LBM 2007 program

Thursday, 6 Dec 2007

9:00 – 9:15 Welcome address
9:15 –10:15	Keynote 1 (Chaired by Jong C. Park) Terminological systems in biomedicine: From terminology integration to information integration Olivier Bodenreider
10:15 – 10:45 Tea Break
10:45 – 12:15 Session 1A: Terminology and Named Entity, chaired by Nigel Collier
10:45 – 11:15	Normalizing biomedical terms by minimizing ambiguity and variability Yoshimasa Tsuruoka, John McNaught, Sophia Ananiadou
11:15 – 11:45	Assessment of diseases named entity recognition on a corpus of annotated sentences Antonio Jimeno, Ernesto Jimenez-Ruiz, Vivian Lee, Sylvain Gaudan, Rafael Berlanga-Llavori, Dietrich Rebholz-Schuhmann
11:45-12:00	Analysis and enhancement of conditional random fields gene mention taggers in BioCreative II Challenge Evaluation Yu-Ming Chang, Cheng-Ju Kuo, Han-Shen Huang, Yu-Shi Lin, Chun-Nan Hsu
12:00-1:00 Lunch Break
1:00-2:00	Keynote 2 (Chaired by Su Jian) Delivering text mining services for the biosciences Sophia Ananiadou
2:00-3:00 Session 1B: Text Classification (I), chaired by Hongfang Liu
2:00-2:30	Exploiting and integrating rich features for biological literature classification Hongning Wang, Minlie Huang, Shilin Ding, Xiaoyan Zhu
2:30-2:45	The integration of multiple feature representations for protein-protein interaction classification task Man Lan and Chew Lim Tan
2:45-3:00	Protein-protein interaction abstract identification with contextual bag of words Richard Tzong-Han Tsai, Hsieh-Chuan Hung, Hong-Jie Dai and Yi-Wen Lin
3:00-3:30 Tea Break
3:30-5:00 Session 1C: Text Mining, chaired by Dietrich Rebholz-Schuhmann
3:30-4:00	New challenges for text mining: Mapping between text and manually curated pathways Kanae Oda, Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii
4:00-4:30	A comparative analysis of five protein-protein interaction corpora Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter ,Tapio Salakoski
4:30-4:45	Syntactic features for protein-protein interaction extraction Rune Saetre, Kenji Sagae and Jun'ichi Tsujii
4:45-5:00	Recognition of multisentence n-ary subcellular localization mentions in biomedical abstracts Gabor Melli, Martin Ester, Anoop Sarkar
19:00-10:00 Conference Banquet @ Made In China Museum, Haw Par Villa Bus leaves from Biopolis to Haw Par Villa at 5:20 pm. Delegates are invited to tour the museum before banquet

Friday, 7 Dec 2007

9:00-10:00	Keynote 3 (Chaired by Christopher Baker) Aligning biomedical ontologies Patrick Lambrix
10:00-10:30 Tea Break
10:30-12:15 Session 2A: Ontologies and Logic, chaired by Mark Schreiber
10:30-11:00	Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability Jong C. Park, Tak-eun Kim, Jinah Park
11:00-11:30	Structuring an event ontology for disease outbreak detection Ai Kawazoe, Hutchatai Chanlekha, Mika Shigematsu, Nigel Collier
11:30-12:00	Combining Gene Ontology and argumentative features for automatic geneRIF extraction Julien Gobeill, Patrick Ruch
12:00-12:15	Decentralised clinical guidelines modelling with lightweight coordination calculus Bo Hu, Srinandan Dasmahapatra, David Robertson, Paul Lewis
12:15-1:30 Lunch Break
1:30-2:45 Session 2B: Text Classification (II), chaired by Minlie Huang
1:30-2:00	Automatic construction of rule-based ICD-9-CM coding systems Richard Farkas, Gyorgy Szarvas
2:00-2:30	Identification of transcription factor contexts in literature using machine learning approaches Hui Yang, Goran Nenadic
2:30-2:45	Classifier ensemble for biomedical document retrieval Manabu Torii, Hongfang Liu
2:45-3:30 Tea Break
3:30-5:00 Panel Discussion	Biomedical language and biomedical knowledge: Emerging synergies Panel: Jun-ichi Tsujii (chair), Olivier Bodenreider, Sophia Ananiadou, Patrick Lambrix
5:00-5:15 Closing address

* Papers for LBM BMC special issue  and long oral presentations are in black.  Short oral presentations are in blue.