program reg forms st int conf on intell sys for molecular biology 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 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 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 rockville pike nih building a bethesda md 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 wisconsin avenue bethesda md a special room rate has been negotiated with the hotel of day expires attendees must make their own reservations by writing the hotel or calling 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 copies will be distributed at the conference to registered attendees and will be available for purchase from the publisher afterwards talks wednesday july am continental breakfast am opening remarks am invited talk statistics protein cores and predicted structures prof temple smith boston university am break am constructive induction and protein structure prediction t r ioerger l rendell s surbramaniam am protein secondary structure modeling with probabilistic networks a l delcher s kasif h r goldberg w hsu pm lunch pm protein secondary structure using two level case based reasoning b leng b g buchanan h b nicholas pm 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 pm 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 pm break pm protein classification using neural networks e a ferran b pflugfelder p ferrara pm neural networks for molecular sequence classification c wu m berry y s fung j mclarty pm computationally efficient cluster representation in molecular sequence megaclassification d j states n harris l hunter pm poster setup pm reception poster session thursday july am continental breakfast am invited talk large scale dna sequencing a tale of mice and men prof leroy hood university of washington am break am pattern recognition for automated dna sequencing i on line signal conditioning and feature extraction for basecalling j b bolden iii d torgersen c tibbetts am genetic algorithms for sequence assembly r parsons s forrest c burks am a partial digest approach to restriction site mapping s s skiena g sundaram pm lunch pm integrating order and distance relationships from heterogeneous maps m graves pm discovering sequence similarity by the algorithmic significance method a milosavljevic pm identification of human gene functional regions based on oligonucleotide composition v v solovyev c b lawrence pm knowledge discovery in genbank j s aaronson j haas g c overton pm break pm an expert system to generate machine learning experiments learning with dna crystallography data d cohen c kulikowski h berman pm detection of correlations in trna sequences with structural implications t m klingler d brutlag pm probabilistic structure calculations a three dimensional trna structure from sequence correlation data r b altman friday july am continental breakfast am invited talk artificial intelligence and a grand unified theory of biochemistry prof harold morowitz george mason university am break am testing hiv molecular biology in in silico physiologies h b sieburg c baray am identification of localized and distributed bottlenecks in metabolic pathways m l mavrovouniotis am fine grain databases for pattern discovery in gene regulation s m veretnik b r schatz pm lunch pm representation for discovery of protein motifs d conklin s fortier j glasgow pm finding relevant biomolecular features l hunter t klein pm database techniques for biological materials and methods k baclawski r futrelle n fridman m j pescitelli pm a multi level description scheme of protein conformation k onizuka k asai m ishikawa s t c wong pm break pm protein topology prediction through parallel constraint logic programming d a clark c j rawlings j shirazi a veron m reeve pm a constraint reasoning system for automating sequence specific resonance assignments in multidimensional protein nmr spectra d zimmerman c kulikowski g t montelione pm closing remarks poster session the following posters will be on display at the bethesda ramada hotel from pm wednesday july the induction of rules for predicting chemical carcinogenesis in rodents d bahler d bristol senex a clos clim application for molecular pathology s s ball v h mah flash a fast look up algorithm for string homology a califano i rigoutsos toward multi strategy parallel learning in sequence analysis p k chan s j stolfo protein structure prediction selecting salient features from large candidate pools k j cherkauer j w shavlik comparison of two approaches to the prediction of protein folding patterns i dubchak s r holbrook s h kim a modular learning environment for protein modeling j gracy l chiche j sallantin inference of order in genetic systems j n guidi t h roderick palm a pattern language for molecular biology c helgesen p r sibbald grammatical formalization of metabolic processes r hofestedt representations of metabolic knowledge p d karp m riley protein sequencing experiment planning using analogy b kettler l darden design of an object oriented database for reverse genetics k j kochut j arnold j a miller w d potter a small automaton for word recognition in dna sequences c lefevre j e ikeda multimap an expert system for automated genetic linkage mapping t c matise m perlin a chakravarti constructing a distributed object oriented system with logical constraints for fluorescence activated cell sorting t matsushima prediction of primate splice junction gene sequences with a cooperative knowledge acquisition system e m nguifo j sallantin object oriented knowledge bases for the analysis of prokaryotic and eukaryotic genomes g perriere f dorkeld f rechenmann c gautier petri net representations in metabolic pathways v n reddy m l mavrovouniotis m l liebman minimizing complexity in cellular automata models of self replication j a reggia h h chou s l armentrout y peng building large knowledge bases in molecular biology o schmeltzer c medigue p uvietta f rechenmann f dorkeld g perriere c gautier a service oriented information sources database for the biological sciences g k springer t b patrick hidden markov models and iterative aligners study of their equivalence and possibilities h tanaka k asai m ishikawa a konagaya protein structure prediction system based on artificial neural networks j vanhala k kaski 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 pm 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 pm 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 pm 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 pm 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 and is the author of a standard text in the field pm 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 to ismb conference c o j shavlik computer sciences department university of wisconsin west dayton street madison wi 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 registration early late regular student tutorials one two regular student 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
