On the suitability of Biological structure determination by electron microscopy to Grid Computing

The present contribution describes a potential application of Grid Computing in Bioinformatics. High resolution structure determination of biological specimens is critical in BioSciences to understanding the biological function. The problem is computational intensive. Distributed and Grid Computing are thus becoming essential. This contribution analyzes the use of Grid Computing and its potential benefits in the field of electron microscope tomography of biological specimens. Jose-Jesus Fernandez, Ph.D.: He received his M.Sc. and Ph.D. degrees in Computer Science from the University of Granada, Spain, in 1992 and 1997, respectively. He was a Ph.D. student at the Bio-Computing unit of the National Center for BioTechnology (CNB) from the Spanish National Council of Scientific Research (CSIC), Madrid, Spain. He became an Assistant Professor in 1997 and, subsequently, Associate Professor in 2000 in Computer Architecture at the University of Almeria, Spain. He is a member of the supercomputing-algorithms research group. His research interests include high performance computing (HPC), image processing and tomography. Jose-Roman Bilbao-Castro: He received his M.Sc. degree in Computer Science from the University of Almeria in 2001. He is currently a Ph.D. student at the BioComputing unit of the CNB (CSIC) through a Ph.D. CSIC-grant in conjuction with Dept. Computer Architecture at the University of Malaga (Spain). His current research interestsinclude tomography, HPC and distributed and grid computing. Roberto Marabini, Ph.D.: He received the M.Sc. (1989) and Ph.D. (1995) degrees in Physics from the University Autonoma de Madrid (UAM) and University of Santiago de Compostela, respectively. He was a Ph.D. student at the BioComputing Unit at the CNB (CSIC). He worked at the University of Pennsylvania and the City University of New York from 1998 to 2002. At present he is an Associate Professor at the UAM. His current research interests include inverse problems, image processing and HPC. Jose-Maria Carazo, Ph.D.: He received the M.Sc. degree from the Granada University, Spain, in 1981, and got his Ph.D. in Molecular Biology at the UAM in 1984. He left for Albany, NY, in 1986, coming back to Madrid in 1989 to set up the BioComputing Unit of the CNB (CSIC). He was involved in the Spanish Ministry of Science and Technology as Deputy General Director for Research Planning. Currently, he keeps engaged in his activities at the CNB, the Scientific Park of Madrid and Integromics S.L. Immaculada Garcia, Ph.D.: She received her B.Sc. (1977) and Ph.D. (1986) degrees in Physics from the Complutense University of Madrid and University of Santiago de Compostela, respectively. From 1977 to 1987 she was an Assistant professor at the University of Granada, from 1987 to 1996 Associate professor at the University of Almeria and since 1997 she is a Full Professor and head of Dept. Computer Architecture. She is head of the supercomputing-algorithms research group. Her research interest lies in HPC for irregular problems related to image processing, global optimization and matrix computation.     

Temporal disjunctive logic programming

In this paper we introduce the logic programming languageDisjunctive Chronolog which combines the programming paradigms of temporal and disjunctive logic programming. Disjunctive Chronolog is capable of expressing dynamic behaviour as well as uncertainty, two notions that are very common in a variety of real systems. We present the minimal temporal model semantics and the fixpoint semantics for the new programming language and demonstrate their equivalence. We also show how proof procedures developed for disjunctive logic programs can be easily extended to apply to Disjunctive Chronolog programs. Manolis Gergatsoulis, Ph.D.: He received his B.Sc. in Physics in 1983, the M.Sc. and the Ph.D. degrees in Computer Science in 1986 and 1995 respectively all from the University of Athens, Greece. Since 1996 he is a Research Associate in the Institute of Informatics and Telecommunications, NCSR ‘Demokritos’, Athens. His research interests include logic and temporal programming, program transformations and synthesis, as well as theory of programming languages. Panagiotis Rondogiannis, Ph.D.: He received his B.Sc. from the Department of Computer Engineering and Informatics, University of Patras, Greece, in 1989, and his M.Sc. and Ph.D. from the Department of Computer Science, University of Victoria, Canada, in 1991 and 1994 respectively. From 1995 to 1996 he served in the Greek army. From 1996 to 1997 he was a visiting professor in the Department of Computer Science, University of Ioannina, Greece, and since 1997 he is a Lecturer in the same Department. In January 2000 he was elected Assistant Professor in the Department of Informatics at the University of Athens. His research interests include functional, logic and temporal programming, as well as theory of programming languages. Themis Panayiotopoulos, Ph.D.: He received his Diploma on Electrical Engineering from the Department of Electrical Engineering, National Technical Univesity of Athens, in 1984, and his Ph.D. on Artificial Intelligence from the above mentioned department in 1989. From 1991 to 1994 he was a visiting professor at the Department of Mathematics, University of the Aegean, Samos, Greece and a Research Associate at the Institute of Informatics and Telecommunications of “Democritos” National Research Center. Since 1995 he is an Assistant Prof. at the Department of Computer Science, University of Piraeus. His research interests include temporal programming, logic programming, expert systems and intelligent agent architectures.     

