From: shavlik@cs.wisc.edu (Jude Shavlik)
Subject: Program & Reg Forms: 1st Int Conf on Intell Sys for Molecular Biology
Keywords: computational biology, artificial intelligence
Organization: U of Wisconsin CS Dept
Lines: 482

[For those attending the AAAI conf this summer, note that
this conference is immediately preceding it.]


         PRELIMINARY PROGRAM AND REGISTRATION MATERIALS

              First International Conference on
          Intelligent Systems for Molecular Biology

                       Washington, D.C.
                        July 6-9, 1993

Sponsored by:
  The National Institutes of Health, 
     National Library of Medicine

  The Department of Energy, 
     Office of Health and Environmental Research

  The Biomatrix Society

  The American Association for Artificial Intelligence (AAAI)

Poster Session and Tutorials:  
  Bethesda Ramada Hotel

Technical Sessions:
  Lister Hill Center Auditorium, National Library of Medicine

For more information contact ISMB@nlm.nih.gov or FAX (608)262-9777

                           PURPOSE
This, the First International Conference on Intelligent Systems 
for Molecular Biology, is the inaugural meeting in a series 
intended to bring together scientists who are applying the 
technologies of artificial intelligence, robotics, machine 
learning, massively parallel computing, advanced data modelling, 
and related 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."  

                          FACILITIES
The conference will be held at
   Lister Hill Center 
   National Library of Medicine
   8600 Rockville Pike
   NIH, Building 38A
   Bethesda MD 20894
Seating in the conference center is strictly limited, so 
registrations will be accepted on a first-come, first-serve basis. 
Accomodations, as well as a reception and poster session, will be 
at the
   Bethesda Ramada Hotel 
   8400 Wisconsin Avenue
   Bethesda MD 20814
A special room rate has been negotiated with the hotel, of $92/day 
(expires 6/21).  Attendees must make their own reservations, by 
writing the hotel or calling (800)331-5252 and mentioning the 
ISMB conference.  To participate in a roommate-matching service, 
e-mail opitz@cs.wisc.edu.

                         TRANSPORTATION
The two facilities are within easy walking distance, convenient to 
the subway (Metro Red Line, Medical Center stop), and from there 
to the Amtrak station.  Nearby airports include Dulles, National, 
and Baltimore-Washington International. 

                           PROCEEDINGS
Full-length papers from both talks and posters will be published in
archival proceedings.  The citation is: 

  Proceedings of the First International 
  Conference on Intelligent Systems for 
  Molecular Biology (eds. L. Hunter, 
  D. Searls, and J. Shavlik) AAAI/MIT
  Press, Menlo Park CA, 1993.  

Copies will be distributed at the conference to registered 
attendees, and will be available for purchase from the publisher 
afterwards.

                             TALKS
Wednesday, July 7, 1993
-----------------------------------------------------------------
8:00-9:00am     Continental Breakfast

9:00-9:15am     Opening Remarks

9:15-10:30am    Invited Talk
 "Statistics, Protein Cores, and Predicted Structures"
 Prof. Temple Smith (Boston University)

10:30-11:00am	Break

11:00am	"Constructive Induction and Protein Structure Prediction"
 T.R. Ioerger, L. Rendell, & S. Surbramaniam

11:30am	"Protein Secondary-Structure Modeling with Probabilistic 
 Networks"  A.L. Delcher, S. Kasif, H.R. Goldberg, & W. Hsu

12:00-1:30pm	Lunch

1:30pm	"Protein Secondary Structure using Two-Level Case-Based 
 Reasoning"  B. Leng, B.G. Buchanan, & H.B. Nicholas

2:00pm 	"Automatic Derivation of Substructures Yields Novel 
 Structural Building Blocks in Globular Proteins" 
 X. Zhang, J.S. Fetrow, W.A. Rennie, D.L. Waltz, & G. Berg

2:30pm 	"Using Dirichlet Mixture Priors to Derive Hidden Markov 
 Models for Protein Families" M. Brown, R. Hughey, A. Krogh, 
 I.S. Mian, K. Sjolander, & D. Haussler

3:00-3:30pm	Break

3:30pm	"Protein Classification using Neural Networks" 
 E.A. Ferran, B. Pflugfelder, & P. Ferrara

4:00pm	"Neural Networks for Molecular Sequence Classification"
 C. Wu, M. Berry, Y-S. Fung, & J. McLarty

4:30pm	"Computationally Efficient Cluster Representation in 
 Molecular Sequence Megaclassification"  D.J. States, N. Harris, 
 & L. Hunter

