From ismb@camis.stanford.edu Thu Feb 17 12:37:41 EST 1994 Article: 20716 of comp.ai Xref: glinda.oz.cs.cmu.edu comp.ai:20716 Path: honeydew.srv.cs.cmu.edu!fs7.ece.cmu.edu!europa.eng.gtefsd.com!library.ucla.edu!agate!headwall.Stanford.EDU!nntp!brutlag From: brutlag@cmgm.stanford.edu (Doug Brutlag) Newsgroups: comp.ai Subject: Intelligent Systems for Molecular Biology Conference Followup-To: comp.ai Date: Thu, 17 Feb 94 08:58:02 GMT Organization: Stanford University Lines: 86 Message-ID: Reply-To: ismb@camis.stanford.edu NNTP-Posting-Host: biochem1-fp-dynamic.stanford.edu X-Newsreader: VersaTerm Link v1.1.1 ***************** SECOND CALL FOR PAPERS ***************** The Second International Conference on Intelligent Systems for Molecular Biology August 15-17, 1994 Stanford University Organizing Committee Deadlines Russ Altman, Stanford U, Stanford Papers due: March 11, 1994 Doug Brutlag, Stanford U, Stanford Replies to authors: April 29, 1994 Peter Karp, SRI, Menlo Park Revised papers due: May 27, 1994 Richard Lathrop, MIT, Cambridge David Searls, U Penn, Philadelphia Program Committee K. Asai, ETL, Tsukuba A. Lapedes, LANL, Los Alamos D. Benson, NCBI, Bethesda M. Mavrovouniotis, Northwestern U, Evanston B. Buchanan, U of Pittsburgh G. Michaels, George Mason U, Fairfax C. Burks, LANL, Los Alamos G. Myers, U. Arizona, Tucson D. Clark, ICRF, London K. Nitta, ICOT, Tokyo F. Cohen, UCSF, San Francisco C. Rawlings, ICRF, London T. Dietterich, OSU, Corvallis J. Sallatin, LIRM, Montpellier S. Forrest, UNM, Albuquerque C. Sander, EMBL, Heidelberg J. Glasgow, Queen's U., Kingston J. Shavlik, U Wisconsin, Madison P. Green, Wash U, St. Louis D. States, Wash U, St. Louis M. Gribskov, SDSC, San Diego G. Stormo, U Colorado, Boulder D. Haussler, UCSC, Santa Cruz E. Uberbacher, ORNL, Oak Ridge S. Henikoff, FHRC, Seattle M. Walker, Stanford U, Stanford L. Hunter, NLM, Bethesda T. Webster, Stanford U, Stanford T. Klein, UCSF, San Francisco X. Zhang, TMC, Cambridge The Second International Conference on Intelligent Systems for Molecular Biology will take place at Stanford University in the San Francisco Bay Area, August 14-17, 1994. The ISMB conference, held for the first time last summer in Bethesda, MD, attracted an overflow crowd, yielded an excellent 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 will continue the tradition of pre-published, rigorously refereed proceedings, and opportunities for fruitful personal interchange. The conference will bring together scientists who are applying the technologies of advanced data modeling, artificial intelligence, machine learning, probabilistic reasoning, massively parallel computing, robotics, and related computational methods to problems in molecular biology. We invite participation from both developers and users of any novel system, provided it supports 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." The four-day conference will feature introductory tutorials (August 14), presentations of original refereed papers and invited talks (August 15-17). Paper submissions should be single-spaced, 12 point type, 12 pages maximum including title, abstract, figures, tables, and bibliography with titles. The first page should include the full postal address, electronic mailing address, telephone and FAX number of each author. Also, please list five to ten keywords describing the methods and concepts discussed in the paper. State whether you wish the paper to be considered for oral presentation only, poster presentation only or for either presentation format. Submit 6 copies to the address below. For more information, please contact ismb@camis.stanford.edu. Proposals for introductory tutorials must be well documented, including the purpose and intended audience of the tutorial as well as previous experience of the author in presenting such material. Those considering submitting tutorial proposals are strongly encouraged to submit a one-page outline, before the deadline, to enable early feed-back regarding topic and content suitability. The conference will pay an honorarium and support, in part, the travel expenses of tutorial speakers. Limited funds are available to support travel to ISMB-94 for those students, post-docs, minorities and women who would otherwise be unable to attend.. Please submit