TEG—a hybrid approach to information extraction

This paper describes a hybrid statistical and knowledge-based information extraction model, able to extract entities and relations at the sentence level. The model attempts to retain and improve the high accuracy levels of knowledge-based systems while drastically reducing the amount of manual labour by relying on statistics drawn from a training corpus. The implementation of the model, called TEG (trainable extraction grammar), can be adapted to any IE domain by writing a suitable set of rules in a SCFG (stochastic context-free grammar)-based extraction language and training them using an annotated corpus. The system does not contain any purely linguistic components, such as PoS tagger or shallow parser, but allows to using external linguistic components if necessary. We demonstrate the performance of the system on several named entity extraction and relation extraction tasks. The experiments show that our hybrid approach outperforms both purely statistical and purely knowledge-based systems, while requiring orders of magnitude less manual rule writing and smaller amounts of training data. We also demonstrate the robustness of our system under conditions of poor training-data quality. Ronen Feldman is a senior lecturer at the Mathematics and Computer Science Department of Bar-Ilan University in Israel, and the Director of the Data Mining Laboratory. He received his B.Sc. in Math, Physics and Computer Science from the Hebrew University, M.Sc. in Computer Science from Bar-Ilan University, and his Ph.D. in Computer Science from Cornell University in NY. He was an Adjunct Professor at NYU Stern Business School. He is the founder of ClearForest Corporation, a Boston based company specializing in development of text mining tools and applications. He has given more than 30 tutorials on next mining and information extraction and authored numerous papers on these topics. He is currently finishing his book “The Text Mining Handbook” to the published by Cambridge University Press. Benjamin Rosenfeld is a research scientist at ClearForest Corporation. He received his B.Sc. in Mathematics and Computer Science from Bar-Ilan University. He is the co-inventor of the DIAL information extraction language. Moshe Fresko is finalizing his Ph.D. in Computer Science Department at Bar-Ilan University in Israel. He received his B.Sc. in Computer Engineering from Bogazici University, Istanbul/Turkey on 1991, and M.Sc. on 1994. He is also an adjunct lecturer at the Computer Science Department of Bar-Ilan University and functions as the Information-Extraction Group Leader in the Data Mining Laboratory.     

Seeing things: Inventive reasoning with geometric analogies and topographic maps

This paper examines two seemingly unrelated qualitative spatial reasoning domains; geometric proportional analogies and topographic (land-cover) maps. We present a Structure Matching algorithm that combines Gentner’s structuremapping theory with an attributematching process. We use structure matching to solve geometric analogy problems that involve manipulating attribute information, such as colors and patterns. Structure matching is also used to creatively interpret topographic (land-cover) maps, adding a wealth of semantic knowledge and providing a far richer interpretation of the raw data. We return to the geometric proportional analogies, identify alternate attribute matching processes that are required to solve different categories of problems. Finally, we assess some implications for computationally creative and inventive models. Diarmuid P. O’Donoghue, Ph.D.: He received his B.Sc. and M.Sc. from University College Cork in 1988 and 1990, and his Ph.D. from University College Dublin. He has been a lecturer at the Department of Computer Science NUI Maynooth since 1996 and is also an associate of the National Centre for Geocomputation. His interests are in artificial intelligence, analogical reasoning, topology, and qualitative spatial reasoning. Amy Bohan, B.Sc, M.Sc.: She received her B.Sc. from the National University of Ireland, Maynooth in 2000. She received her M.Sc. in 2003 from University College Dublin where she also recently completed her Ph.D. She is a member of the Cognitive Science society. Her interests are in cognitive science, analogical argumentation, geometric proportional analogies and computational linguistics. Prof. Mark T. Keane: He is Chair of Computer Science and Associate Dean of Science at University College Dublin. He is also Director of ICT, at Science Foundation Ireland. Prof. Keane has made significant contributions in the areas of analogy, case-based reasoning and creativity. He has published over 100 publications, including 16 books, that are cited widely. He is co-author of a Cognitive Science textbook, written with Mike Eysenck (University of London) that has been translated into Portuguese, Hungarian, Italian and Chinese and is now entering its fifth edition. Prof. Keane is a fellow of ECCAI (European Co-ordinating Committee on Artificial Intelligence) and received the Special Award for Merit from the Psychology Society of Ireland, for his work on human creativity.     

Adaptive solutions to the mutual exclusion problem

Summary Algorithms for mutual exclusion that adapt to the current degree of contention are developed. Afilter and a leader election algorithm form the basic building blocks. The algorithms achieve system response times that are independent of the total number of processes and governed instead by the current degree of contention. The final algorithm achieves a constant amortized system response time. Manhoi Choy was born in 1967 in Hong Kong. He received his B.Sc. in Electrical and Electronic Engineerings from the University of Hong Kong in 1989, and his M.Sc. in Computer Science from the University of California at Santa Barbara in 1991. Currently, he is working on his Ph.D. in Computer Science at the University of California at Santa Barbara. His research interests are in the areas of parallel and distributed systems, and distributed algorithms. Ambuj K. Singh is an Assistant Professor in the Department of Computer Science at the University of California, Santa Barbara. He received a Ph.D. in Computer Science from the University of Texas at Austin in 1989, an M.S. in Computer Science from Iowa State University in 1984, and a B.Tech. from the Indian Institute of Technology at Kharagpur in 1982. His research interests are in the areas of adaptive resource allocation, concurrent program development, and distributed shared memory.A preliminary version of the paper appeared in the 12th Annual ACM Symposium on Principles of Distributed ComputingWork supported in part by NSF grants CCR-9008628 and CCR-9223094     

Determination of user interfaces in adaptive systems using a rough classification-based method

This paper presents a novel method for user classification in adaptive systems based on rough classification. Adaptive systems could be used in many areas, for example in a user interface construction or e-Learning environments for learning strategy selection. In this paper the adaptation of web-based system user interface is presented. The goal of rough user classification is to select the most essential attributes and their values that group together users who are very much alike concerning the system logic. In order to group users we exploit their usage data taken from the user model of the adaptive web-based system user interface. We presented three basic problems for attribute selection that generates the following partitions: that is included, that includes and that is the closest to the given partition. Ngoc Thanh Nguyen, Ph.D., D.Sc.: He currently works as an associate professor at the Faculty of Computer Science and Management, Wroclaw University of Technology in Poland. He received his diplomas of M.Sc, Ph.D. and D.Sc. in Computer Science in 1986, 1989 and 2002, respectively. Actually, he is working on intelligent technologies for conflict resolution and inconsistent knowledge processing and e-learning methods. His teaching interests consist of database systems and distributed systems. He is a co-editor of 4 special issues in international journals, author of 3 monographs, editor of one book and about 110 other publications (book chapters, journal and refereed conference papers). He is an associate editor of the following journals: “International Journal of Computer Science & Application”; “Journal of Information Knowledge System Management”; and “International Journal of Knowledge-Based & Intelligent Engineering Systems”. He is a member of societies: ACM, IFIP WG 7.2, ISAI, KES International, and WIC. Janusz Sobecki, Ph.D.: He is an Assistant Professor in Institute of Applied Informatics (IAI) at Wroclaw University of Technology (WUT). He received his M. Sc. in Computer Science from Faculty of Computer Science and Management at WUT in 1986 and Ph.D. in Computer Science from Faculty of Electronics at WUT in 1994. For 1986–1996 he was an Assistant at the Department of Information Systems (DIS) at WUT. For 1988–1996 he was also a head of the laboratory at DIS. For 1996–2004 he was an Assistant Professor in DIS and since fall of 2004 at IAI, both at WUT. His research interests include information retrieval, multimedia information systems, system usability and recommender systems. He is on the editorial board of New Generation Computing and was a co-editor of two journal special issues. He is a member of American Association of Machinery.     

