Where Mathematics, Computer Science, Linguistics and Biology Meet: Essays in honour of Gheorghe Păun PDF
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WHERE MATHEMATICS, COMPUTER SCIENCE, LINGUISTICS AND BIOLOGY MEET Where Mathematics, Computer Science, Linguistics and Biology Meet Essays in honour of Gheorghe Paun Edited by Carlos Martin-Vide Rovira i Virgili University, Tarragona, Spain and Victor Mitrana University of Bucharest, Bucharest, Romania Springer Science+Business Media, B.V. AA CC..II..PP.. CCaattaalloogguuee rreeccoorrdd ffoorr tthhiiss bbooookk iiss aavvaaiillaabbllee ffrroomm tthhee LLiibbrraarryy ooff CCoonnggrreessss.. ISBN 978-90-481-5607-8 ISBN 978-94-015-9634-3 (eBook) DOI 10.1007/978-94-015-9634-3 PPrriinntteedd oann aacciidd--ffrreeee ppaappeerr AAIlIl RRiigghhttss RReesseerrvveedd ©© 22000011 SSpprriinnggeerr SScciieennccee++BBuussiinneessss MMeeddiiaa DDoorrddrreecchhtt OOrriiggiinnaallllyy ppuubblliisshheedd bbyy KKlluuwweerr AAccaaddeemmiicc PPuubblliisshheerrss iinn 22000011 SSooffttccoovveerr rreepprriinntt ooff tthhee hhaarrddccoovveerr 11ss tt eeddiittiioonn 22000011 NNoo ppaarrtt ooff tthhee mmaatteerriiaall pprrootteecctteedd bbyy tthhiiss ccooppyyrriigghhtt nnoottiiccee mmaayy bbee rreepprroodduucceedd aorr uuttiilliizzeedd iinn aannyy ffoorrmm oorr bbyy aannyy mmeeaannss,, eelleeccttrroonniicc aorr mmeecchhaanniiccaall,, iinncdluuddiinngg pphhoottooccooppyyiinngg,, rreeccoarrddiinngg aorr bbyy aannyy iinnffaorrmmaattiioonn ssttoorraaggee aanndd rreettrriieevvaall ssyysstteemm,, wwiitthhoouutt wwrriitttteenn ppeerrmmiiss ssiioonn ffrroomm tthhee ccooppyyrriigghhtt oowwnneerr.. Contents Preface ix Contributing Authors xiii 1 The Games of His Life 1 Solomon Marcus Part I GRAMMARS AND GRAMMAR SYSTEMS 2 Deterministic Stream X-Machines Based on Grammar Systems 13 Tudor Biiliinescu, Marian Gheorghe, Mike Holcombe 3 Some Ghosts that Arise in a Spliced Linguistic String: 25 Evidence from Catalan Gemma Bel-Enguix 4 On Size Complexity of Context-Free Returning Parallel 37 Communicating Grammar Systems Erzsebet Csuhaj-Varju 5 Subregularly Controlled Derivations: Restrictions by 51 Syntactic Parameters liirgen Dassow 6 Neo-Modularity and Colonies 63 loze! Kelemen, Alica Kelemenowi, Victor Mitrana v vi WHERE MATHEMATICS, COMPUTER SCIENCE, liNGUISTICS ... 7 Sewing Contexts and Mildly Context-Sensitive Languages 75 Carlos Martln-Vide, Alexandru Mateescu, Arto Salomaa 8 Towards Grammars of Decision Algorithms 85 Leck Polkowski, Andrzej Skowron Part II AUTOMATA 9 Computational Complementarity for Probabilistic Automata 99 Cristian S. Calude, Elena Calude, Karl Svozil 10 Acceptance of w-Languages by Communicating Deterministic 115 Thring Machines Rudolf Freund, LudWig Staiger 11 Counter Machines and the Safety and Disjointness Problems for 127 Database Queries with Linear Constraints Oscar H. Ibarra, Jianwen Su, Constantinos Bartzis 12 Automata Arrays and Context-Free Languages 139 Martin Kutrib 13 On Special Forms of Restarting Automata 149 FrantiJek Mraz, Martin Platek, Martin Prochazka 14 The Time Dimension of Computation Models 161 Sheng Yu Part ill LANGUAGES AND COMBINATORICS 15 An Infinite Sequence of Full AFL-Structures, Each of Which 175 Possesses an Infinite Hierarchy Peter R.J. Asveld 16 Trellis Languages 187 Adrian Atanasiu 17 Pictures, Layers, Double Stranded Molecules: On 199 Multi-Dimensional Sentences Paolo Bottoni Contents vii 18 Transduction in Polypodes 211 Symeon Bozapalidis 19 Some Algebraic Properties of Contexts and Their Applications to 219 Contextual Languages Rodica Ceterchi 20 On Fatou Properties of Rational Languages 227 Christian Choffrut, Juhani Karhumiiki 21 Multiple Keyword Patterns in Context-Free Languages 237 Pal DOmOsi, Masami Ito 22 Reading Words in Graphs Generated by Hyperedge Replacement 243 Frank Drewes, Hans-Jorg Kreowski 23 Regularly Controlled Formal Power Series 253 Henning Fernau, Werner Kuich 24 Forbidden Subsequences and Permutations