On inverse deterministic pushdown transductions

AbstractClasses of source languages which can be mapped by a deterministic pushdown (DPDA) transduction into a given object language (while their complement is mapped into the complement of the object language) are studied. Such classes of source languages are inverse DPDA transductions of the given object language. Similarly for classes of object languages. The inverse DPDA transductions of the Dyck sets are studied in greater detail: they can be recognized in deterministic storage (log n)' but do not comprise all context free languages; their emptiness problem is unsolvable and their closure under homomorphism constitutes the r.e. sets. For each object language L we can exhibit a storage hardest language for the class of inverse DPDA transductions of L; similarly for the classes of regular, deterministic context free, and context free object languages. Last, we classify the classes of inverse DPDA transductions of the regular, deterministic context free, context free and deterministic context sensitive languages

Efficient String Matching on Coded Texts

The so called "four Russians technique'' is often used to speed up algorithms by encoding several data items in a single memory cell. Given a sequence of n symbols over a constant size alphabet, one can encode the sequence into O(n / lambda) memory cells in O(log(lambda) ) time using n / log(lambda) processors. This paper presents an efficient CRCW-PRAM string-matching algorithm for coded texts that takes O(log log(m/lambda)) time making only O(n / lambda ) operations, an improvement by a factor of lambda = O(log n) on the number of operations used in previous algorithms. Using this string-matching algorithm one can test if a string is square-free and find all palindromes in a string in O(log log n) time using n / log log n processors

Algorithms and lower bounds in finite automata size complexity

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.Includes bibliographical references (p. 97-99).In this thesis we investigate the relative succinctness of several types of finite automata, focusing mainly on the following four basic models: one-way deterministic (1)FAs), one-way nondeterministic (1NFAs), two-way deterministic (2DFAS), and two-way nondeterministic (2NFAS). First, we establish the exact values of the trade-offs for all conversions from two-way to one-way automata. Specifically, we prove that the functions ... return the exact values of the trade-offs from 2DFAS to 1DFAS, from 2NFAS to 1DFAs, and from 2DFAs or 2NFAS to 1NFAs, respectively. Second, we examine the question whether the trade-offs from NFAs or 2NFAS to 2DiFAs are polynomial or not. We prove two theorems for liveness, the complete problem for the conversion from 1NFAS to 2DFAS. We first focus on moles, a restricted class of 2NFAs that includes the polynomially large 1NFAS which solve liveness. We prove that, in contrast, 2DFA moles cannot solve liveness, irrespective of size.(cont.) We then focus on sweeping 2NFAS, which can change the direction of their input head only on the end-markers. We prove that all sweeping 2NFAs solving the complement of liveness are of exponential size. A simple modification of this argument also proves that the trade-off from 2DFAS to sweeping 2NFAS is exponential. Finally, we examine conversions between two-way automata with more than one head-like devices (e.g., heads, linearly bounded counters, pebbles). We prove that, if the automata of some type A have enough resources to (i) solve problems that no automaton of some other type B can solve, and (ii) simulate any unary 2DFA that has additional access to a linearly-bounded counter, then the trade-off from automata of type A to automata of type B admits no recursive upper bound.by Christos Kapoutsis.Ph.D

Formal models of the extension activity of DNA polymerase enzymes

The study of formal language operations inspired by enzymatic actions on DNA is part of ongoing efforts to provide a formal framework and rigorous treatment of DNA-based information and DNA-based computation. Other studies along these lines include theoretical explorations of splicing systems, insertion-deletion systems, substitution, hairpin extension, hairpin reduction, superposition, overlapping concatenation, conditional concatenation, contextual intra- and intermolecular recombinations, as well as template-guided recombination. First, a formal language operation is proposed and investigated, inspired by the naturally occurring phenomenon of DNA primer extension by a DNA-template-directed DNA polymerase enzyme. Given two DNA strings u and v, where the shorter string v (called the primer) is Watson-Crick complementary and can thus bind to a substring of the longer string u (called the template) the result of the primer extension is a DNA string that is complementary to a suffix of the template which starts at the binding position of the primer. The operation of DNA primer extension can be abstracted as a binary operation on two formal languages: a template language L1 and a primer language L2. This language operation is called L1-directed extension of L2 and the closure properties of various language classes, including the classes in the Chomsky hierarchy, are studied under directed extension. Furthermore, the question of finding necessary and sufficient conditions for a given language of target strings to be generated from a given template language when the primer language is unknown is answered. The canonic inverse of directed extension is used in order to obtain the optimal solution (the minimal primer language) to this question. The second research project investigates properties of the binary string and language operation overlap assembly as defined by Csuhaj-Varju, Petre and Vaszil as a formal model of the linear self-assembly of DNA strands: The overlap assembly of two strings, xy and yz, which share an overlap y, results in the string xyz. In this context, we investigate overlap assembly and its properties: closure properties of various language families under this operation, and related decision problems. A theoretical analysis of the possible use of iterated overlap assembly to generate combinatorial DNA libraries is also given. The third research project continues the exploration of the properties of the overlap assembly operation by investigating closure properties of various language classes under iterated overlap assembly, and the decidability of the completeness of a language. The problem of deciding whether a given string is terminal with respect to a language, and the problem of deciding if a given language can be generated by an overlap assembly operation of two other given languages are also investigated

Proceedings of JAC 2010. Journées Automates Cellulaires

The second Symposium on Cellular Automata “Journ´ees Automates Cellulaires” (JAC 2010) took place in Turku, Finland, on December 15-17, 2010. The first two conference days were held in the Educarium building of the University of Turku, while the talks of the third day were given onboard passenger ferry boats in the beautiful Turku archipelago, along the route Turku–Mariehamn–Turku. The conference was organized by FUNDIM, the Fundamentals of Computing and Discrete Mathematics research center at the mathematics department of the University of Turku. The program of the conference included 17 submitted papers that were selected by the international program committee, based on three peer reviews of each paper. These papers form the core of these proceedings. I want to thank the members of the program committee and the external referees for the excellent work that have done in choosing the papers to be presented in the conference. In addition to the submitted papers, the program of JAC 2010 included four distinguished invited speakers: Michel Coornaert (Universit´e de Strasbourg, France), Bruno Durand (Universit´e de Provence, Marseille, France), Dora Giammarresi (Universit` a di Roma Tor Vergata, Italy) and Martin Kutrib (Universit¨at Gie_en, Germany). I sincerely thank the invited speakers for accepting our invitation to come and give a plenary talk in the conference. The invited talk by Bruno Durand was eventually given by his co-author Alexander Shen, and I thank him for accepting to make the presentation with a short notice. Abstracts or extended abstracts of the invited presentations appear in the first part of this volume. The program also included several informal presentations describing very recent developments and ongoing research projects. I wish to thank all the speakers for their contribution to the success of the symposium. I also would like to thank the sponsors and our collaborators: the Finnish Academy of Science and Letters, the French National Research Agency project EMC (ANR-09-BLAN-0164), Turku Centre for Computer Science, the University of Turku, and Centro Hotel. Finally, I sincerely thank the members of the local organizing committee for making the conference possible. These proceedings are published both in an electronic format and in print. The electronic proceedings are available on the electronic repository HAL, managed by several French research agencies. The printed version is published in the general publications series of TUCS, Turku Centre for Computer Science. We thank both HAL and TUCS for accepting to publish the proceedings.Siirretty Doriast