A framework for protein structure prediction on the grid

The large number of protein sequences, provided by genomic projects at an increasing pace, constitutes a challenge for large scale computational studies of protein structure and thermodynamics. Grid technology is very suitable to face this challenge, since it provides a way to access the resources needed in compute and data intensive applications. In this paper, we show the procedure to adapt to the Grid an algorithm for the prediction of protein thermodynamics, using the GridWay tool. GridWay allows the resolution of large computational experiments by reacting to events dynamically generated by both the Grid and the application. Eduardo Huedo, Ph.D.: He is a Computer Engineer (1999) and Ph.D. in Computer Architecture (2004) by the Universidad Complutense de Madrid (UCM). He is Scientist in the Advanced Computing Laboratory at Centro de Astrobiología (CSIC-INTA), associated to NASA Astrobiology Institute. He had one appointment in 2000 as a Summer Student in High Performance Computing and Applied Mathematics at ICASE (NASA Langley Research Center). His research areas are Performance Management and Tuning, High Performance Computing and Grid Technology. Ugo Bastolla, Ph.D.: He received his degree and Ph.D. in Physics in Rome University, with L. Peliti and G. Parisi respectively. He was interested from the beginning in biologically motivated problems, therefore, studied models of Population Genetics, Boolean Networks, Neural Networks, Statistical Mechanics of Polymers, Ecological and Biodiversity. His main research interest is constituted by studies of protein folding thermodynamics and evolution. Thereby, he set up an effective energy function allowing prediction of protein folding thermodynamics, and applied it to protein structure prediction, to simulate protein evolution and to analyze protein sequences from a thermodynamical point of view. He is currently in the Bioinformatic Unit of the Centro de Astrobiología of Madrid. Rubén S. Montero, Ph.D.: He received his B.S. in Physics (1996), M.S in Computer Science (1998) and Ph.D. in Computer Architecture (2002) from the Universidad Complutense de Madrid (UCM). He is Assistant Professor of Computer Architecture and Technology at UCM since 1999. He has held several research appointments at ICASE (NASA Langley Research Center), where he worked on computational fluid dynamics, parallel multigrid algorithms and Cluster computing. Nowadays, his research interests lie mainly in Grid Technology, in particular in adaptive scheduling, adaptive execution and distributed algorithms. Ignacio M. Llorente, Ph.D.: He received his B.S. in Physics (1990), M.S in Computer Science (1992) and Ph.D. in Computer Architecture (1995) from the Universidad Complutense de Madrid (UCM). He is Executive M.B.A. by Instituto de Empresa since 2003. He is Associate Professor of Computer Architecture and Technology in the Department of Computer Architecture and System Engineering at UCM and Senior Scientist at Centro de Astrobiología (CSIC-INTA), associated to NASA Astrobiology Institute. He has held several appointments since 1997 as a Consultant in High Performance Computing and Applied Mathematics at ICASE (NASA Langley Research Center). His research areas are Information Security, High Performance Computing and Grid Technology.     

Verification of distributed programs using representative interleaving sequences

Summary We present a formal proof method for distributed programs. The semantics used to justify the proof method explicitly identifies equivalence classes of execution sequences which are equivalent up to permuting commutative operations. Each equivalence class is called an interleaving set or a run. The proof rules allow concluding the correctness of certain classes of properties for all execution sequences, even though such properties are demonstrated directly only for a subset of the sequences. The subset used must include a representative sequence from each interleaving set, and the proof rules, when applicable, guarantee that this is the case. By choosing a subset with appropriate sequences, simpler intermediate assertions can be used than in previous formal approaches. The method employs proof lattices, and is expressed using the temporal logic ISTL. Shmuel Katz received his B.A. in Mathematics and English Literature from U.C.L.A., and his M.Sc. and Ph.D. in Computer Science (1976) from the Weizmann Institute in Rechovot, Israel. From 1976 to 1981 he was at the IBM Israel Scientific Center. Presently, he is on the faculty of the Computer Science Department at the Technion in Haifa, Israel. In 1977–1978 he visited for a year at the University of California, Berkeley, and in 1984–1985 was at the University of Texas at Austin. He has been a consultant and visitor at the MCC Software Technology Program, and in 1988–1989 was a visiting scientist at the I.B.M. Watson Research Center. His research interests include the methodology of programming, specification methods, program verification and semantics, distributed programming, data structures, and programming languages. Doron Peled was born in 1962 in Haifa. He received his B.Sc. and M.Sc. in Computer Science from the Technion, Israel in 1984 and 1987, respectively. Between 1987 and 1991 he did his military service. He also completed his D.Sc. degree in the Technion during these years. Dr. Peled was with the Computer Science department at Warwick University in 1991–1992. He is currently a member of the technical staff with AT & T Bell Laboratories. His main research interests are specification and verification of programs, especially as related to partial order models, fault-tolerance and real-time. He is also interested in semantics and topology.This research was carried out while the second author was at the Department of Computer Science, The Technion, Haifa 32000, Israel     

