Sponsored by: Department of Energy National Center for Human Genome Research (NIH) National Library of Medicine (NIH)
The Second International Conference on Intelligent Systems for Molecular Biology (ISMB) will take place at Stanford University, Palo Alto, California on August 14-17, 1994. The ISMB conference is intended to bring together scientists who are applying the technologies of advanced data modeling, machine learning, artificial intelligence, robotics, parallel computing, and other computational methods to problems in molecular biology. The scope extends to any computational or robotic system supporting a biological task that is cognitively challenging, involves a synthesis of information from multiple sources at multiple levels, or in some other way exhibits the abstraction and emergent properties of an "intelligent system." Last year's conference in Bethesda, MD attracted an overflow crowd, yielded a diverse offering of papers, invited speakers, posters and tutorials, provided an exciting opportunity for researchers to meet and exchange ideas, and was an important forum for the developing field. We are continuing the tradition of pre-published, rigorously refereed proceedings, and opportunities for fruitful personal interchange. The four-day conference will feature introductory and advanced tutorials (on August 14), and presentations of original refereed papers and invited talks (on August 15-17). A preliminary program is included in this document (see PRELIMINARY PROGRAM). More information can be gathered about
Russ Altman, Stanford University Doug Brutlag, Stanford University Peter Karp SRI Richard Lathrop Massachusetts Institute of Technology David Searls U. of Pennsylvania
Kiyoshi Asai Electrotechnical University Dennis Benson National Center for Biotechnology Information Soren Brunak The Technical University of Denmark Bruce Buchanan University of Pittsburgh Christian Burks Los Alamos National Laboratory Dominic Clark Imperial Cancer Research Fund Fred Cohen University of California, San Francisco Thomas G. Dietterich Oregon State University Stephanie Forrest University of New Mexico Janice Glasgow Queen's University Philip Green Washington University Michael Gribskov San Diego Supercomputer Center David Haussler University of California, Santa Cruz Steve Henikoff Frederick Hutchinson Cancer Research Center Lawrence Hunter National Library of Medicine Teri Klein University of California, San Francisco Alan Lapedes Los Alamos National Laboratory Michael Mavrovouniotis Northwestern University Gene Myers University of Arizona Katsumi Nitta Institute for New Generation Computer Technology Christopher Rawlings Imperial Cancer Research Fund Jean Sallantin Laboratoire D'Informatique de Robotique et de Microelectronique de Montpellier Chris Sander European Molecular Biology Laboratory Jude Shavlik University of Wisconsin David States Washington University Gary Stormo University of Colorado Ed Uberbacher Oak Ridge National Laboratory Michael Walker Stanford University Teresa Webster Stanford University Xiru Zhang Thinking Machines Incorporated
Full-length papers from both talks and posters will be published in archival proceedings. Copies will be distributed at the conference to registered attendees, and extra copies will be available for purchase from the publisher subsequently. The citation is:Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology (eds. R. Altman, D. Brutlag, P. Karp, R. Lathrop and D. Searls) AAAI Press, Menlo Park CA, 1994.
In addition to covering the cost of the proceedings, the registration fee covers refreshments and general program expenses.
Accommodations are available for the conference at the Governor's Corner
student housing facility on Stanford's Campus (corner of Santa Teresa St.
and Campus Drive West). The housing facility and dining room are a 10 to 15
minute walk from the main conference venue, Fairchild Auditorium. A special
combined room and board rate has been negotiated with the conference
center. By conference center policy, it is not possible for attendees to
make reservations for a room alone, without meals. The food provided at
Governor's Corner receives excellent reviews and is considered to be a
"deluxe" service. Room and board reservations must be made by July 19,
1994.
Note: The conference will last the entire day of Wednesday, August 17, and
so checkout from conference facilities is scheduled for the morning of
Thursday, August 18.
There are two packages available for out of town participants:
1A. Arrival on Saturday, August 13, with checkout on morning of
Thursday, August 18. Breakfast, lunch and dinner provided for August 14
through August 17.
