News	(Last updated 15 May 2003)

Accepted papers. See below.

 

Workshop Description

(Last updated 25 Sep 2002)

Recent advances in experimental tools for computational genomics have led to sharp growth in data resources for bioinformatics problems such as modeling of gene expression and gene-protein interaction. This provides an interesting application domain for intelligent systems that learn graphical models from data for causal modeling, time series simulation and prediction, and classification and regression problems in computational life sciences.

In response, we propose a workshop to bring together researchers in intelligent systems who are interested in:

• probabilistic reasoning and learning with the primary focus of:
  • learning the structure of graphical models from data,
  • new graphical models such as types of dynamic Bayesian networks, stochastic and other approximation algorithms for inference,
  • structure learning;
• constraint-based knowledge representation;
• parameter estimation on graphical models and dynamical systems.

The emphasis would be on solutions for problems in:

• functional genomics, which includes:
  • modeling of gene regulatory dynamics,
  • data mining from DNA hybridization microarrays,
  • other gene modeling tools such as northern blots;
• building simulation models for metabolomics on:
  • biochemical pathways,
  • environmental stress-response,
  • cellular process regulation;
• proteomics, such as:
  • secondary and tertiary fold prediction
  • gene-protein interaction;
• other contemporary bioinformatics problems, such as:
  • intelligent systems for pharmacology,
  • plant science and crop simulation,
  • decision support systems for human and veterinary medicine,
  • phylogenetic modeling.

Workshop Audience

(Last updated 25 Sep 2002)

This workshop is intended for researchers and practitioners in the area of bioinformatics and uncertain reasoning using graphical models for computational genomics.

Researchers with an interest in machine learning, medical informatics, microbiology, biophysics, and knowledge discovery in databases (KDD) will also find this workshop of interest.

Workshop Agenda (Tentative)

(Last updated 15 May 2003)

8:30AM - 9:00AM	Reception
9:00AM - 9:45AM	Short tutorial on overview of current problems and solutions in computational genomics
9:45AM - 10:45AM	Paper Session I (2 full-length papers)
10:45AM - 11:00AM	[Short break] (15 minutes)
11:00AM - 11:30AM	Discussion Session I
11:30AM - 12:00PM	Paper Session II (1 full-length paper)
12:00PM - 1:00PM	====[Lunch break]====
1:00PM - 2:00PM	Paper Session III (2 full-length papers)
2:00PM - 2:30PM	Discussion Session II
2:30PM - 2:45PM	[Short break] (15 minutes)
2:45PM - 3:45PM	Paper Session IV (2 full-length papers)
3:45PM - 4:00PM	Discussion Session III
4:00PM - 4:45PM	Paper Session V (1 full-length paper and 1 short paper)
4:45PM - 5:00PM	[Short break] (15 minutes)
5:00PM - 5:15PM	Discussion Session IV
5:15PM - 5:30PM	Wrap-up discussion

 

Important Dates

(Last updated 25 Sep 2002)

Full Papers due:	Past due.
Short Papers due:	Past due.
Acceptance notification:	Past due.
Camera-ready copy due:	Fri 16 May 2003
Workshop	Sat 09 Aug 2003

Registration for the workshop through the Acapulco conferences is open to ALL attendees of IJCAI-2003.

To be invited to register, send e-mail to: ijcai-2003-bioinformatics@kddresearch.org containing a short (one-paragraph) statement of interests in the areas of bioinformatics and learning graphical models for computational genomics. Please state your current institutional affiliation as well.

Call for Papers and Submission Procedure

(Last updated 25 Sep 2002)

We encourage submissions containing original theoretical and applied concepts in artificial intelligence with applications to computational genomics, proteomics, and metabolomics. Experimental results are also encouraged, especially on fielded applications, even if they are only preliminary. We therefore invite two categories of paper submissions:

• research papers
• should not exceed 12 pages including title page
• due: N/A
• short summaries (including position papers)
• should not exceed 2 pages
• due: N/A

DUAL SUBMISSION POLICY: Submission of short (2-page OR 6-8 page) synopses of articles currently in preparation, under review, or accepted for publication as journals or book chapters is permitted. Submission of full-length papers currently under review for other conferences and workshops is also permitted. However, these papers shall be published in the working notes for this workshop if and only if they are compliant with the dual-submission guidelines of the other conference or workshop.