A logic-based integration of active and deductive databases

A logic-based approach to the specification of active database functionality is presented which not only endows active databases with a well-defined and well-understood formal semantics, but also tightly integrates them with deductive databases. The problem of endowing deductive databases with rule-based active behaviour has been addressed in different ways. Typical approaches include accounting for active behaviour by extending the operational semantics of deductive databases, or, conversely, accounting for deductive capabilities by constraining the operational semantics of active databases. The main contribution of the paper is an alternative approach in which a class of active databases is defined whose operational semantics is naturally integrated with the operational semantics of deductive databases without either of them strictly subsuming the other. The approach is demonstrated via the formalization of the syntax and semantics of an active-rule language that can be smoothly incorporated into existing deductive databases, due to the fact that the standard formalization of deductive databases is reused, rather than altered or extended. One distinctive feature of the paper is its use of ahistory, as defined in the Kowalski-Sergot event-calculus, to define event occurrences, database states and actions on these. This has proved to be a suitable foundation for a comprehensive logical account of the concept set underpinning active databases. The paper thus contributes a logical perspective to the ongoing task of developing a formal theory of active databases. Alvaro Adolfo Antunes Fernandes, Ph.D.: He received a B.Sc. in Economics (Rio de Janeiro, 1984), an M.Sc. in Knowledge-Based Systems (Edinburgh, 1990) and a Ph.D. in Computer Science (Heriot-Watt, 1995). He worked as a Research Associate at Heriot-Watt University from December 1990 until December 1995. In January 1996 he joined the Department of Mathematical and Computing Sciences at Goldsmiths College, University of London, as a Lecturer. His current research interests include advanced data- and knowledge-base technology, logic programming, and software engineering. M. Howard Williams, Ph.D., D.Sc.: He obtained his Ph.D. in ionospheric physics and recently a D.Sc. in Computer Science. He was appointed as the first lecturer in Computer Science at Rhodes University in 1970. During the following decade he rose to Professor of Computer Science and in 1980 was appointed as Professor of Computer Science at Heriot-Watt University. From 1980 to 1988 he served as Head of Department and then as director of research until 1992. He is now head of the Database Research Group at Heriot-Watt University. His current research interests include active databases, deductive objectoriented databases, spatial databases, parallel databases and telemedicine. Norman W. Paton, Ph.D.: He received a B.Sc. in Computing Science from the University of Aberdeen in 1986. From 1986 to 1989 he worked as a Research Assistant at the University of Aberdeen, receiving a Ph. D. in 1989. From 1989 to 1995 he was a Lecturer in Computer Science at Heriot-Watt University. Since July 1995, he has been a Senior Lecturer in Department of Computer Science at the University of Manchester. His current research interests include active databases, deductive object-oriented databases, spatial databases and database interfaces.     

XCQ: A queriable XML compression system

XML has already become the de facto standard for specifying and exchanging data on the Web. However, XML is by nature verbose and thus XML documents are usually large in size, a factor that hinders its practical usage, since it substantially increases the costs of storing, processing, and exchanging data. In order to tackle this problem, many XML-specific compression systems, such as XMill, XGrind, XMLPPM, and Millau, have recently been proposed. However, these systems usually suffer from the following two inadequacies: They either sacrifice performance in terms of compression ratio and execution time in order to support a limited range of queries, or perform full decompression prior to processing queries over compressed documents.In this paper, we address the above problems by exploiting the information provided by a Document Type Definition (DTD) associated with an XML document. We show that a DTD is able to facilitate better compression as well as generate more usable compressed data to support querying. We present the architecture of the XCQ, which is a compression and querying tool for handling XML data. XCQ is based on a novel technique we have developed called DTD Tree and SAX Event Stream Parsing (DSP). The documents compressed by XCQ are stored in Partitioned Path-Based Grouping (PPG) data streams, which are equipped with a Block Statistics Signature (BSS) indexing scheme. The indexed PPG data streams support the processing of XML queries that involve selection and aggregation, without the need for full decompression. In order to study the compression performance of XCQ, we carry out comprehensive experiments over a set of XML benchmark datasets. Wilfred Ng obtained his M.Sc.(Distinction) and Ph.D. degrees from the University of London. His research interests are in the areas of databases and information Systems, which include XML data, database query languages, web data management, and data mining. He is now an assistant professor in the Department of Computer Science, the Hong Kong University of Science and Technology (HKUST). Further Information can be found at the following URL: . Wai-Yeung Lam obtained his M.Phil. degree from the Hong Kong University of Science and Technology (HKUST) in 2003. His research thesis was based on the project “XCQ: A Framework for Querying Compressed XML Data.” He is currently working in industry. Peter Wood received his Ph.D. in Computer Science from the University of Toronto in 1989. He has previously studied at the University of Cape Town, South Africa, obtaining a B.Sc. degree in 1977 and an M.Sc. degree in Computer Science in 1982. Currently he is a senior lecturer at Birkbeck and a member of the Information Management and Web Technologies research group. His research interests include database and XML query languages, query optimisation, active and deductive rule languages, and graph algorithms. Mark Levene received his Ph.D. in Computer Science in 1990 from Birkbeck College, University of London, having previously been awarded a B.Sc. in Computer Science from Auckland University, New Zealand in 1982. He is currently professor of Computer Science at Birkbeck College, where he is a member of the Information Management and Web Technologies research group. His main research interests are Web search and navigation, Web data mining and stochastic models for the evolution of the Web. He has published extensively in the areas of database theory and web technologies, and has recently published a book called ‘An Introduction to Search Engines and Web Navigation’.     

A Numerical Scheme for the Curvature Equation Near the Singularities

In this paper we propose a modification in the usual numerical method for computing the solutions of the curvature equation in the plane . This modification takes place near the singularities of the image. We propose to use zero as the vertical speed at a saddle point and, at an extremum, the geometric mean of the eigenvalues of the Hessian matrix. This modification is theoretically justified and the preliminary experimental results show that it makes the algorithm more reliable.Marcos Craizer has a degree in mathematics from UFRJ (Rio de Janeiro), a M.Sc. from IMPA (Rio de Janeiro) and received his Ph.D. in mathematics also from IMPA, in 1989. His research interests in image processing includes image representation, curve evolution and PDE applications. Since 1988, he has been working at the math department of PUC-Rio, Brazil.Sinésio Pesco is an Assistant Professor of the Department of Mathematics at Pontifical Catholic University of Rio de Janeiro (PUCRio). He received his Ph.D. and MS degree in Applied Mathematics at PUC-Rio and a B.S. degree in mathematics from State University of Maringa Brasil. He has visiting positions at Lawrence Livermore National Laboratory, CSE/OGI School of Science and Engineering (Oregon Health & Science University) and Scientific Computation and Imaging Insititute (University of UTAH). His main research interests are in Computational Topology, Image Processing and Scientific Visualization. Since 1991, he has been working in the development of a CAD system for petroleum reservoir modeling.Ralph Teixeira has a degree in Computer Engineering from IME (in Rio), a M.Sc. from IMPA (also in Rio) and received his Ph.D. in Mathematics from Harvard University in 1998. His research interests in Computer Vision include shape representations by skeletons (medial axis and similar objects), curve evolutions and PDE applications. Since 2001, he has been working at Fundação Getulio Vargas in Rio de Janeiro, Brazil.     

