Basic research in computer science and software engineering at SKLCS

The State Key Laboratory of Computer Science (SKLCS) is committed to basic research in computer science and software engineering. The research topics of the laboratory include: concurrency theory, theory and algorithms for real-time systems, formal specifications based on context-free grammars, semantics of programming languages, model checking, automated reasoning, logic programming, software testing, software process improvement, middleware technology, parallel algorithms and parallel software, computer graphics and human-computer interaction. This paper describes these topics in some detail and summarizes some results obtained in recent years.     

Basic research in computer science and software engineering at SKLCS

The State Key Laboratory of Computer Science (SKLCS) is committed to basic research in computer science and software engineering. The research topics of the laboratory include: concurrency theory, theory and algorithms for real-time systems, formal specifications based on context-free grammars, semantics of programming languages, model checking, automated reasoning, logic programming, software testing, software process improvement, middleware technology, parallel algorithms and parallel software, computer graphics and human-computer interaction. This paper describes these topics in some detail and summarizes some results obtained in recent years.     

Step semantics for “true” concurrency with recursion

We present a variety of denotational linear time semantics for a language with recursion and true concurrency in a form of synchronous co-operation, which in the literature is known as step semantics. We show that this can be done by a generalization of known results for interleaving semantics. A general method is presented to define semantical operators and denotational semantics in the Smyth powerdomain of streams. With this method, first a naive and then more sophisticated semantics for synchronous co-operation are developed, which include such features as interleaving and synchronization. Then we refine the semantics to deal with a bounded number of processors, subatomic actions, maximal parallelism and a real-time operator. Finally, it is indicated how to apply these ideas to branching-time models, where it becomes possible to analyze deadlock behaviour as well as a form of true concurrency. John-Jules Meyer received his Master's degree in Mathematics in 1979 from the University of Leiden, and his Ph.D. degree in 1985 from the Free University Amsterdam. He is currently a Professor of Theoretical Computer Science, both at the Free University Amsterdam and at the University of Nijmegen. His current research interests include semantics of programming languages and logics for computer science, in particular artifical intelligence. Erik de Vink received the M.S. degree in Mathematics from the University of Amsterdam. He is currently a Junior Researcher at the Department of Mathematics and Computer Science of the Free University Amsterdam. At the moment his main research concerns the semantics of concurrent and logic programming languages.     

A unifying approach to goal-directed evaluation

Goal-directed evaluation, as embodied in Icon and Snobol, is built on the notions of backtracking and of generating successive results, and therefore it has always been something of a challenge to specify and implement. In this article, we address this challenge using computational monads and partial evaluation. We consider a subset of Icon and we specify it with a monadic semantics and a list monad. We then consider a spectrum of monads that also fit the bill, and we relate them to each other. For example, we derive a continuation monad as a Church encoding of the list monad. The resulting semantics coincides with Gudeman’s continuation semantics of Icon. We then compile Icon programs by specializing their interpreter (i.e., by using the first Futamura projection), using type-directed partial evaluation. Through various back ends, including a run-time code generator, we generate ML code, C code, and OCaml byte code. Binding-time analysis and partial evaluation of the continuation-based interpreter automatically give rise to C programs that coincide with the result of Proebsting’s optimized compiler. Basic Research in Computer Science (www.brics. dk), funded by the Danish National Research Foundation. Olivier Danvy, Ph.D., Habilitation: He is an Associate Professor at the Department of Computer Science at the University of Aarhus, in Denmark. He obtained his Ph.D. degree in 1986 and his Habilitation in 1993 from the Université Pierre et Marie Curie (Paris VI), France. His research interests are in Programming Languages in general and in Partial Evaluation and Continuations in particular. He has published over 75 refereed research papers and edited several proceedings. He has both served on and chaired program committees of scientific meetings in the area of Programming Languages. He is presently chairing the PEPM steering committee at ACM SIGPLAN and serving as external reviewer in computer science for the Danish Universities, as board member in the BRICS PhD School, and as co-Editor-in-Chief of the journal Higher-Order and Symbolic Computation (http://www.wkap.nl/journals/hosc). Bernd Grobauer, M.Sc.: He is a Ph.D. student at the BRICS International Ph.D. school, University of Aarhus, Denmark, and will graduate in the summer of 2001. He obtained his Masters degree from the Munich University of Technology (TUM), Germany. His research interests are in formal methods (especially theorem proving) and programming languages (semantics of programming languages, program analysis, program transformation, types). He serves as editorial assistant for the journal Higher-Order and Symbolic Computation and as chairman of the BRICS Juniorklubben. Morten Rhiger, M.Sc.: He is a Ph.D. student at the BRICS International Ph.D. school, University of Aarhus, Denmark, and will graduate in the summer of 2001. He obtained his Masters degree from the University of Aarhus in 1998. His research interests are in the semantics and implementation of programming languages.     

