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.