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LBM 2007 Last Call for Participation

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      :: LBM 2007 R E G I S T R A T I O N I S O P E N !
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Registration for LBM 2007 is still open. Please go to the LBM 2007 website at

http://lbm2007.biopathway.org

for details.

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      :: Important Dates
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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

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      :: Table of Contents
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1. LBM 2007 in Biopolis, Singapore
2. Welcome Message

3. LBM 2007 Program

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      :: 1. LBM 2007 in Biopolis, Singapore
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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.

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      :: 2. Welcome Message

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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

professionals.

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

papers.

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

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[1]

http://www.visitsingapore.com

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      :: 3. LBM 2007 Program
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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

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