ISMB-94 General and Registration Info

Doug Brutlag brutlag at
Thu Apr 14 21:20:43 EST 1994

General Announcement and Registration Information for the 

          Second International Conference on

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


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 including 
original papers will be distributed in early May.  Tutorials are 
described below.

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 ismb at or using the mailing
address given below. 

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

K. Asai                 ETL, Tsukuba
D. Benson               NCBI, Bethesda
B. Buchanan             U of Pittsburgh
C. Burks                LANL, Los Alamos
S, Brunak               DTN, Lyngby, Denmark
D. Clark                ICRF, London
F. Cohen                UCSF, San Francisco
T. Dietterich           OSU, Corvallis
S. Forrest              UNM, Albuquerque
J. Glasgow              Queen's U., Kingston
P. Green                Wash U, St. Louis
M. Gribskov             SDSC, San Diego
D. Haussler             UCSC, Santa Cruz
S. Henikoff             FHRC, Seattle
L. Hunter               NLM, Bethesda
T. Klein                UCSF, San Francisco
A. Lapedes              LANL, Los Alamos
M. Mavrovouniotis       Northwestern U
G. Michaels             George Mason U, Fairfax
G. Myers                U. Arizona, Tucson
K. Nitta                ICOT, Tokyo
C. Rawlings             ICRF, London
J. Sallatin             LIRM, Montpellier
C. Sander               EMBL, Heidelberg
J. Shavlik              U Wisconsin, Madison
D. States               Wash U, St. Louis
G. Stormo               U Colorado, Boulder
E. Uberbacher           ORNL, Oak Ridge
M. Walker               Stanford U, Stanford
T. Webster              Stanford U, Stanford
X. Zhang                PHZ Parnters, Cambridge

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. 


All tutorials will be offered on Sunday, August 14. There will be parallel
sessions geared for introductory issues and advanced issues. Tutorials
costs are $50 for a single tutorial and $70 for two tutorials.

AM Tutorials (August 14, 1994, 9:00 AM - 12:00 PM)

Introductory AM Tutorials:

                Dr. Douglas Brutlag (Stanford University)
                will provide an introduction to and overview of
                the methods of information science particularly
                relevant to molecular biology. These include
                multiple representations, machine learning, search
                and constraint methods, sequence analysis techniques,
                and pattern matching, with specific examples.

                Dr. Gary Stormo (University of Colorado, Boulder)
                will provide an introduction to and overview of
                the basic concepts of modern molecular biology
                particularly relevant to computational methods.
                These include the fundamentals of DNA, RNA and
                protein sequences, their structures and functions,
                concepts of homology and phylogenetic relationships,
                and basic cell biology and metabolism. In addition,
                information will be provided about experimental methods,   
                databases, and the genome project.

     Advanced AM Tutorials:

                Dr. Aleksandar Milosavljevic (Argonne National
                Laboratory) will introduce the minimal length
                encoding (MLE) method to computational biologists
                who are designing sequence analysis algorithms, to
                computer scientists who are in interested in learning
                more about macromolecular sequence analysis, and to
                biologists who are more advanced users of sequence
                analysis programs. The emphasis will be on the use of
                the MLE method as a tool for comparative analysis.

                BIOLOGY. Dr. Pierre Baldi (California Institute of         
                Technology) will provide an introduction to the basic
                machine learning methods often used in sequence analysis:
                including hidden markov models,  neural networks,
                the Bayesian framework and maximum likelihood estimation, 
                model fitting and model classes, learning and optimization 
                algorithms, and applications.  (This tutorial is the first
                of a two-part sequence with T9.  The cost for T4
                and T9 is $70.)

PM Tutorials (August 14, 1994, 1:30 PM to 4:30 PM)

    Introductory PM Tutorials:

                MOLECULAR BIOLOGY. Drs. Russ Altman (Stanford University)
                and Peter Karp (SRI) will provide a breadth first survey
                of important application areas within ISMB, and discuss
                outstanding accomplishments and challenges. Topics will    
                include biological databases, sequence analysis, protein  
                and nucleic acid structure prediction, signal to symbol    
                transformations, molecular evolution, metabolic pathways,  
                and machine learning. (T1 or T2 or equivalent recommended)

                Dr. David Bisant (Stanford University)
                will teach the basics of neural network models.
                The session will also highlight the application
                of neural networks to sequence analysis and other
                problems in molecular biology. The tutorial will start
                with the most basic concepts and proceed from there.

    Advanced PM Tutorials:

                Drs. Christopher Rawlings and Dominic Clark
                (Imperial Cancer Research Fund) will show how
                a wide variety of biological problems, especially those
                with very large hypothesis spaces, can be formulated
                as constraint satisfaction problems. They will discuss
                solution methods for constraint satisfaction
                problems using ideas (such as search, optimization and
                network consistency) from classical artificial
                intelligence as well as more recent developments
                from related disciplines.

                Dr. John Koza (Stanford University)
                will introduce the genetic algorithm, an
                increasingly popular approach to highly non-linear
                multidimensional optimization problems, that was
                originally inspired by a biological metaphor. This
                tutorial will cover both the biological motivations, and
                the actual implementation and characteristics of the
                algorithm. Genetic programming (an extension for
                problems in which the size and shape of the solution
                is a major part of the problem) will also be addressed.

        T9. HOW TO USE HIDDEN MARKOV MODELS, STOCHASTIC                    
                Dr. David Haussler (U.C. Santa Cruz)
                will provide a solid foundation in the use of hidden
                Markov and related statistical models, including theory
                and key algorithms, the time series model, stochastic
                graph grammars, segment models, practical issues and
                limitations, and detailed examples of biological   
                applications.  (This tutorial is the second of a two-part 
                sequence with T4.  The cost for T4 and T9 is $70.)


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)

Return Registration Form (with payment) to 

c/o Russ Altman
Section on Medical Informatics
Stanford, CA 94305-5479

For questions: ismb at
       or Fax: (415) 725-7944

************************************************************* ISMB-94


Affiliation: __________________________________________ 




Phone: ___________________ Fax: ____________________ 

Email: _____________________________________________ 

Status: ________ Student _______ Non-student
        ________ Male    _______ Female

_____  Check if you would like information about travel support.

>Registration (Early = before 7/15)......................$_______ 

                  Early      Late
Non-student       $100       $125
Student            $75       $100

>Tutorials (select one or two tutorials).................$_______ 

                   One     Two
Regular            $50     $70
Student            $25     $35

AM 8/14:
__ T1: Information Science for Molecular Biologists 
__ T2: Molecular Biology for Computer Scientists 
__ T3: Minimal Length Encoding in Molecular Biology 
__ T4: Machine Learning in Molecular Biology 

PM 8/14:
__ T5: Computational Challenges for ISMB 
__ T6: Neural Networks
__ T7: Constraint Satisfaction in Molecular Biology 
__ T8: Genetic Algorithms and Genetic Programming 
__ T9: Hidden Markov Models, SCFGs, and Related Models 

>Room/Board (see detailed descriptions)..................$_______ 

         Single Occupancy         Double Occupancy
___1A.    $455                 $392
___1B.    $352                 $302

___2A. Lunch only, 8/14-8/17 $75
___2B. Lunch only, 8/15-8/17 $57

>>Total (Check or money order $US made to ISMB-94)... ...$_______

Doug Brutlag                             (415) 723-6593
Department of Biochemistry               (415) 328-7837  FAX
Beckman Center, B400                     brutlag at
Stanford University School of Medicine                   
Stanford, California 94305-5307

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