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Priscilla Rasmussen <[log in to unmask]>
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Priscilla Rasmussen <[log in to unmask]>
Mon, 26 Nov 2007 15:03:11 -0500
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              LBM 2007 Last Call for Participation


     :: LBM 2007  R E G I S T R A T I O N   I S   O P E N !

Registration for LBM 2007 is still open.  Please go to the LBM 2007 website at for details.

     :: Important Dates

Hotel reservation deadline: November 15, 2007 (closed)
Early registration deadline: November 15, 2007 (closed)
On-site registration available
Panel Discussion: December 7, 2007
Banquet:    December 6, 2007
Symposium:    December 6-7, 2007

     :: Table of Contents

1. LBM 2007 in Biopolis, Singapore
2. Welcome Message
3. LBM 2007 Program

     :: 1. LBM 2007 in Biopolis, Singapore

The 2nd International Symposium on Languages in Biology and Medicine (LBM) 
will be held at Creation Theatrette, Matrix, Biopolis, Singapore, located near the 
Ministry of Education and on 30 Biopolis Street. The symposium banquet will take 
place at Made in China Museum, Haw Par Villa, on Thursday 6 December. The 
participants to LBM2007 are also welcome at the banquet for the International 
Conference on Genome Informatics (GIW), as well as for the conference itself, 
to be held on December 3-5 back-to-back with LBM 2007. 

     :: 2. Welcome Message

On behalf of the committees of the symposium, we would like to welcome you 
to Singapore, a world of unique contrasts!  Being a dynamic city rich in contrast 
and colour, you will find a harmonious blend of culture, cuisine, arts and 
architecture in Singapore.[1] 

Language is a powerful tool that in its many manifestations is a system, used for 
communication, comprising a finite set of arbitrary symbols and a set of rules 
(or grammar) by which the manipulation of these symbols is governed.  In biology 
and medicine, the importance of languages used to represent knowledge, 
communicate and query information is immense.  Likewise auxiliary tasks such 
as translation, summarization and information extraction play important roles 
supporting scientific research.  The automation of such tasks has significantly 
advanced knowledge discovery in biomedicine.

Incumbent technologies that discover, read and process language are continually 
stretched by the vigorous demands of bio-medical scientists and there is the continual 
need and incentive for language techniques to evolve.  Despite this, the distinct 
communities involved in language processing rarely borrow from one another or
look over the fence to see what other approaches are in use.  And yet synergistic 
interactions across methodological disciplines and across different topics are 
frequently the harbingers of revolutionary technologies.  In this context, it is imperative 
that we adopt diversification, more lateral and creative interaction between language 

The 2nd International Symposium on Languages in Biology and Medicine (LBM2007) 
seeks to provide a renewed opportunity for interaction between language professionals 
with different methodological backgrounds.  LBM was established in 2005 and the remit 
of this event remains highly relevant today.  The symposium focuses on the languages 
that are in active use for biology and medicine.  

The programme for LBM2007 comprises (a) 3 invited keynote lectures by Olivier 
Bodenreider, Sophia Ananiadou, and Patrick Lambrix; (b) a panel discussion chaired 
by Junichi Tsujii on emerging synergies of biomedical language and biomedical 
knowledge; and  (c) 5 sessions of oral presentations selected from 47 submitted 

We wish to express our deep appreciation for the programme committee members 
and the additional reviewers who have gone through the review process of all the submitted 
papers.  We also wish to express our gratitude to our supporting organizations: Institute 
for Infocom Research and Bioinformatics Institute, A*STAR; School of Computing and 
OLS Bioinformatics Programme, National University of Singapore; and  KAIST, Korea and 
BK21 Project, Korea.  Lastly, we look forward to seeing you again in Korea for LBM2009.  
Please stay tuned for forthcoming announcements on LBM2009. 

Rajaraman Kanagasabai
Local Organizing Chair

Christopher J. O. Baker and Su Jian
Programme Committee Chairs

Jong C. Park and Limsoon Wong
General Chairs

     :: 3. 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 
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
Lunch Break
Keynote 2 (Chaired by Su Jian)
Delivering text mining services for the biosciences
Sophia Ananiadou
Session 1B: Text Classification (I), chaired by Hongfang Liu
2:00-2:30 Exploiting and integrating rich features for biological literature 
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
Tea Break
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 
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
Keynote 3 (Chaired by Christopher Baker)
Aligning biomedical ontologies
Patrick Lambrix
Tea Break
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 
Bo Hu, Srinandan Dasmahapatra, David Robertson, Paul Lewis
Lunch Break
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
Tea Break
Panel Discussion Biomedical language and biomedical knowledge: Emerging synergies
Panel: Jun-ichi Tsujii (chair), Olivier Bodenreider, Sophia Ananiadou, Patrick Lambrix
Closing address

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