papers and tutorial proposals to: Intelligent Systems for Molecular Biology c/o Dr. Douglas L. Brutlag Beckman Center, B400 Department of Biochemistry Stanford University School of Medicine Stanford, California 94305-5307 Article 21026 of comp.ai: Xref: glinda.oz.cs.cmu.edu comp.ai:21026 Path: honeydew.srv.cs.cmu.edu!fs7.ece.cmu.edu!europa.eng.gtefsd.com!gatech!swrinde!sgiblab!rpal.rockwell.com!headwall.Stanford.EDU!nntp!brutlag From: brutlag@cmgm.stanford.edu (Doug Brutlag) Newsgroups: comp.ai Subject: New Submission Deadline for ISMB '94 Conference Followup-To: comp.ai Date: Thu, 10 Mar 94 13:34:37 GMT Organization: Stanford University Lines: 90 Message-ID: Reply-To: ismb@camis.stanford.edu NNTP-Posting-Host: biochem1-fp-dynamic.stanford.edu X-Newsreader: VersaTerm Link v1.1.1 *************** CHANGE IN SUBMISSION DEADLINE ***************** Due to late advertisement and numerous requests, we are changing the deadline for submission of papers to March 25, 1994. Papers must be received by March 25 to be considered. The Second International Conference on Intelligent Systems for Molecular Biology August 15-17, 1994 Stanford University Organizing Committee New Deadlines Russ Altman, Stanford U, Stanford Papers due: March 25, 1994 Doug Brutlag, Stanford U, Stanford Replies to authors: May 6, 1994 Peter Karp, SRI, Menlo Park Revised papers due: June 3, 1994 Richard Lathrop, MIT, Cambridge David Searls, U Penn, Philadelphia Program Committee K. Asai, ETL, Tsukuba A. Lapedes, LANL, Los Alamos D. Benson, NCBI, Bethesda M. Mavrovouniotis, Northwestern U, Evanston B. Buchanan, U of Pittsburgh G. Michaels, George Mason U, Fairfax C. Burks, LANL, Los Alamos G. Myers, U. Arizona, Tucson D. Clark, ICRF, London K. Nitta, ICOT, Tokyo F. Cohen, UCSF, San Francisco C. Rawlings, ICRF, London T. Dietterich, OSU, Corvallis J. Sallatin, LIRM, Montpellier S. Forrest, UNM, Albuquerque C. Sander, EMBL, Heidelberg J. Glasgow, Queen's U., Kingston J. Shavlik, U Wisconsin, Madison P. Green, Wash U, St. Louis D. States, Wash U, St. Louis M. Gribskov, SDSC, San Diego G. Stormo, U Colorado, Boulder D. Haussler, UCSC, Santa Cruz E. Uberbacher, ORNL, Oak Ridge S. Henikoff, FHRC, Seattle M. Walker, Stanford U, Stanford L. Hunter, NLM, Bethesda T. Webster, Stanford U, Stanford T. Klein, UCSF, San Francisco X. Zhang, TMC, Cambridge The Second International Conference on Intelligent Systems for Molecular Biology will take place at Stanford University in the San Francisco Bay Area, August 14-17, 1994. The ISMB conference, held for the first time last summer in Bethesda, MD, attracted an overflow crowd, yielded an excellent 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 will continue the tradition of pre-published, rigorously refereed proceedings, and opportunities for fruitful personal interchange. The conference will bring together scientists who are applying the technologies of advanced data modeling, artificial intelligence, machine learning, probabilistic reasoning, massively parallel computing, robotics, and related computational methods to problems in molecular biology. We invite participation from both developers and users of any novel system, provided it supports 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." The four-day conference will feature introductory tutorials (August 14), presentations of original refereed papers and invited talks (August 15-17). Paper submissions should be single-spaced, 12 point type, 12 pages maximum including title, abstract, figures, tables, and bibliography with titles. The first page should include the full postal address, electronic mailing address, telephone and FAX number of each author. Also, please list five to ten keywords describing the methods and concepts discussed in the paper. State whether you wish the paper to be considered for oral presentation only, poster presentation only or for either presentation format. Submit 6 copies to the address below. For more information, please contact ismb@camis.stanford.edu. Proposals for introductory tutorials must be well documented, including the purpose and intended audience of the tutorial as well as previous experience of the author in presenting such material. Those considering submitting tutorial proposals are strongly encouraged to submit a one-page outline, before