Single occupancy packaged price is $455
Double occupancy packaged price is $392
1B. Arrival on Sunday, August 14, with checkout on morning of
Thursday, August 18. Breakfast, lunch and dinner provided for August 15
through August 17.
Single occupancy packaged price is $352
Double occupancy packaged price is $302
There are two lunch packages for participants who are commuting to the
conference. These will take place in Governor's corner facility, during
2A. Lunches on Sunday, August 14 through
Wednesday, August 17, (Price: $75)
2B. Lunches on Monday, August 15 through
Wednesday, August 17. (Price: $57)
Keynote Speaker, August 15, 1994: Bruce Buchanan University of Pittsburg Plenary Speaker, August 16, 1994: Lawrence Hunter National Library of Medicine Plenary Speaker, August 17, 1994: Richard Roberts New England BioLabs
ISMB-94 ANNOUNCES:
"Promising and Early"
SPECIAL OPEN POSTER SESSION
August 16, 1994
7:30 PM - 9:30 PM
Fairchild Auditorium
Stanford University
Stanford, CA
In addition to a poster session on the evening of August 15, for which
full length manuscripts will be included in the proceedings,
ISMB-94 will host a special open poster session on August 16 for informal
presentations of promising and early research in the area of complex
software systems for molecular biology applications. Appropriate posters
for this session would highlight creative approaches, novel problem
formulations, and interesting recent results; and should present
material that will be new to most of the audience.
The primary goal of the Conference is the high quality of its formal
presentations and published Proceedings. However, another major goal
is to foster productive professional interactions. This special
poster session is intended to bring researchers into informal contact
with each other and with the latest work in their area of interest.
The special poster session is unreviewed and open to all, but
participants must register in advance to ensure that space will be
available. Registration will be taken on a first-come first-served
basis, and will continue until all available slots are filled.
Space is limited, and early registration is encouraged.
To register for this special poster session, send email giving name,
contact information and an abstract to ISMB@camis.stanford.edu.
Conference registration material is included in this document.
Second International Conference on Intelligent Systems for Molecular Biology, Stanford University. **Preliminary** Program August 14: Tutorials August 15-17: Scientific Sessions. Monday, August 15 8:30 - 8:40 Welcome and Introduction of Speaker 8:35 - 9:30 Keynote Speaker: Bruce Buchanan, University of Pittsburgh 9:30 - 9:45 Break Session 1: Databases and Metabolism 09:45 - 10:15 Describing Multiple Levels of Abstraction in the Metabolism (Mavrovouniotis) 10:15 - 10:45 Representations of Metabolic Knowledge: Pathways (Karp and Paley) 10:45 - 11:15 Creating a Knowledge Base of Biological Research Papers (Hafner, Baclawski, Futrelle, Fridman, and Sampath) 11:15 - 11:45 Prototyping a Genetics Deductive Database (Hearne, Cui and Parsons) 11:45 - 1:00 Lunch Session 2: Sequence Analysis I 1:00 - 1:30 Sequence comparisons via algorithmic mutual information (Milosavljevic) 1:30 - 2:00 RNA Modeling Using Gibbs Sampling and Stochastic Context-Free Grammars (Grate, Herbster, Hughey, Mian, Noller and Haussler) 2:00 - 2:30 Neural Networks for Determining Protein Specificity and Multiple Alignment of Binding Sites (Heumann, Lapedes and Stormo) 2:30 - 2:45 Break Session 3: Gene Recognition and Prediction 2:45 - 3:15 An Improved System for Exon Recognition and Gene Modeling in Human DNA Sequences (Xu, Einstein, Mural, Shah and Uberbacher) 3:15 - 3:45 The prediction of internal