, Vivian K. Lee, James G. Mork, Aurelie Neveol, Lee Peters and Willie J. Rogers
  Poster session
17:35-19:00 Automatically Restructuring Practice Guidelines using the GEM DTD
Amanda Bouffier and Thierry Poibeau
A Study of Structured Clinical Abstracts and the Semantic Classification of Sentences
Grace Chung and Enrico Coiera
Automatic Code Assignment to Medical Text
Koby Crammer, Mark Dredze, Kuzman Ganchev, Partha Pratim Talukdar and Steven Carroll
Interpreting comparative constructions in biomedical text
Marcelo Fiszman, Dina Demner-Fushman, Francois M. Lang, Philip Goetz and Thomas C. Rindflesch
The Extraction of Enriched Protein-Protein Interactions from Biomedical Text
Barry Haddow and Michael Matthews
What's in a gene name? Automated refinement of gene name dictionaries
Jörg Hakenberg
Exploring the Use of NLP in the Disclosure of Electronic Patient Records
David Hardcastle and Catalina Hallett
BaseNPs that contain gene names: domain specificity and genericity
Ian Lewin
Challenges for extracting biomedical knowledge from full text
Tara McIntosh and James R. Curran
Adaptation of POS Tagging for Multiple BioMedical Domains
John E. Miller, Manabu Torii and K. Vijay-Shanker
Information Extraction from Patients' Free Form Documentation
Agnieszka Mykowiecka and Malgorzata Marciniak
Automatic Indexing of Specialized Documents: Using Generic vs. Domain-Specific Document Representations
Aurelie Neveol, James G. Mork and Alan R. Aronson
Developing Feature Types for Classifying Clinical Notes
Jon Patrick, Yitao Zhang and Yefeng Wang
Quantitative Data on Referring Expressions in Biomedical Abstracts
Michael Poprat and Udo Hahn
Discovering contradicting protein-protein interactions in text
Olivia Sanchez and Massimo Poesio
Marking time in developmental biology
Gail Sinclair and Bonnie Webber
Evaluating and combining and biomedical named entity recognition systems
Andreas Vlachos
Unsupervised Learning of the Morpho-Semantic Relationship in MEDLINE
W. John Wilbur
Reranking for Biomedical Named-Entity Recognition
Kazuhiro Yoshida and Jun'ichi Tsujii

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