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LINGUIST List 18.3507

Fri Nov 23 2007

Confs: Computational Linguistics/Singapore

Editor for this issue: Stephanie Morse <morselinguistlist.org>

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        1.    Jian Su, Languages in Biology and Medicine

Message 1: Languages in Biology and Medicine
Date: 23-Nov-2007
From: Jian Su <sujiani2r.a-star.edu.sg>
Subject: Languages in Biology and Medicine
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Languages in Biology and Medicine
Short Title: LBM 2007

Date: 06-Dec-2007 - 07-Dec-2007
Location: Singapore, Singapore
Contact: Jian Su
Contact Email: sujiani2r.a-star.edu.sg
Meeting URL: http://lbm2007.biopathway.org/

Linguistic Field(s): Computational Linguistics

Meeting Description:

The International Symposium on Languages in Biology and Medicine (LBM) 2007
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. We are
calling for original research papers on, but not limited to the topics listed
below. Papers focusing on application aspects of languages in biology and
medicine are also invited.

Natural language: text mining, retrieval and management;

Ontology language: ontology construction, extension and management;

Logic language: knowledge representation and induction;

Sequence language: RNA structure prediction, protein domain prediction;

Database language: database interface, query language;

Visualization language: information visualization, molecular visualization.

LBM 2007 Last Call for Participation

Registration is open!

Registration for LBM 2007 is still open. Please go to the LBM 2007 website at
http://lbm2007.biopathway.org 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

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.

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 orlook 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 (LBM 2007)
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

[1] http://www.visitsingapore.com

LBM 2007 Programme

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

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

Exploiting and integrating rich features for biological literature
Hongning Wang, Minlie Huang, Shilin Ding, Xiaoyan Zhu

The integration of multiple feature representations for protein-protein
interaction classification task
Man Lan and Chew Lim Tan

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

New challenges for text mining: Mapping between text and manually
curated pathways
Kanae Oda, Jin-Dong Kim, Tomoko Ohta, Yuka Tateisi, Jun'ichi Tsujii

A comparative analysis of five protein-protein interaction corpora
Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter ,Tapio

Syntactic features for protein-protein interaction extraction
Rune Saetre, Kenji Sagae and Jun'ichi Tsujii

Recognition of multisentence n-ary subcellular localization mentions
in biomedical abstracts
Gabor Melli, Martin Ester, Anoop Sarkar

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

Structuring an event ontology for disease outbreak detection
Ai Kawazoe, Hutchatai Chanlekha, Mika Shigematsu, Nigel Collier

Combining Gene Ontology and argumentative features for automatic
geneRIF extraction
Julien Gobeill, Patrick Ruch

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

Automatic construction of rule-based ICD-9-CM coding systems
Richard Farkas, Gyorgy Szarvas

Identification of transcription factor contexts in literature using machine
learning approaches
Hui Yang, Goran Nenadic

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

Closing address

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