One-bit algorithms

Many algorithms in distributed systems assume that the size of a single message depends on the number of processors. In this paper, we assume in contrast that messages consist of a single bit. Our main goal is to explore how the one-bit translation of unbounded message algorithms can be sped up by pipelining. We consider two problems. The first is routing between two processors in an arbitrary network and in some special networks (ring, grid, hypercube). The second problem is coloring a synchronous ring with three colors. The routing problem is a very basic subroutine in many distributed algorithms; the three coloring problem demonstrates that pipelining is not always useful. Amotz Bar-Noy received his B.Sc. degree in Mathematics and Computer Science in 1981, and his Ph.D. degree in Computer Science in 1987, both from the Hebrew University of Jerusalem, Israel. Between 1987 and 1989 he was a post-doctoral fellow in the Department of Computer Science at Stanford University. He is currently a visiting scientist at the IBM Thomas J. Watson Research Center. His current research interests include the theoretical aspects of distributed and parallel computing, computational complexity and combinatorial optimization. Joseph (Seffi) Naor received his B.A. degree in Computer Science in 1981 from the Technion, Israel Institute of Technology. He received his M.Sc. in 1983 and Ph.D. in 1987 in Computer Science, both from the Hebrew University of Jerusalem, Israel. Between 1987 and 1988 he was a post-doctoral fellow at the University of Southern California, Los Angeles, CA. Since 1988 he has been a post-doctoral fellow in the Department of Computer Science at Stanford University. His research interests include combinatorial optimization, randomized algorithms, computational complexity and the theoretical aspects of parallel and distributed computing. Moni Naor received his B.A. in Computer Science from the Technion, Israel Institute of Technology, in 1985, and his Ph.D. in Computer Science from the University of California at Berkeley in 1989. He is currently a visiting scientist at the IBM Almaden Research Center. His research interests include computational complexity, data structures, cryptography, and parallel and distributed computation.Supported in part by a Weizmann fellowship and by contract ONR N00014-85-C-0731Supported by contract ONR N00014-88-K-0166 and by a grant from Stanford's Center for Integrated Systems. This work was done while the author was a post-doctoral fellow at the University of Southern California, Los Angeles, CAThis work was done while the author was with the Computer Science Division, University of California at Berkeley, and Supported by NSF grant DCR 85-13926     

Program transformation system based on generalized partial computation

Generalized Partial Computation (GPC) is a program transformation method utilizing partial information about input data, abstract data types of auxiliary functions and the logical structure of a source program. GPC uses both an inference engine such as a theorem prover and a classical partial evaluator to optimize programs. Therefore, GPC is more powerful than classical partial evaluators but harder to implement and control. We have implemented an experimental GPC system called WSDFU (Waseda Simplify-Distribute-Fold-Unfold). This paper demonstrates the power of the program transformation system as well as its theorem prover and discusses some future works. Yoshihiko Futamura, Ph.D.: He is Professor of Department of Information and Computer Science and the director of the Institute for Software Production Technology (ISPT) of Waseda University. He received his BS in mathematics from Hokkaido University in 1965, MS in applied mathematics from Harvard University in 1972 and Ph.D. degree from Hokkaido University in 1985. He joined Hitachi Central Research Laboratory in 1965 and moved to Waseda University in 1991. He was a visiting professor of Uppsala University from 1985 to 1986 and a visiting scholar of Harvard University from 1988 to 1989. Automatic generation of computer programs and programming methodology are his main research fields. He is the inventor of the Futamura Projections in partial evaluation and ISO8631 PAD (Problem Analysis Diagram). Zenjiro Konishi: He is a visiting lecturer of Institute for Software Production Technology, Waseda University. He received his M. Sc. degree in mathematics from Waseda University in 1995. His research interests include automated theorem proving. He received JSSST Takahashi Award in 2001. He is a member of JSSST and IPSJ. Robert Glück, Ph.D., Habil.: He is an Associate Professor of Computer Science at the University of Copenhagen. He received his Ph.D. and Habilitation (venia docendi) from the Vienna University of Technology in 1991 and 1997. He was research assistant at the City University of New York and received twice the Erwin-Schrodinger-Fellowship of the Austrian Science Foundation (FWF). After being an Invited Fellow of the Japan Society for the Promotion of Science (JSPS), he is now funded by the PRESTO21 program for basic research of the Japan Science and Technology Corporation (JST) and located at Waseda University in Tokyo. His main research interests are advanced programming languages, theory and practice of program transformation, and metaprogramming.     