7:00-7:30pm     Poster Setup
7:30-10:00pm    Reception & Poster Session 

Thursday, July 8, 1993
-----------------------------------------------------------------
8:00-9:00am     Continental Breakfast

9:00-10:15am    Invited Talk
 "Large-Scale DNA Sequencing:  A Tale of Mice and Men"
 Prof. Leroy Hood (University of Washington)

10:15-10:45am	Break

10:45am	"Pattern Recognition for Automated DNA Sequencing: 
 I. On-Line Signal Conditioning and Feature Extraction for 
 Basecalling"  J.B. Bolden III, D. Torgersen, & C. Tibbetts

11:15am	"Genetic Algorithms for Sequence Assembly" 
 R. Parsons, S. Forrest, & C. Burks

11:45am	"A Partial Digest Approach to Restriction Site Mapping"
 S.S. Skiena & G. Sundaram

12:15-2:00pm	Lunch

2:00pm	"Integrating Order and Distance Relationships from 
 Heterogeneous Maps"  M. Graves 

2:30pm	"Discovering Sequence Similarity by the Algorithmic 
 Significance Method"  A. Milosavljevic

3:00pm	"Identification of Human Gene Functional Regions Based on 
 Oligonucleotide Composition"  V.V. Solovyev & C.B. Lawrence

3:30pm	"Knowledge Discovery in GENBANK"
 J.S. Aaronson, J. Haas, & G.C. Overton

4:00-4:30pm	Break

4:30pm	"An Expert System to Generate Machine Learning 
 Experiments: Learning with DNA Crystallography Data"
 D. Cohen, C. Kulikowski, & H. Berman 

5:00pm 	"Detection of Correlations in tRNA Sequences with 
 Structural Implications"  T.M. Klingler & D. Brutlag

5:30pm	"Probabilistic Structure Calculations: A Three-
 Dimensional tRNA Structure from Sequence Correlation Data" 
 R.B. Altman

Friday, July 9, 1993
-----------------------------------------------------------------
8:00-9:00am     Continental Breakfast

9:00-10:15am    Invited Talk
 "Artificial Intelligence and a Grand Unified Theory of 
 Biochemistry" Prof. Harold Morowitz (George Mason University)

10:15-10:45am	Break

10:45am	"Testing HIV Molecular Biology in in silico Physiologies" 
 H.B. Sieburg & C. Baray

11:15am	"Identification of Localized and Distributed Bottlenecks 
 in Metabolic Pathways"  M.L. Mavrovouniotis

11:45am	"Fine-Grain Databases for Pattern Discovery in Gene 
 Regulation"  S.M. Veretnik & B.R. Schatz

12:15-2:00pm	Lunch

2:00pm	"Representation for Discovery of Protein Motifs"
 D. Conklin, S. Fortier, & J. Glasgow

2:30pm	"Finding Relevant Biomolecular Features"  
 L. Hunter & T. Klein

3:00pm	"Database Techniques for Biological Materials and 
 Methods"  K. Baclawski, R. Futrelle, N. Fridman, 
 & M.J. Pescitelli

3:30pm	"A Multi-Level Description Scheme of Protein 
 Conformation"  K. Onizuka, K. Asai, M. Ishikawa, & S.T.C. Wong

4:00-4:30pm	Break

4:30pm	"Protein Topology Prediction through Parallel Constraint 
 Logic Programming"  D.A. Clark, C.J. Rawlings, J. Shirazi, 
 A. Veron, & M. Reeve

5:30pm	"A Constraint Reasoning System for Automating Sequence-
 Specific Resonance Assignments in Multidimensional Protein
 NMR Spectra"  D. Zimmerman, C. Kulikowski, & G.T. Montelione

5:30-5:45pm	Closing Remarks

                         POSTER SESSION
The following posters will be on display at the Bethesda Ramada 
Hotel from 7:30-10:00pm, Wednesday, July 7.

[1] "The Induction of Rules for Predicting Chemical
 Carcinogenesis in Rodents"  D. Bahler & D. Bristol

[2] "SENEX: A CLOS/CLIM Application for Molecular Pathology"  
 S.S. Ball & V.H. Mah

[3] "FLASH: A Fast Look-Up Algorithm for String Homology"
 A. Califano & I. Rigoutsos

[4] "Toward Multi-Strategy Parallel Learning in Sequence 
 Analysis"  P.K. Chan & S.J. Stolfo

[5] "Protein Structure Prediction: Selecting Salient Features 
 from Large Candidate Pools"  K.J. Cherkauer & J.W. Shavlik

[6] "Comparison of Two Approaches to the Prediction of Protein 
 Folding Patterns"  I. Dubchak, S.R. Holbrook, & S.-H. Kim

