The workshop on Knowledge, Language, and Learning in Bioinformatics (KLLBI)

in conjunction with

The Tenth Pacific Rim International Conference on Artificial Intelligence (PRICAI 2008)

December 15-19, 2008, Hanoi, Vietnam

 



THANK YOU!

The workshop has been successfully finished with attractive talks and fruitful discussions. If you couldn't participate in it, please enjoy the following movie clips.

KLLBI-talks
KLLBI-others
(reception, street, cafe, water puppet show, HUT campus, Van Mieu, museum of ethnology, dinner)

WORKSHOP DATE

December 16

ABOUT PRESENTATION

As you can see in the program below, a speaker of regular paper can use 30 minutes (25 for talk + 5 for Q&A). For invited talk, 60 minutes are available (55 minutes for talk + 5 for Q&A). Basically, only a digital projector is available. If you bring your laptop, you can use it for presentation. Otherwise, please bring your presentation file by USB stick. At least, the following laptop will be available (it's mine):
    OS: Windows Vista Basic (Japanese)
    Display: XGA
    Software: Adobe Reader, PowerPoint 2007, Word 2007, etc. (all Japanese version)
Currently I'm not sure whether English version of laptop will be available or not.

ACCEPTED  PAPERS

DisLex: a Transformation for Discontiguous Suffix Array Construction
Paul B. Horton, Szymon M. Kielbasa, and Martin C. Frith

Probabilistic Graphical Modeling for Large-scale Combinatorial Regulation of Transcription Factors
Sung-Joon Park, Natsuhiro Ichinose, and Tetsushi Yada

Predicting Protein Folding from Primary Structure Using Inductive Logic Programming
Tohgoroh Matsui, Hayato Ohwada, and Kazuyuki Kuchitsu

Combinatorial Effects of Histone Modifications and DNA Sequences on Nucleosome Dynamics
Ngoc Tu Le, Dang Hung Tran, and Tu Bao Ho

A Fast Algorithm for Genome Pairwise Alignment with Rearrangements
Thang N. Dinh, Huan X. Hoang, Le Sy Vinh

Biological Non-Commutativity Operating Paradigm In E. coli Metabolic Network
Dat H. Nguyen, Cuong Cao Dang

Limits of Maximum Likelihood Models for Protein Phylogenetics
Le Si Quang and Le Sy Vinh

WORKSHOP PROGRAM

10:00 Opening

10:00-12:00 Morning session


DisLex: a Transformation for Discontiguous Suffix Array Construction
Paul B. Horton, Szymon M. Kie lbasa, Martin C. Frith

A Fast Algorithm for Genome Pairwise Alignment with Rearrangements
Thang N. Dinh, Huan X. Hoang, Le Sy Vinh

Limits of Maximum Likelihood Models for Protein Phylogenetics
Le Si Quang, Le Sy Vinh

Predicting Protein Folding from Primary Structure Using Inductive Logic Programming
Tohgoroh Matsui, Hayato Ohwada, Kazuyuki Kuchitsu

12:00-14:00 Lunch break

14:00-15:00 Invited talk

Data Mining in Medicine
Hideto Yokoi, Katsuhiko Takabayashi, Takahiro Suzuki, Tu Bao Ho

15:00-15:30 Coffee break

15:30-17:00 Afternoon session

Biological Non-Commutativity Operating Paradigm In E. coli Metabolic Network
Dat H. Nguyen, Cuong Cao Dang

Probabilistic Graphical Modeling for Large-scale Combinatorial Regulation of Transcription Factors
Sung-Joon Park, Natsuhiro Ichinose, Tetsushi Yada

Combinatorial Effects of Histone Modifications and DNA Sequences on Nucleosome Dynamics
Ngoc Tu Le, Dang Hung Tran, Tu Bao Ho

17:00 Closing

PURPOSE and SCOPE

To handle the torrents of data yielded by high-throughput experiments like genome sequencing and gene expression measurement, today’s biologists are expanding their scientific capability by computer and internet. Huge amount of biological data are well-organized, stored, and searched at database sites. Due to the rich information stored in databases, statistical methods including machine learning and data mining are of increasing importance. In addition to such intelligent algorithms, text data and ontologies are strongly supporting today’s biologists. For instance, recent application software for gene expression analysis tends to combine statistical algorithms (clutering, PCA, etc.), concepts represented as ontologies (e.g. Gene Ontology), and text data from literature (PubMed, etc.) to help scientists data analysis and hypothesis verification. Because of this situation, the workshop aims to provide a forum for more detailed discussion on the following computational technologies (but not limited) applied to biological or medical data.

- Knowledge representation

- Knowledge management

- Knowledge discovery

- Data mining

- Text mining

- Text classification

- Natural language processing

- Ontology construction

- Ontology utilization

- Machine learning

 

SUBMISSION GUIDELINE

Format: Springer LNAI format (http://www.springer.com/computer/lncs?SGWID=0-164-7-72376-0)

Length: 10-15 pages

Submission: Please send your manuscript in PDF to the workshop organizer (ken@t.kanazawa-u.ac.jp) by the submission deadline.

 

IMPORTANT DATES

Submission deadline:    September 30

Notification of acceptance:    October 15  -> October 20

Camera ready deadline:    November 4

Workshop date: December 16

 

REVIEW

All papers submitted to this workshop will be reviewed by at least two reviewers. Acceptance will be based primarily on originality and contribution.

 

PUBLICATION

All the accepted *and* presented papers will be included in the proceedings available on-site during the workshop. To be included in the proceedings, at least one of the authors must confirm his/her attendance to the workshop and present the paper.  Authors of accepted papers must complete a confirmation form and submit it with the camera-ready version of the paper. Selected best papers will be published as the special issue of this workshop in Journal of Software (http://www.academypublisher.com/jsw/) after the extension so that they contain at least 30% of new material.

 

WORKSHOP ORGANIZERS

Kenji Satou (Kanazawa University, Japan)

Masanori Arita (The University of Tokyo, Japan)

 

PROGRAM COMMITTEE

Jose C. Clemente (NIG)

Ken-ichiro Fukuda (CBRC)

Susumu Goto (Kyoto University)

Paul Horton (CBRC)

Takeshi Nagashima (RIKEN) 

Tomoko Ohta (The University of Tokyo)

Tho Hoan Pham (Hanoi National University of Education) 

Nguyen Thanh Phuong (Microsoft)

Yuka Tateishi (Kogakuin Univeristy)

Tetsushi Yada (Kyoto University)

Yasunori Yamamoto (DBCLS) 

WORKSHOP WEBSITE

http://www.jaist.ac.jp/~ken/KLLBI/