| ACL 2007 CD | WORKSHOP ON CD | ACL 2007 ONLINE | ACL ONLINE |
WORKSHOP PROGRAM
Friday, June 29, 2007 | |
| 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 |
| 12:30–2:30 | Lunch |
| Keynote speech | |
| 2:30–3:25 | Keynote speaker |
| Interfaces and usability in BioNLP | |
| 3:25–3:45 | Exploring the Efficacy of Caption Search for Bioscience Journal Search Interfaces Marti Hearst, Anna Divoli, Ye Jerry and Michael Wooldridge |
| 3:45–4:15 | Coffee break |
| Information extraction in BioNLP | |
| 4:15–4:35 | ConText: An Algorithm for Identifying Contextual Features from Clinical Text Wendy Chapman, John Dowling and David Chu |
| 4:35–4:55 | BioNoculars: Extracting Protein-Protein Interactions from Biomedical Text Amgad Madkour, Kareem Darwish, Hany Hassan, Ahmed Hassan and Ossama Emam |
| Shared tasks in BioNLP | |
| 4:55–5:15 | 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 |
| 5:15–5:35 | 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 | |
| 5:35–7:00 | Poster session |
| 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 | |