[7] "A Modular Learning Environment for Protein Modeling"
 J. Gracy, L. Chiche & J. Sallantin

[8] "Inference of Order in Genetic Systems" 
 J.N. Guidi & T.H. Roderick

[9] "PALM - A Pattern Language for Molecular Biology"
 C. Helgesen & P.R. Sibbald

[10] "Grammatical Formalization of Metabolic Processes"  
 R. Hofestedt

[11] "Representations of Metabolic Knowledge"  
 P.D. Karp & M. Riley

[12] "Protein Sequencing Experiment Planning Using Analogy"
 B. Kettler & L. Darden

[13] "Design of an Object-Oriented Database for Reverse Genetics"  
 K.J. Kochut, J. Arnold, J.A. Miller, & W.D. Potter

[14] "A Small Automaton for Word Recognition in DNA Sequences"
 C. Lefevre & J.-E Ikeda

[15] "MultiMap:  An Expert System for Automated Genetic Linkage 
 Mapping"  T.C. Matise, M. Perlin & A. Chakravarti

[16] "Constructing a Distributed Object-Oriented System with 
Logical Constraints for Fluorescence-Activated Cell Sorting"
 T. Matsushima

[17] "Prediction of Primate Splice Junction Gene Sequences with 
 a Cooperative Knowledge Acquisition System"
 E.M. Nguifo & J. Sallantin

[18] "Object-Oriented Knowledge Bases for the Analysis of 
 Prokaryotic and Eukaryotic Genomes" 
 G. Perriere, F. Dorkeld, F. Rechenmann, & C. Gautier

[19] "Petri Net Representations in Metabolic Pathways"
 V.N. Reddy, M.L. Mavrovouniotis, & M.L. Liebman

[20] "Minimizing Complexity in Cellular Automata Models of 
 Self-Replication"  J.A. Reggia, H.-H. Chou, S.L. Armentrout, 
 & Y. Peng

[21] "Building Large Knowledge Bases in Molecular Biology"
 O. Schmeltzer, C. Medigue, P. Uvietta, F. Rechenmann, 
 F. Dorkeld, G. Perriere, & C. Gautier

[22] "A Service-Oriented Information Sources Database for the 
 Biological Sciences"  G.K. Springer & T.B. Patrick

[23] "Hidden Markov Models and Iterative Aligners: Study of their 
 Equivalence and Possibilities" H. Tanaka, K. Asai, M. Ishikawa,
 & A. Konagaya

[24] "Protein Structure Prediction System Based on Artificial 
 Neural Networks"  J. Vanhala & K. Kaski

[25] "Transmembrane Segment Prediction from Protein Sequence 
 Data"  S.M. Weiss, D.M. Cohen & N. Indurkhya

                      TUTORIAL PROGRAM
Tutorials will be conducted at the Bethesda Ramada Hotel on 
Tuesday, July 6.

12:00-2:45pm "Introduction to Molecular Biology for Computer 
 Scientists"  Prof. Mick Noordewier (Rutgers University)

This overview of the essential facts of molecular biology is 
intended as an introduction to the field for computer scientists 
who wish to apply their tools to this rich and complex domain.  
Material covered will include structural and informational 
molecules, the basic organization of the cell and of genetic 
material, the "central dogma" of gene expression, and selected 
other topics in the area of structure, function, and regulation as 
relates to current computational approaches.  Dr. Noordewier has 
appointments in both Computer Science and Biology at Rutgers, and 
has extensive experience in basic biological research in addition 
to his current work in computational biology.

12:00-2:45pm "Introduction to Artificial Intelligence for 
 Biologists"  Dr. Richard Lathrop (MIT & Arris Corp.)

An overview of the field of artificial intelligence will be 
presented, as it relates to actual and potential biological 
applications.  Fundamental techniques, symbolic programming 
languages, and notions of search will be discussed, as well as 
selected topics in somewhat greater detail, such as knowledge 
representation, inference, and machine learning.  The intended 
audience includes biologists with some computational background, 
but no extensive exposure to artificial intelligence.  Dr. 
Lathrop, co-developer of ARIADNE and related technologies, has 
worked in the area of artificial intelligence applied to 
biological problems in both academia and industry.

3:00-5:45pm "Neural Networks, Statistics, and Information Theory 
 in Biological Sequence Analysis" Dr. Alan Lapedes (Los Alamos 
 National Laboratory) 

This tutorial will cover the most rapidly-expanding facet of 
intelligent systems for molecular biology, that of machine 
learning techniques applied to sequence analysis.  Closely 
interrelated topics to be addressed include the use of artifical 
neural networks to elicit both specific signals and general 
characteristics of sequences, and the relationship of such 
approaches to statistical techniques and information-theoretic 
views of sequence data.  Dr. Lapedes, of the Theoretical 
Division at Los Alamos, has long been a leader in the use of such 
techniques in this domain.