A Graphical μ—Calculus and Local Model Checking

A graphical notation for the propositional μ-calculus,called modal graphs,is presented.It is shown that both the textual an equational presentations of the μ-calculus can be translated into modal graphs.A model checking algorithm based on such graphs is proposed.The algorithm is truly local in the sense that it only generates the parts of the underlying search space which are necessary for the computation of the final result.The correctness of the algorithm is proven and its complexity analysed.     

Model Checking Real-Time Value-Passing Systems

In this paper, to model check real-time value-passing systems, a formal language Timed Symbolic Transition Graph and a logic system named Timed Predicate p-Calculus are proposed. An algorithm is presented which is local in that it generates and investigates the reachable state space in top-down fashion and maintains the partition for time evaluations as coarse as possible while on-the-fly instantiating data variables. It can deal with not only data variables with finite value domain, but also the so called data independent variables with infinite value domain. To authors knowledge, this is the first algorithm for model checking timed systems containing value-passing features.     

Testing Congruence for Mobile Processes

Testing equivalence on πprocesses has been studied in literature.The equivalence is not closed under the iuput prefix operator and is therefore not a congruence relation.This note takes a look at testing congruence on fipite π processes.A complete equational system is given for the congruence relation.     

Exploiting edge semantics in citation graphs using efficient, vertical ARM

Graphs are increasingly becoming a vital source of information within which a great deal of semantics is embedded. As the size of available graphs increases, our ability to arrive at the embedded semantics grows into a much more complicated task. One form of important hidden semantics is that which is embedded in the edges of directed graphs. Citation graphs serve as a good example in this context. This paper attempts to understand temporal aspects in publication trends through citation graphs, by identifying patterns in the subject matters of scientific publications using an efficient, vertical association rule mining model. Such patterns can (a) indicate subject-matter evolutionary history, (b) highlight subject-matter future extensions, and (c) give insights on the potential effects of current research on future research. We highlight our major differences with previous work in the areas of graph mining, citation mining, and Web-structure mining, propose an efficient vertical data representation model, introduce a new subjective interestingness measure for evaluating patterns with a special focus on those patterns that signify strong associations between properties of cited papers and citing papers, and present an efficient algorithm for the purpose of discovering rules of interest followed by a detailed experimental analysis. Imad Rahal is a newly appointed assistant professor in the Department of Computer Science at the College of Saint Benedict ∣ Saint John's University, Collegeville, MN, and a Ph.D. candidate at North Dakota State University, Fargo, ND. In August 2003, he earned his master's degree in computer science from North Dakota State University. Prior to that, he graduated summa cum laude from the Lebanese American University, Beirut, Lebanon, in February 2001 with a bachelor's degree in computer science. Currently, he is completing the final requirements for his Ph.D. degree in computer science on an NSF ND-EPSCoR doctoral dissertation assistantship with August of 2005 as a projected completion date. He is very active in research, proposal writing, and publications; his research interests are largely in the broad areas of data mining, machine learning, databases, artificial intelligence, and bioinformatics. Dongmei Ren is working for the Database Technology Institute for z/OS, IBM Silicon Valley Lab, San Jose, CA, as a staff software engineer. She holds a Ph.D. degree from North Dakota State University, Fargo, ND, and master's and bachelor's degrees from TianJin University, TianJin, China. She has been a software engineer at DaTang Telecommunications, Beijing, China. Her areas of expertise are outlier analysis, data mining and knowledge discovery, database systems, machine learning, intelligent systems, wireless networks and bioinformatics. She has been awarded the Siemens Scholarship research enhancement for excellent performance in study and research. She is a member of ACM, IEEE. Weihua Wu is a network monitoring & managed services analyst at Hewlett-Packard Co. in Canada. He holds a master's degree from North Dakota State University and a bachelor's degree from Nanjing University, both in computer science. His research areas of interest include data mining, knowledge discovery, data warehousing, information technology, network security, and bioinformatics. He has participated in various projects supported by NSF, DARPA, NASA, USDA, and GSA grants. Anne Denton is an assistant professor in computer science at North Dakota State University. Her research interests are in data mining, knowledge discovery in scientific data, and bioinformatics. Specific interests include data mining of diverse data, in which objects are characterized by a variety of properties such as numerical and categorical attributes, graphs, sequences, time-dependent attributes, and others. She received her Ph.D. in physics from the University of Mainz, Germany, and her M.S. in computer science from North Dakota State University, Fargo, ND. Christopher Besemann received his M.Sc. in computer science from North Dakota State University in Fargo, ND, 2005. Currently, he works in data mining research topics including association mining and relational data mining with recent work in model integration as a research assistant. He is accepted under a fellowship program for Ph.D. study at North Dakota State University. William Perrizo is a professor of computer science at North Dakota State University. He holds a Ph.D. degree from the University of Minnesota, a master's degree from the University of Wisconsin and a bachelor's degree from St. John's University. He has been a research scientist at the IBM Advanced Business Systems Division and the U.S. Air Force Electronic Systems Division. His areas of expertise are data mining, knowledge discovery, database systems, distributed database systems, high speed computer and communications networks, precision agriculture and bioinformatics. He is a member of ISCA, ACM, IEEE, IAAA, and AAAS.     