P transducers

We introduce in this paper four classes of P transducers: arbitrary, initial, isolated arbitrary, isolated and initial. The first two classes are universal, they can compute the same word functions as Turing machines, the latter two are incomparable with finite state sequential transducers, generalized or not. We study the effect of the composition, and show that iteration increases the power of these latter classes, also leading to a new characterization of recursively enumerable languages. The “Sevilla carpet” of a computation is defined for P transducers, giving a representation of the control part for these P transducers. Gabriel Ciobanu, Ph.D.: He has graduated from the Faculty of Mathematics, “A.I.Cuza” University of Iasi, and received his Ph.D. from the same university. He is a senior researcher at the Institute of Computer Science of the Romanian Academy. He has wide-ranging interests in computing including distributed systems and concurrency, computational methods in biology, membrane computing, and theory of programming (semantics, formal methods, logics, verification). He has published around 90 papers in computer science and mathematics, a book on programming semantics and a book on network programming. He is a co-editor of three volumes. He has visited various universities in Europe, Asia, and North America, giving lectures and invited talks. His webpage is http://www.info.uaic.ro/gabriel Gheorghe Păun, Ph.D.: He has graduated from the Faculty of Mathematics, University of Bucharest, in 1974 and received his Ph.D. from the same university in 1977. Curently he works as senior researcher in the Institute of Mathematics of the Romanian Academy, as well as a Ramon y Cajal researcher in Sevilla University, Spain. He has repeatedly visited numerous universities in Europe, Asia, and North America. His main research areas are formal language theory and its applications, computational linguistics, DNA computing, and membrane computing (a research area initiated by him). He has published over 400 research papers (collaborating with many researchers worldwide), has lectured at over 100 universities, and gave numerous invited talks at recognized international conferences. He has published 11 books in mathematics and computer science, has edited about 30 collective volumes, and also published many popular science books and books on recreational mathematics (games). He is on the editorial boards of fourteen international journals in mathematics, computer science, and linguistics, and was/is involved in the program/steering/organizing commitees for many recognized conferences and workshops. In 1997 he was elected a member of the Romanian Academy. Gheorghe Ştefănescu, Ph.D.: He received his B.Sc./M.Sc./Ph.D. degrees in Computer Science from the University of Bucharest. Currently, he is a Professor of Computer Science at the University of Bucharest and a Senior Fellow at the National University of Singapore. Previously, he was a researcher at the Institute of Mathematics of the Romanian Academy and has held visiting positions in The Netherlands, Germany, and Japan. His current research focuses on formal methods in computer science, particularly on process and network algebras, formal methods for interactive, real-time, and object-oriented systems. Some of his results may be found in his book on “Network Algebra,” Springer, 2000.     

Evolvable hardware: A robot navigation system testbed

Recently there has been great interest in the design and study of evolvable systems based on Artificial Life principles in order to monitor and control the behavior of physically embedded systems such as mobile robots, plants and intelligent home devices. At the same time new integrated circuits calledsoftware-reconfigurable devices have been introduced which are able to adapt their hardware almost continuously to changes in the input data or processing. When the configuration phase and the execution phase are concurrent, the software-reconfigurable device is calledevolvable hardware (EHW). This paper examines an evolutionary navigation system for a mobile robot using a Boolean function approach implemented on gate-level evolvable hardware (EHW). The task of the mobile robot is to reach a goal represented by a colored ball while avoiding obstacles during its motion. We show that the Boolean function approach using dedicated evolution rules is sufficient to build the desired behavior and its hardware implementation using EHW allows to decrease the learning time for on-line training. We demonstrate the effectiveness of the generalization ability of the Boolean function approach using EHW due to its representation and evolution mechanism. The results show that the evolvable hardware configuration learned off-line in a simple environment creates a robust robot behavior which is able to perform the desired behaviors in more complex environments and which is insensitive to the gap between the real and simulated world. Didier Keymeulen, Ph.D.: He currently works as a senior research engineer at the Computer Science Division of Electrotechnical Laboratory, AIST, MITI, Japan. His research interests are in the design of adaptive physically embedded systems using biologically inspired complex dynamical systems. He studied electrical and computer science engineering at the Universite Libre de Bruxelles in 1987. He obtained his M. Sc. and PH. D. in Computer Science from the Artificial Intelligence Laboratory of the Vrije Universiteit Brussel, directed by Dr. Luc Steels, respectively in 1991 and 1994. He was the Belgium laureate of the Japanese JSPS Postdoctoral Fellowship for Foreign Researchers in 1995. Masaya Iwata, Ph.D.: He currently works as a researcher at the Computer Science Division of Electrotechnical Laboratory, AIST, MITI, Japan. His research interests are in developing adaptive hardware devices using genetic algorithms, and in their applications to pattern recognition and image compression. He received his B. E. in 1988, his M. E. in 1990, and his Ph. D. in 1993 in applied physics from the Osaka University. He was a postdoctoral fellow in optical computing at ONERA-CERT, Toulouse, France in 1993. Kenji Konaka: He is currently working as a software research engineer at the Humanoid Interaction Laboratory of the Intelligent Systems Division of Electrotechnical Laboratory, AIST, MITI, Japan. His current research interest is on real-time vision-based mobile robots working in cooperative mode. He has developped a highly interactive distributed real-time software and hardware platform for controlling a group of robots. Yasuo Kuniyoshi, Ph.D.: He is currently a senior research scientist and head of the Humanoid Interaction Laboratory at the Intelligent Systems Division of Electrotechnical Laboratory, AIST, MITI, Japan. His current research interest is on emergence of stable structures out of complex sensory-motor interactions by a humanoid robot. He received IJCAI93 Outstanding Paper A ward and several other awards in the field of intelligent robotics. He received the B. Eng. in applied physics in 1985, M. Eng. and Ph. D. in information engineering in 1988 and 1991 respectively, all from the University of Tokyo. Tetsuya Higuchi, Ph.D.: He heads the Evolvable Systems Laboratory in Electrotechnical Laboratory, AIST, MITI, Japan. He received B. E., M. E., Ph. D. degrees all in electrical engineering from Keio University in 1978, 1980, and 1984, respectively. His current interests include envolvable hardware systems, parallel processing architecture in artificial intelligence, and adaptive systems. He is also in charge of the adaptive devices group in the MITI national project, Real World Computing Project.     

Scheduling algorithms based on weakly hard real-time constraints

The problem of scheduling weakly hard real-time tasks is addressed in this paper.The paper first analyzes the characters of μ-pattern and weakly hard real-time constraints,then,presents two scheduling algorithms,Meet Any Algorithm and Meet Row Algorithm,for weakly hard real-time systems.Different from traditional algorithms used to guarantee deadlines,MeetAny Algorithm and Meet Row Algorithm can guarantee both deadlines and constraints.Meet Any Algorithm and Meet Row Algorithm try to find out the probabilities of tasks breaking constraints and increase task‘s priority in advance,but not till the last moment.Simulation results show that these two algorithms are better than other scheduling algorithms dealing with constraints and can largely decrease worst-case computation time of real-time tasks.     