3:00-5:45pm "Genetic Algorithms and Genetic Programming" 
 Prof. John Koza (Stanford University)

The genetic algorithm, an increasingly popular approach to highly 
non-linear multi-dimensional optimization problems, 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 well-suited to problems where the discovery of the size 
and shape of the solution is a major part of the problem, will 
also be addressed.  Particular attention will be paid to 
biological applications, and to identifying resources and software 
that will permit attendees to begin using the methods.  Dr. Koza, 
a Consulting Professor of Computer Science at Stanford, has taught 
this subject since 1988 and is the author of a standard text in 
the field.

3:00-5:45pm "Linguistic Methods in Sequence Analysis" 
 Prof. David Searls (University of Pennsylvania) 
 & Shmuel Pietrokovski (Weizmann Institute)

Approaches to sequence analysis based on linguistic methodologies 
are increasingly in evidence.  These involve the adaptation of 
tools and techniques from computational linguistics for syntactic 
pattern recognition and gene prediction, the classification of 
genetic structures and phenomena using formal language theory, the 
identification of significant vocabularies and overlapping codes 
in sequence data, and sequence comparison reflecting taxonomic and 
functional relatedness.  Dr. Searls, who holds research faculty 
appointments in both Genetics and Computer Science at Penn, 
represents the branch of this field that considers higher-order 
syntactic approaches to sequence data, while Shmuel Pietrokovski 
has studied and published with Prof. Edward Trifinov in the area 
of word-based analyses.

                      REGISTRATION FORM
Mail, with check made out to "ISMB-93", to:

               ISMB Conference, c/o J. Shavlik
               Computer Sciences Department
               University of Wisconsin
               1210 West Dayton Street
               Madison, WI 53706  USA

        ================================================

        Name____________________________________________
	
        Affiliation_____________________________________
	
        Address_________________________________________

        ________________________________________________

        ________________________________________________

        ________________________________________________

        Phone___________________________________________

        FAX_____________________________________________

        Electronic Mail_________________________________
	
        Registration Status: ____ Regular   ____ Student

        Presenting?          ____ Talk      ____  Poster
        ================================================
        TUTORIAL REGISTRATION 

        ____"Molecular Biology for Computer Scientists"
         or
        ____"Artificial Intelligence for Biologists"
         -  -  -  -  -  -  -  -  -  -  -  -  -  -  -  - 
        ____"Neural Networks, Statistics, and 
         or     Information Theory in Sequence Analysis"
        ____"Genetic Algorithms and Genetic Programming"
         or 
        ____"Linguistic Methods in Sequence Analysis"
        ================================================
        PAYMENT       (Early Registration Before June 1)

        Registration:  Early   Late	    $___________
              Regular  $100    $125	
              Student  $75     $100	
        Tutorials:     One      Two         $___________
              Regular  $50      $65	
              Student  $25      $35	
        Total:                              $___________
        ================================================
        Registration fees include conference proceedings, 
        refreshments, and general program expenses. 


                      ORGANIZING COMMITTEE
        Lawrence Hunter                              NLM 
        David Searls                  U. of Pennsylvania
        Jude Shavlik                     U. of Wisconsin

                        PROGRAM COMMITTEE
        Douglas Brutlag                      Stanford U.
        Bruce Buchanan                  U. of Pittsburgh
        Christian Burks          Los Alamos National Lab
        Fred Cohen                    U.C.-San Francisco
        Chris Fields           Inst. for Genome Research
        Michael Gribskov                  U.C.-San Diego
        Peter Karp                     SRI International
        Toni Kazic                         Washington U.
        Alan Lapedes             Los Alamos National Lab
        Richard Lathrop                MIT & Arris Corp.
        Charles Lawrence                          Baylor 
        Michael Mavrovouniotis            U. of Maryland
        George Michaels                              NIH
        Harold Morowitz                  George Mason U.
        Katsumi Nitta                               ICOT
        Mick Noordewier                       Rutgers U.
        Ross Overbeek               Argonne National Lab
        Chris Rawlings                              ICRF
        Derek Sleeman                     U. of Aberdeen
        David States                       Washington U.
        Gary Stormo                       U. of Colorado
        Ed Uberbacher             Oak Ridge National Lab
        David Waltz              Thinking Machines Corp.