The narrowing-driven approach to functional logic program specialization

Partial evaluation is a semantics-based program optimization technique which has been investigated within different programming paradigms and applied to a wide variety of languages. Recently, a partial evaluation framework for functional logic programs has been proposed. In this framework, narrowing—the standard operational semantics of integrated languages—is used to drive the partial evaluation process. This paper surveys the essentials of narrowing-driven partial evaluation. Elvira Albert, Ph.D.: She is an associate professor in Computer Science at the Technical University of Valencia, Spain. She received her bachelors degree in computer science in 1998 and her Ph.D. in computer science in 2001, both from the Technical University of Valencia. She has investigated on program optimization and on partial evaluation for declarative multi-paradigm programming languages. Her current research interests include term rewriting, multi-paradigm declarative programming, and formal methods, in particular semantics-based program analysis, transformation, specification, verification, and debugging. Germán Vidal, Ph.D.: He is an associate professor in Computer Science at the Technical University of Valencia, Spain. He obtained his bachelors degree in computer science in 1992 and his Ph.D. in computer science in 1996, both from the Technical University of Valencia. He is active on several research topics in Functional Logic Programming. He has worked on compositionality, on abstract interpretation, and on program transformation techniques for functional logic programs. Currently, his research interests include declarative multi-paradigm programming languages, term rewriting, and semantics-based program manipulation, in particular partial evaluation.     

PRIME: A Mass Spectrum Data Mining Tool for <Emphasis Type="Italic">De Nova</Emphasis> Sequencing and PTMs Identification

De novo sequencing is one of the most promising proteomics techniques for identification of protein posttranslation modifications (PTMs) in studying protein regulations and functions. We have developed a computer tool PRIME for identification of b and y ions in tandem mass spectra, a key challenging problem in de novo sequencing. PRIME utilizes a feature that ions of the same and different types follow different mass-difference distributions to separate b from y ions correctly. We have formulated the problem as a graph partition problem. A linear integer-programming algorithm has been implemented to solve the graph partition problem rigorously and efficiently. The performance of PRIME has been demonstrated on a large amount of simulated tandem mass spectra derived from Yeast genome and its power of detecting PTMs has been tested on 216 simulated phosphopeptides.     

Fairness and hyperfairness in multi-party interactions

Summary In this paper, a new fairness notion is proposed for languages withmulti-party interactions as the sole interprocess synchronization and communication primitive. The main advantage of this fairness notion is the elimination of starvation occurring solely due to race conditions (i.e., ordering of independent actions). Also, this is the first fairness notion for such languages which is fully adequate with respect to the criteria presented in [2]. The paper defines the notion, proves its properties, and presents examples of its usefulness. Orna Grumberg received her B.Sc. degree, M.Sc. and Ph.D. in the Computer Science Department at the Technion—Israel Institute of Technology. Since 1984 she is a faculty member in the Computer Science Department at the Technion. Her research interests include verification of distributed systems, computer-aided verification, model checking, temporal logics and automata. Paul Attie received a B.A. degree in engineering science from the University of Oxford, and an M.Sc. degree in computer science from the University of London. Since 1986, Paul has been with the Microelectronics and Computer Technology Corporation, where he is currently a member of technical staff. He is also a candidate for the Ph.D. in computer science degree at the University of Texas at Austin. His research interests include temporal logic, fairness, algebraic process theory, formal semantics, and concurrent program verification.The photograph and autobiography of Dr. Nissim Francez were published in Volume 2, Issue No. 4, 1988 on page 226     

Topology in Process Calculus (Ⅰ):Limit Behaviour of Agents

This paper introduces the modifications on actions of a topology on names of actions and te simplest topology on agents induced by a topology on names of actions and shows that the limit behaviour of some agents is compatible with transitional semantics.     