Finite-horizon scheduling of radar dwells with online template construction

Timing constraints for radar tasks are usually specified in terms of the minimum and maximum temporal distance between successive radar dwells. We utilize the idea of feasible intervals for dealing with the temporal distance constraints. In order to increase the freedom that the scheduler can offer a high-level resource manager, we introduce a technique for nesting and interleaving dwells online while accounting for the energy constraint that radar systems need to satisfy. Further, in radar systems, the task set changes frequently and we advocate the use of finite horizon scheduling in order to avoid the pessimism inherent in schedulers that assume a task will execute forever. The combination of feasible intervals and online dwell packing allows modular schedule updates whereby portions of a schedule can be altered without affecting the entire schedule, hence reducing the complexity of the scheduler. Through extensive simulations we validate our claims of providing greater scheduling flexibility without compromising on performance when compared with earlier work based on templates constructed offline. We also evaluate the impact of two parameters in our scheduling approach: the template length (or the extent of dwell nesting and interleaving) and the length of the finite horizon. Sathish Gopalakrishnan is a visting scholar in the Department of Computer Science, University of Illinois at Urbana-Champaign, where he defended his Ph.D. thesis in December 2005. He received an M.S. in Applied Mathematics from the University of Illinois in 2004 and a B.E. in Computer Science and Engineering from the University of Madras in 1999. Sathish’s research interests concern real-time and embedded systems, and the design of large-scale reliable systems. He received the best student paper award for his work on radar dwell scheduling at the Real-Time Systems Symposium 2004. Marco Caccamo graduated in computer engineering from the University of Pisa in 1997 and received the Ph.D. degree in computer engineering from the Scuola Superiore S. Anna in 2002. He is an Assistant Professor of the Department of Computer Science at the University of Illinois. His research interests include real-time operating systems, real-time scheduling and resource management, wireless sensor networks, and quality of service control in next generation digital infrastructures. He is recipient of the NSF CAREER Award (2003). He is a member of ACM and IEEE. Chi-Sheng Shih is currently an assistant professor at the Graduate Institute of Networking and Multimedia and Department of Computer Science and Information Engineering at National Taiwan University since February 2004. He received the B.S. in Engineering Science and M.S. in Computer Science from National Cheng Kung University in 1993 and 1995, respectively. In 2003, he received his Ph.D. in Computer Science from the University of Illinois at Urbana-Champaign. His main research interests are embedded systems, hardware/software codesign, real-time systems, and database systems. Specifically, his main research interests focus on real-time operating systems, real-time scheduling theory, embedded software, and software/hardware co-design for system-on-a-chip. Chang-Gun Lee received the B.S., M.S. and Ph.D. degrees in computer engineering from Seoul National University, Korea, in 1991, 1993 and 1998, respectively. He is currently an Assistant Professor in the Department of Electrical Engineering, Ohio State University, Columbus. Previously, he was a Research Scientist in the Department of Computer Science, University of Illinois at Urbana-Champaign from March 2000 to July 2002 and a Research Engineer in the Advanced Telecomm. Research Lab., LG Information & Communications, Ltd. from March 1998 to February 2000. His current research interests include real-time systems, complex embedded systems, QoS management, and wireless ad-hoc networks. Chang-Gun Lee is a member of the IEEE Computer Society. Lui Sha graduated with the Ph.D. degree from Carnegie-Mellon University in 1985. He was a Member and then a Senior Member of Technical Staff at Software Engineering Institute (SEI) from 1986 to 1998. Since Fall 1998, he has been a Professor of Computer Science at the University of Illinois at Urbana Champaign, and a Visiting Scientist of the SEI. He was the Chair of IEEE Real Time Systems Technical Committee from 1999 to 2000, and has served on its Executive Committee since 2001. He was a member of National Academy of Science’s study group on Software Dependability and Certification from 2004 to 2005, and is an IEEE Distinguished Visitor (2005 to 2007). Lui Sha is a Fellow of the IEEE and the ACM.     

Life sciences grid in EUROGRID and GRIP projects

In this paper we describe deployment of most important life sciences applications on the grid. The build grid is heterogenous and consist of systems of different architecture as well as operating systems and various middleware. We have used UNICORE infrastructure as framework for development dedicated user interface to the number of existing computational chemistry codes and molecular biology databases. Developed solution allows for access to the resources provided with UNICORE as well as Globus with exactly the same interface which gives access to the general grid functionality such as single login, job submission and control mechanism. Jarosław Wypychowski: He is a student at the Faculty of Mathematics and Computer Science, Warsaw University, Poland. He is involved in the development of grid tools. He has been working as programmer in the private company. Jarosław Pytliński, M.Sc.: He received his M.Sc. in 2002 from Department of Mathematic and Computer Science of Nicolaus Copernicus University in Torun. His thesis on “Quantum Chemistry Computations in Grid Environment” was distincted in XIX Polish Contest for the best M.Sc. Thesis of Computer Science. He also worked in Laboratory of High Performance Systems at UCI, Torun. His interests are Artificial Intelligence and GRID technology. Łukasz Skorwider, M.Sc.: He is programmer in the private pharmaceutical company. He obtained M.Sc. degree from the Faculty of Mathematics and Computer Science N. Copernicus University. As graduate student he was involved in the development of grid tools for drug design. His private and professional interest is Internet technology. Mirosław Nazaruk, M.Sc.: He is a senior computer and network administrator at ICM Warsaw University. He provides professional support for the users of the high performance facilities located at the ICM. He obtained M.Sc. in Computer Science from Warsaw University in 1991. Before joining ICM, he was a member of technical staff at Institute of Applied Mathematics, Warsaw University. Krzysztof Benedyczak: He is a student at the Faculty of Mathematics and Computer Science, N. Copernicus University, Torun, Poland. He is involved in the development of grid tools. Michał Wroński: He is a student at the Faculty of Mathematics and Computer Science, N. Copernicus University, Torun, Poland. He is involved in the development of grid tools. Piotr Bała, Ph.D.: He is an adiunkt at Faculty of Mathematics and Computer Science N. Copernicus University, Torun, Poland, and tightly cooperates with ICM, Warsaw University. He obtained Ph.D. in Physics in 1993 in Institute of Physics, N. Copernicus University and in 2000 habilitation in physics. From 2001 he was appointed director of Laboratory of Parallel and Distributed Processing at Faculty of Mathematics, N. Copernicus University. His main research interest is development and application of Quantum-Classical Molecular Dynamics and Approximated Valence Bond method to study of enzymatic reactions in biological systems. In the last few years, he has been involved in development of parallel and grid tools for large scale scientific applications.     

