[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