Sortable on Two 267 Parallel Stacks Tero Harju, Lucian !lie 25 Approximate Identification and Finite Elasticity 277 Satoshi Kobayashi, Yasubumi Sakakibara, Takashi Yokomori 26 Insertion of Languages and Differential Semirings 287 Gabriel Thierrin Part IV MODELS OF MOLECULAR COMPUTING 27 Molecular Structures 299 Gabriel Ciobanu 28 A Characterization of Non-Iterated Splicing with Regular Rules 319 Ray Dassen, Hendrik Jan Hoogeboom, Nike van Vugt 29 Universal and Simple Operations for Gene Assembly in Ciliates 329 Andrzej Ehrenfeucht, Ion Petre, David M. Prescott, Grzegorz Rozenberg viii WHERE MATHEMATICS, COMPUTER SCIENCE, LINGUISTICS ... 30 Semi-Simple Splicing Systems 343 Elizabeth Goode, Dennis Pixton 31 Writing By Methylation Proposed For Aqueous Computing 353 Tom Head 32 Context-Free Recombinations 361 Jarkko Kari, Lila Kari 33 Simplified Simple H Systems 377 Kamala Krithivasan, Arvind Arasu 34 On Some Forms of Splicing 387 Vincenzo Manca 35 Time-Varying Distributed H -Systems of Degree 2 Generate All 399 Recursively Enumerable Languages Maurice Margenstern, Yurii Rogozhin 36 On Membrane Computing Based on Splicing 409 Andrei Piiun, Mihaela Piiun 37 Is Evolutionary Computation Using DNA Strands Feasible? 423 Jose Rodrigo, Juan Castellanos, Fernando Arroyo, Luis Fernando Mingo 38 Splicing Systems Using Merge and Separate Operations 435 Claudio Zandron, Giancarlo Mauri, Claudio Ferretti, Paola Bonizzoni Preface In the last years, it was observed an increasing interest of computer scientists in the structure of biological molecules and the way how they can be manipulated in vitro in order to define theoretical models of computation based on genetic engineering tools. Along the same lines, a parallel interest is growing regarding the process of evolution of living organisms. Much of the current data for genomes are expressed in the form of maps which are now becoming available and permit the study of the evolution of organisms at the scale of genome for the first time. On the other hand, there is an active trend nowadays throughout the field of computational biology toward abstracted, hierarchical views of biological sequences, which is very much in the spirit of computational linguistics. In the last decades, results and methods in the field of formal language theory that might be applied to the description of biological sequences were pointed out. Let us briefly provide an example. The structural representation of the syntactic information used by any parsing algorithm is a parse tree, which would appear to any biologist to be a reasonable representation of the hierarchical construction of a typical gene. We can fairly ask, then, to what extent a grammar-based approach could be generalized. Moreover, is such an approach suitable to be used for computing? It may be assumed that the distin.ction between the structural and the func tional or informational view of biological sequences corresponds to the conven tional (and controversial) one drawn between syntax and semantics of natural languages. The functional view will allow us to expand our horizons beyond the local phenomena of syntactic structure to large regions of DNA. It appears crucial, in this respect, to define the semantics of DNA, which is mainly based on evolutionary selection, in order to linguistically reason about the processes of evolution as well as about computational capacity matters. We may certainly say that a new field has emerged at the crossroads of molec ular biology, linguistics and formal language theory. It can be considered as ix x WHERE MATHEMATICS, COMPUTER SCIENCE, UNGUlSTlCS ... a young brother of another field born in the last decade, that of Bioinfonnat ics. At the same time, such a field is a part of a set of biologically-inspired, fonnally rigorous new disciplines that shows close connections with linguistics and includes neural networks, genetic algorithms, etc. Our volume has two goals. One is to present some