Symmetric π-Calculus

An alternative presentation of the π－calculus is given.This version of the π-calculus is symmetric in the sense that communications are symmetric and there is no difference between input and output prefixes.The point of the symmetric π-calculus is that it has no abstract names.The set of closed names is therefore homogeneous.The π－calculus can be fully embedded into the symmetric π-calculus.The symmetry changes the emphasis of the communication mechanism of the π-calculus and opens up possibility for further variations.     

Event-based operational semantics and a consistency result for real-time concurrent processes with action refinement

In this paper an event-based operational interleaving semantics is proposed for real-time processes,for which action refinement and a denotational true concurrency semantics are developed and defined in terms of timed event structures. The authors characterize the timed event traces that are generated by the operational semantics in a denotational way, and show that this operational semantics is consistent with the denotational semantics in the sense that they generate the same set of timed event traces, thereby eliminating the gap between the true concurrency and interleaving semantics.     

Hierarchies of parallel rewriting P systems — A survey

The paper is about some families of rewriting P systems, where the application of evolution rules is extended from the classical sequential rewriting to the parallel one (as, for instance, in Lindenmayer systems). As a result, consistency problems for the communication of strings may arise. Three variants of parallel rewriting P systems (already present in the literature) are considered here, together with the strategies they use to face the communication problem, and some parallelism methods for string rewriting are defined. We give a survey of all known results about each variant and we state some relations among the three variants, thus establishing hierarchies of parallel rewriting P systems. Various open problems related to the subject are also presented. Danicla Besozzi: She is assistant professor at the University of Milano. She received her M.S. in Mathematics (2000) from the University of Como and Ph.D. in Computer Science (2004) from the University of Milano. Her research interests cover topics in Formal Language Theory, Molecular Computing, Systems Biology. She is member of EATCS (European Association for Theoretical Computer Science) and EMCC (European Molecular Computing Consortium). Giancarlo Mauri: He is full professor of Computer Science at the University of Milano-Bicocca. His research interests are mainly in the area of theoretical computer science, and include: formal languages and automata, computational complexity, computational learning theory, soft computing techniques, cellular automata, bioinformatics and molecular computing. On these subjects, he published more than 150 scientific papers in international journals, contributed volumes and conference proceedings. Claudio Zandron: He received Ph.D. in Computer Science at the University of Milan, Italy, in 2001. Since 2002 he is assistant professor at the University of Milano-Bicocca, Italy. He is member of the EATCS (European Association for Theoretical Computer Science) and of EMCC (European Molecular Computing Consortium). His research interests are Molecular Computing (DNA and Membrane Computing) and Formal Languages.     

Category-based modularisation for equational logic programming

Although modularisation is basic to modern computing, it has been little studied for logic-based programming. We treat modularisation for equational logic programming using the institution of category-based equational logic in three different ways: (1) to provide a generic satisfaction condition for equational logics; (2) to give a category-based semantics for queries and their solutions; and (3) as an abstract definition of compilation from one (equational) logic programming language to another. Regarding (2), we study soundness and completeness for equational logic programming queries and their solutions. This can be understood as ordinary soundness and completeness in a suitable “non-logical” institution. Soundness holds for all module imports, but completeness only holds for conservative module imports. Category-based equational signatures are seen as modules, and morphisms of such signatures as module imports. Regarding (3), completeness corresponds to compiler correctness. The results of this research applies to languages based on a wide class of equational logic systems, including Horn clause logic, with or without equality; all variants of order and many sorted equational logic, including working modulo a set of axioms; constraint logic programming over arbitrary user-defined data types; and any combination of the above. Most importantly, due to the abstraction level, this research gives the possibility to have semantics and to study modularisation for equational logic programming developed over non-conventional structures. Received April 15, 1994/April 12, 1995     

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.     

On the completeness of SLDENF-resolution

SLDENF-resolution combines the negation-as-failure principle for logic programs involving negation, and SLDE-resolution for logic programs with an underlying equational theory. Recently, J. Shepherdson proved the soundness of this resolution principle wrt. an extended completion semantics. In this note, we investigate the particular problems of obtaining completeness which are caused by adding equational theories. As a concrete result we show to what extent the classical result for hierarchical and allowed nonequational programs can be generalized.