The Second International Conference on

Intelligent Systems for Molecular Biology

August 14-17, 1994
Stanford University
Stanford, California
Fairchild Auditorium

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 
  • TUTORIALS. The conference will be held at: Fairchild Auditorium Stanford University Medical Center Stanford, California Stanford is in the San Francisco Bay area, approximately 25 minutes south of San Francisco International Airport and approximately 25 minutes north of San Jose International Airport. Limited funds are available to support travel to ISMB-94 for students and post-docs, as well as for women and minority scientists. Applications are available by contacting or using the mailing address given below. ISMB-95 will be held in Cambridge, England and will be hosted by Drs. Dominic Clark and Chris Rawlings of the Imperial Cancer Research Fund.
  • Organizing Committee

    Russ Altman,            Stanford University
    Doug Brutlag,           Stanford University
    Peter Karp              SRI
    Richard Lathrop         Massachusetts Institute of Technology
    David Searls            U. of Pennsylvania

    Program Committee

    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.

    Housing and Meals

    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,
    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
    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
    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 
    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 
    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 
    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 
    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 /