Ranking-based evaluation of regression models

We suggest the use of ranking-based evaluation measures for regression models, as a complement to the commonly used residual-based evaluation. We argue that in some cases, such as the case study we present, ranking can be the main underlying goal in building a regression model, and ranking performance is the correct evaluation metric. However, even when ranking is not the contextually correct performance metric, the measures we explore still have significant advantages: They are robust against extreme outliers in the evaluation set; and they are interpretable. The two measures we consider correspond closely to non-parametric correlation coefficients commonly used in data analysis (Spearman's ρ and Kendall's τ); and they both have interesting graphical representations, which, similarly to ROC curves, offer useful various model performance views, in addition to a one-number summary in the area under the curve. An interesting extension which we explore is to evaluate models on their performance in “partially” ranking the data, which we argue can better represent the utility of the model in many cases. We illustrate our methods on a case study of evaluating IT Wallet size estimation models for IBM's customers. Saharon Rosset is Research Staff Member in the Data Analytics Research Group at IBM's T. J. Watson Research Center. He received his B.S. in Mathematics and M.Sc., in Statistics from Tel Aviv University in Israel, and his Ph.D. in Statistics from Stanford University in 2003. In his research, he aspires to develop practically useful predictive modeling methodologies and tools, and apply them to solve problems in business and scientific domains. Currently, his major projects include work on customer wallet estimation and analysis of genetic data. Claudia Perlich has received a M.Sc. in Computer Science from Colorado University at Boulder, a Diploma in Computer Science from Technische Universitaet in Darmstadt, and her Ph.D. in Information Systems from Stern School of Business, New York University. Her Ph.D. thesis concentrated on probability estimation in multi-relational domains that capture information of multiple entity types and relationships between them. Her dissertation was recognized as an additional winner of the International SAP Doctoral Support Award Competition. Claudia joined the Data Analytics Research group at IBM's T.J. Watson Research Center as a Research Staff Member in October 2004. Her research interests are in statistical machine learning for complex real-world domains and business applications. Bianca Zadrozny is currently an associate professor at the Computer Science Department of Federal Fluminense University in Brazil. Her research interests are in the areas of applied machine learning and data mining. She received her B.Sc. in Computer Engineering from the Pontifical Catholic University in Rio de Janeiro, Brazil, and her M.Sc. and Ph.D. in Computer Science from the University of California at San Diego. She has also worked as a research staff member in the data analytics research group at IBM T.J. Watson Research Center.     

S-Club: an overlay-based efficient service discovery mechanism in CROWN Grid

Information service plays a key role in grid system, handles resource discovery and management process. Employing existing information service architectures suffers from poor scalability, long search response time, and large traffic overhead. In this paper, we propose a service club mechanism, called S-Club, for efficient service discovery. In S-Club, an overlay based on existing Grid Information Service (GIS) mesh network of CROWN is built, so that GISs are organized as service clubs. Each club serves for a certain type of service while each GIS may join one or more clubs. S-Club is adopted in our CROWN Grid and the performance of S-Club is evaluated by comprehensive simulations. The results show that S-Club scheme significantly improves search performance and outperforms existing approaches. Chunming Hu is a research staff in the Institute of Advanced Computing Technology at the School of Computer Science and Engineering, Beihang University, Beijing, China. He received his B.E. and M.E. in Department of Computer Science and Engineering in Beihang University. He received the Ph.D. degree in School of Computer Science and Engineering of Beihang University, Beijing, China, 2005. His research interests include peer-to-peer and grid computing; distributed systems and software architectures. Yanmin Zhu is a Ph.D. candidate in the Department of Computer Science, Hong Kong University of Science and Technology. He received his B.S. degree in computer science from Xi’an Jiaotong University, Xi’an, China, in 2002. His research interests include grid computing, peer-to-peer networking, pervasive computing and sensor networks. He is a member of the IEEE and the IEEE Computer Society. Jinpeng Huai is a Professor and Vice President of Beihang University. He serves on the Steering Committee for Advanced Computing Technology Subject, the National High-Tech Program (863) as Chief Scientist. He is a member of the Consulting Committee of the Central Government’s Information Office, and Chairman of the Expert Committee in both the National e-Government Engineering Taskforce and the National e-Government Standard office. Dr. Huai and his colleagues are leading the key projects in e-Science of the National Science Foundation of China (NSFC) and Sino-UK. He has authored over 100 papers. His research interests include middleware, peer-to-peer (P2P), grid computing, trustworthiness and security. Yunhao Liu received his B.S. degree in Automation Department from Tsinghua University, China, in 1995, and an M.A. degree in Beijing Foreign Studies University, China, in 1997, and an M.S. and a Ph.D. degree in computer science and engineering at Michigan State University in 2003 and 2004, respectively. He is now an assistant professor in the Department of Computer Science and Engineering at Hong Kong University of Science and Technology. His research interests include peer-to-peer computing, pervasive computing, distributed systems, network security, grid computing, and high-speed networking. He is a senior member of the IEEE Computer Society. Lionel M. Ni is chair professor and head of the Computer Science and Engineering Department at Hong Kong University of Science and Technology. Lionel M. Ni received the Ph.D. degree in electrical and computer engineering from Purdue University, West Lafayette, Indiana, in 1980. He was a professor of computer science and engineering at Michigan State University from 1981 to 2003, where he received the Distinguished Faculty Award in 1994. His research interests include parallel architectures, distributed systems, high-speed networks, and pervasive computing. A fellow of the IEEE and the IEEE Computer Society, he has chaired many professional conferences and has received a number of awards for authoring outstanding papers.