Thursday, June 19, 2008 |
| 8:45–8:50 | Opening Remarks |
| | Session 1: Relations Extraction and Text Mining |
| 8:50–9:15 | A Graph Kernel for Protein-Protein Interaction Extraction
Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter and Tapio Salakoski |
| 9:15–9:40 | Extracting Clinical Relationships from Patient Narratives
Angus Roberts, Robert Gaizauskas and Mark Hepple |
| 9:40–10:05 | Using Automated Feature Optimisation to Create an Adaptable Relation Extraction System
Barry Haddow |
| 10:05–10:30 | Mining the Biomedical Literature for Genic Information
Catalina O Tudor, K Vijay-Shanker and Carl J Schmidt |
| 10:30–11:00 | Coffee break |
| 11:00–11:40 | Keynote I: John
Hutton, Enhancing the role of clinical decision support systems by
integrating computational linguistics: The needs of a large academic medical center. |
| | Session 2: Annotation Issues and Uncertainty Detection |
| 11:45–12:10 | Accelerating the Annotation of Sparse Named Entities by Dynamic Sentence Selection
Yoshimasa Tsuruoka, Jun’ichi Tsujii and Sophia Ananiadou |
| 12:10–12:35 | The BioScope corpus: annotation for negation, uncertainty and their scope in biomedical texts
György Szarvas, Veronika Vincze, Richárd Farkas and János Csirik |
| 12:35–13:00 | Recognizing Speculative Language in Biomedical Research Articles: A Linguistically Motivated Perspective
Halil Kilicoglu and Sabine Bergler |
| 13:00–14:00 | Lunch |
| | Session 3: Named Entity Recognition |
| 14:00–14:25 | Cascaded Classifiers for Confidence-Based Chemical Named Entity Recognition
Peter Corbett and Ann Copestake |
| 14:25–14:50 | How to Make the Most of NE Dictionaries in Statistical NER
Yutaka Sasaki, Yoshimasa Tsuruoka, John McNaught and Sophia Ananiadou |
| 14:50–15:30 | Keynote II: Hon Pak |
| 15:30–16:00 | Coffee break |
| | Session 4: Word Sense Disambiguation |
| 16:00–16:25 | Species Disambiguation for Biomedical Term Identification
Xinglong Wang and Michael Mattews |
| 16:25–16:50 | Knowledge Sources for Word Sense Disambiguation of Biomedical Text
Mark Stevenson, Yinkun Guo, Robert Gaizauskas and David Martinez |
| | 17:00–18:00 Poster Session |
| | Automatic inference of indexing rules for MEDLINE
Aurelie Neveol, Sonya Shooshan and Vincent Claveau |
| | Prediction of Protein Sub-cellular Localization using Information from Texts and Sequences.
Hong-Woo Chun, Chisato Yamasaki, Naomi Saichi, Masayuki Tanaka, Teruyoshi Hishiki, Tadashi Imanishi, Takashi Gojobori, Jin-Dong Kim, Jun’ichi Tsujii and Toshihisa Takagi |
| | A Pilot Annotation to Investigate Discourse Connectivity in Biomedical Text
Hong Yu, Nadya Frid, Susan McRoy, Rashmi Prasad, Alan Lee and Aravind Joshi |
| | Conditional Random Fields and Support Vector Machines for Disorder Named Entity Recognition in Clinical Texts
Dingcheng Li, Guergana Savova and Karin Kipper-Schuler |
| | Using Natural Language Processing to Classify Suicide Notes
John Pestian, Pawel Matykiewicz, Jacqueline Grupp-Phelan, Sarah Arszman Lavanier, Jennifer Combs and Robert Kowatch |
| | Extracting Protein-Protein Interaction based on Discriminative Training of the Hidden Vector State Model
Deyu Zhou and Yulan He |
| | A preliminary approach to extract drugs by combining UMLS resources and USAN naming conventions
Isabel Segura-Bedmar, Paloma Martínez and Doaa Samy |
| | Mapping Clinical Notes to Medical Terminologies at Point of Care
Yefeng Wang and Jon Patrick |
| | An Approach to Reducing Annotation Costs for BioNLP
Michael Bloodgood and K Vijay-Shanker |
| | Temporal Annotation of Clinical Text
Danielle Mowery, Henk Harkema and Wendy Chapman |
| | CBR-Tagger: a case-based reasoning approach to the gene/protein mention problem
Mariana Neves, Monica Chagoyen, José María Carazo and Alberto Pascual-Montano |
| | Textual Information for Predicting Functional Properties of the Genes
Oana Frunza and Diana Inkpen |
| | Determining causal and non-causal relationships in biomedical text by classifying verbs using a Naive Bayesian Classifier
Pieter van der Horn, Bart Bakker, Gijs Geleijnse, Jan Korst and Sergei Kurkin |
| | Statistical Term Profiling for Query Pattern Mining
Paul Buitelaar, Pinar Oezden Wennerberg and Sonja Zillner |
| | Using Language Models to Identify Language Impairment in Spanish-English Bilingual Children
Thamar Solorio and Yang Liu |
| | Raising the Compatibility of Heterogeneous Annotations: A Case Study on
Yue Wang, Kazuhiro Yoshida, Jin-Dong Kim, Rune Saetre and Jun’ichi Tsujii |
| | Adaptive Information Extraction for Complex Biomedical Tasks
Donghui Feng, Gully Burns and Eduard Hovy |