the deadline, to enable early feed-back regarding topic and content suitability. The conference will pay an honorarium and support, in part, the travel expenses of tutorial speakers. Limited funds are available to support travel to ISMB-94 for those students, post-docs, minorities and women who would otherwise be unable to attend.. Please submit papers and tutorial proposals to: Intelligent Systems for Molecular Biology c/o Dr. Douglas L. Brutlag Beckman Center, B400 Department of Biochemistry Stanford University School of Medicine Stanford, California 94305-5307 Article 21664 of comp.ai: Xref: glinda.oz.cs.cmu.edu comp.ai:21664 comp.ai.neural-nets:15945 sci.bio:19098 sci.engr.biomed:2036 sci.med:85054 news.announce.conferences:6033 Path: honeydew.srv.cs.cmu.edu!nntp.club.cc.cmu.edu!news.mic.ucla.edu!library.ucla.edu!galaxy.ucr.edu!ihnp4.ucsd.edu!swrinde!sgiblab!sgigate.sgi.com!olivea!biosci!biosci!not-for-mail From: brutlag@cmgm.stanford.edu (Doug Brutlag) Newsgroups: bionet.announce,bionet.software,bionet.molbio.bio-matrix,comp.ai,comp.ai.neural-nets,sci.bio,sci.engr.biomed,sci.med,news.announce.conferences Subject: ISMB-94 General and Registration Info Followup-To: sci.bio Date: 14 Apr 1994 19:20:43 -0700 Organization: Stanford University Lines: 351 Sender: kristoff@net.bio.net Approved: bionews-moderator@net.bio.net Distribution: bionet Message-ID: Reply-To: ismb@camis.stanford.edu NNTP-Posting-Host: net.bio.net ***************************************************************** General Announcement and Registration Information for the Second International Conference on INTELLIGENT SYSTEMS FOR MOLECULAR BIOLOGY (ISMB-94) August 14-17, 1994 Stanford University Stanford, California Fairchild Auditorium PURPOSE 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@camis.stanford.edu or using the mailing address given below. ORGANIZING COMMITTEE Russ Altman, Stanford University Doug Brutlag, Stanford University Peter Karp SRI Richard Lathrop MIT David Searls U. of Pennsylvania PROGRAM COMMITTEE 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 PROCEEDINGS: 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. TUTORIALS: 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: T1. INFORMATION SCIENCE FOR MOLECULAR BIOLOGISTS. 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. T2. MOLECULAR BIOLOGY FOR COMPUTER SCIENTISTS. 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: T3. MINIMAL LENGTH ENCODING IN MOLECULAR BIOLOGY. 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. T4. MACHINE LEARNING APPROACHES IN COMPUTATIONAL MOLECULAR 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: T5. COMPUTATIONAL CHALLENGES FOR INTELLIGENT SYSTEMS IN 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) T6. NEURAL NETWORKS 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: T7. CONSTRAINT SATISFACTION IN MOLECULAR BIOLOGY. 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. T8. GENETIC ALGORITHMS AND GENETIC PROGRAMMING. 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 CONTEXT-FREE GRAMMARS AND OTHER RELATED MODELS 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.) HOUSING AND MEAL PLANS 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, 1994. 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: $57) Return Registration Form (with payment) to ISMB-94 c/o Russ Altman Section on Medical Informatics SUMC, MSOB X-215 Stanford, CA 94305-5479 USA For questions: ismb@camis.stanford.edu or Fax: (415) 725-7944 CUT HERE: ************************************************************* ISMB-94 REGISTRATION FORM: Name:__________________________________________________ Affiliation: __________________________________________ Address:_______________________________________________ _______________________________________________ _______________________________________________ Phone: ___________________ Fax: ____________________ Email: _____________________________________________ Status: ________ Student _______ Non-student ________ Male _______ Female _____ Check if you would like information about travel support. >Registration (Early = before 7/15)......................$_______ 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@cmgm.stanford.edu Stanford University School of Medicine Stanford, California 94305-5307