We request that authors prepare papers in the standard IJCAI format

The first page of submitted papers should include the title; a brief abstract; and author names, affiliations, postal addresses, electronic mail addresses, and telephone and fax numbers.

Papers should be submitted in PostScript, PDF, or Microsoft Word 97/2000/XP file format. Electronic submissions are preferred, but both types of papers may be submitted by one of the following three options:

• E-mail a URL pointer to the paper to ijcai-2003-bioinformatics@www.kddresearch.org
• Attach a PostScript, PDF, or Word file (or .zip, .gz, or .bz2 archive) to ijcai-2003-bioinformatics@www.kddresearch.org
• Mail 5 hard copies printed on 8.5" x 11" or A4 paper with at least 1 inch margins on all sides.

All submissions should be sent to ijcai-2003-bioinformatics@www.kddresearch.org

Note: If for any reason the e-mail address failed, please use the primary contact's e-mails instead. Thanks.

Invited Speakers and Disussion Panels

(Last updated 25 Sep 2002)

(To be determined)

Papers and Presentations

(Last updated 15 May 2003)

Accepted Papers:

• Chu, et. al., "A Statistical Problem for Inference to Regulatory Structure from Associations of Gene Expression Measurements with Microarrays"
• Danks, et. al., "Confirmation versus Search in Gene Regulation: The Complexity of Gene Pertubation Experimentation as a Search Method"
• Bay, et. al., "Temporal Aggregation Bias and Inference of Causal Regulatory Networks"
• Wimberly, et. al., "Experiments on the Accuracy of Algorithms for Inferring the Structure of Genetic Regulatory Networks from Microarray Expression Levels"
• Xing, "An Expressive Modular Probabilistic Model for de novo Motif Detection"
• Tamaddoni-Nezhad, Mugleton, Bang, "A Bayesian Model for Metabolic Pathways"
• Badea, "Inferring Large Gene Networks from Microarray Data: A Constraint-based Approach"
• Hsu, Joehanes, "Learning the Structure of Graphical Models of Gene Regulation from Microarray Data: Survey and Experiments"
• Banerjee, Zhang, "Analysis of Cooperativity Networks of Transcription Factors in S. Cerevisiae"

All accepted paper authors need to submit a camera-ready copy by 16 May 2003. Formatting instructions can be found here.

 

Program Committee (tentative)

(Last updated 30 Jan 2003)

• Peter Bajcsy, National Center for Supercomputing Applications (NCSA), University of Illinois at Urbana-Champaign (UIUC)
• Richard Bruskiewich, International Rice Research Institute (IRRI)
• Mark Craven, University of Wisconsin-Madison
• William H. Hsu, Kansas State University (KSU)
• Dan Geiger, Technion, Israel
• David Gilbert, University of Glasgow
• Haipeng Guo, Kansas State University
• Lei Liu, University of Illinois Urbana-Champaign (UIUC)
• Irene Ong, University of Wisconsin-Madison
• Jude Shavlik, University of Wisconsin-Madison
• Stephen M. Welch, Kansas State University (KSU)

Organizing Committee

(Last updated 27 Sep 2002)

William H. Hsu (primary contact)
Department of Computing and Information Sciences
Kansas State University
234 Nichols Hall
Manhattan, KS 66506-2302
t: (785) 532-6350 ext. 29
f: (785) 539-7180
e: bhsu-AT-cis.ksu.edu
w: http://www.cis.ksu.edu/~bhsu

Roby Joehanes (primary contact)
Department of Computing and Information Sciences
Kansas State University
234 Nichols Hall
Manhattan, KS 66506-2302
t: (785) 532-6350 ext. 55
f: (785) 537-9927
e: robbyjo-AT-cis.ksu.edu
w: http://www.cis.ksu.edu/~robbyjo

C. David Page, Jr.
Department of Biostatistics and Medical Informatics (Medical School) and Department of Computer Sciences
University of Wisconsin-Madison
Medical Science Center, Room 6743
1300 University Avenue
Madison, WI 53706
t: (608) 265-6168
f: (608) 263-0415
e: page-AT-biostat.wisc.edu
w: http://www.cs.wisc.edu/~dpage

Page created: 25 Sep 2002 Last updated 27 Oct 2002 Roby Joehanes