exons by oligonucleotide composition and discriminant analysis of splicible open reading frames (Solovyev, Salamov and Lawrence) 3:45-4:00 Break Session 4: Protein Structure I 4:00 - 4:30 Geometric Problems in Molecular Biology and Robotics (Parsons and Canny) 4:30 - 5:00 Kinematic Manipulation of Molecular Chains Subject to Rigid Constraints (Manocha and Zhu) 5:00 - 5:30 Segmentation and Interpretation of 3D Protein Images (Leherte, Baxter, Glasgow and Fortier) 5:30 Dinner 7:30 Poster Session, Poster papers included in proceedings. -------------------------------------------------------------------------- Tuesday, August 16. 8:30 - 8:35 Introduction of Speaker 8:35 - 9:30 Plenary Address: Lawrence Hunter, National Library of Medicine 9:30- 9:45 Break Session 5: Protein Motifs 09:45 - 10:15 Fitting a mixture model by expectation maximization to discover motifs in biopolymers (Bailey and Elkan) 10:15 - 10:45 Stochastic Motif Extraction Using Hidden Markov Model (Fujiwara, Asogawa and Konagaya) 10:45 - 11:15 Visual-QUEST: A Visual Language for Querying Macromolecular Structural Databases (Cohen, Vadaparty, Dickinson and Salem) 11:15 - 11:45 A Generalized Profile Syntax for Biomolecular Sequence Motifs and its Function in Automatic Sequence Interpretation (Bucher and Bairoch) 11:45 - 1:00 Lunch 1:00 - 2:00 Panel Discussion Session 6: Sequence Analysis II 2:00 - 2:30 An Efficient Method for Multiple Sequence Alignment (Kim and Pramanik) 2:30 - 3:00 An Expert System for Processing Sequence Homology Data (Sonnhammer) 3:00 - 3:30 Induction of Rules for Biological Macromolecular Crystallization (Hennessy, Gopalakrishnan, Buchanan, Rosenberg and Subramanian) 3:30 - 3:45 Break Session 7: Protein Structure II 3:45 - 4:15 Predicting location and structure of beta-sheet regions using stochastic tree grammars (Mamitsuka and Abe) 4:15 - 4:45 Inductive Logic Programming used to Discover Topological Constraints in Protein Structures (King, Clark, Shirazi and Sternberg) 4:45 - 5:15 Finding an average core structure: Application to the globins (Altman and Gerstein) 5:30 Dinner 7:30 Open Poster Session, "Promising and Early" -------------------------------------------------------------------------- Wednesday, August 17 Session 8: Sequence Analysis III 8:30 - 9:00 Aligning Genomes with Inversions and Swaps (Holloway and Cull) 9:00 - 9:30 DNA Sequence Analysis using Hierarchical ART-based classification Networks (LeBlanc, Katholi, Unnasch and Hruska) 9:30 - 10:00 Repeat Pattern Toolkit (RPT): Analysis of the Structure and Evolution of the C. elegans Genome (Agarwal and States) 10:00 - 10:15 Break Session 9: Protein Structure III 10:15 - 10:45 Evolution of a Computer Program for Classifying Protein Segments as Transmembrane Domains Using Genetic Programming (Koza) 10:45 - 11:15 Discovering Side-chain correlations in alpha-helices (Klinger and Brutlag) 11:15 - 11:45 Constraint Satisfaction Techniques for Modeling Large Complexes: Application to Central Domain of the 16S Ribosomal Subunit (Altman, Weiser and Noller) 11:45 - 1:30 Lunch 1:30 - 1:35 Introduction of Speaker 1:35 - 2:30 Plenary Address: Richard Roberts, New England Biolabs Session 10: Mapping and Assembly 2:30 - 3:00 Genetic Map Construction with Constraints (Clark, Rawlings and Doursenot) 3:00 - 3:30 Using Interval Logic for Order Assembly (Cui) 3:30 - 4:00 A restriction mapping engine using constraint logic programming (Dix and Yee) 4:00 - 4:30 Integration of Competing Ancillary Assertions in Genome Assembly (Burks, Parsons and Engle) 4:30 - 4:35 Closing Comments. 5:30 Dinner Thursday morning check out from Stanford housing facility. ISMB-95 in Cambridge, England. Hosted by Imperial Cancer Research Fund.22 April 1994 / mbg@cb-iris.stanford.edu