recent results in active areas of the three domains that converge in the new field. The other one is to celebrate the 50th birthday of Gheorghe Paun, who, from fonnallanguage theory, promoted the new research area and made seminal contributions to it; his scientific career is simply exceptional from any point of view we may look at it, and all people having wished to contribute to this collective work are pride of having him as a friend. The contributions are grouped into four sections, plus an introductory pa per written by Solomon Marcus, who has been Gheorghe Paun's mentor for many years. The first section, Grammars and Grammar Systems, is devoted to grammatical fonnalisms. Classical aspects of fonnal grammar theory are presented, like regulated rewriting in connection with descriptional complexity or contextual grammars, as well as more recent ones as grammar systems and colonies, with motivations coming from robotic systems design. It includes also papers that use grammar fonnalisms for modeling aspects of natural languages, concurrency or data knowledge in multi-agent systems. New trends in a traditional model of computation, that of Automata, are presented in the second section. The papers contained in it show that finite automata, transducers or Turing machines still pose lots of interesting problems. Detenninistic iterated finite transducers, probabilistic automata, and distributed automata that cooperate under strategies similar to those met in the area of grammar systems are investigated from the viewpoint of their computational power. Furthennore, relevant issues in database theory are approached by means of automata. The next section, Languages and Combinatorics, provides recent results about algebraic properties oflanguages, regulated rewriting in the framework of fonnal power series, combinatorics on words, sequences, graphs and language representations suggested by techniques widely utilized in the field of signal coding. Combinatorial algorithms are also discussed for problems that appear in some infonnation processing activities. The last section, Models of Molecular Computing, gives a glimpse of a new and attractive area in computer science that is looking for grammar models of computations based on DNA manipulation. One tries to provide an answer to a hot and quite exciting problem: do molecules compute (and how, if it is the case)? Both enthusiastic and rather pessimistic views are expressed with respect to the possibility of having 'wet' computers using DNA strands. Other molecules that have the potential capacity of computing are presented, too. PREFACE xi Most of the contributions deal with the basic operation of splicing, viewed as a very simple model of DNA recombination. All the papers are contributed by Gheorghe Paun's collaborators, colleagues, friends and students in the five continents, who wanted to show in this way their recognition to him for his tremendous work. We have collected 38 papers by 75 authors here. (Another set of 38 papers by 65 authors will be published soon in the future.) The title of this volume intends to reflect the temporal sequence of Gheorghe Paun's scientific concerns along the time. Summing up, this book makes an interdisciplinary journey from classical formal grammars and automata topics, which still constitute the core of mathe maticallinguistics, to some of their most recent applications in natural language processing and molecular computing. The editors must stress M. Dolores Jimenez-Lopez's crucial collaboration in the technical preparation of the volume as well as Kluwer's wann receptiveness from the very beginning. We hope this book will be a further step in the reviving of formal language theory as an essentially interdisciplinary field, and will be understood as an act of scientific justice and gratitude towards Gheorghe paun. Tarragona, July 2000 Carlos Martin-Vide Victor Mitrana
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