Fundamenta Informaticae - Volume 110, issue 1-4

Authors: , Juhani | Karhumäki, | , Gheorghe | Păun, | Rozenberg, Grzegorz | Salomaa, Arto

Article Type: Other

DOI: 10.3233/FI-2011-523

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. vii-viii, 2011

Authors: Akhtarzada, Ali | Calude, Cristian S. | Hosking, John

Article Type: Research Article

Abstract: Information overload and an abundance of choices create situations where selecting one option becomes extremely difficult or even worse, a guessing game. Collaborative ranking systems are widely used to alleviate this problem by creating intelligent rankings of items based on an aggregation of user opinions. Current ranking systems can still be improved in a number of areas, including accuracy, transparency and flexibility. This paper presents a multi-criteria ranking algorithm that can be used on a non-rigid set of criteria. The system implementing the algorithm fares well with respect to the above qualities.

Keywords: Metric algorithm, intelligent ranking, non-rigid criteria

DOI: 10.3233/FI-2011-524

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 1-11, 2011

Authors: Alhazov, Artiom | Krassovitskiy, Alexander | Rogozhin, Yurii | Verlan, Sergey

Article Type: Research Article

Abstract: It is known that insertion-deletion (P) systems with two symbols context-free insertion and deletion rules are not computationally complete. It is thus interesting to consider conditions that would allow such systems to reach computational completeness. In this paper we consider insertion-deletion P systems with insertion and deletion operations applied only at the ends of string (we call them exo-operations). We show that such systems with one-symbol insertion and deletion of up to two symbols are computationally complete, and so are systems with insertion of up to two symbols and one-symbol deletion. The question about the computational power of insertion-deletion P …systems with one-symbol insertion and one-symbol deletion operations applied at the ends of string is open. However, the tissue P systems reach computationally completeness even in this case. Show more

DOI: 10.3233/FI-2011-525

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 13-28, 2011

Authors: Azimi, Sepinoud | Harju, Tero | Langille, Miika | Petre, Ion | Rogojin, Vladimir

Article Type: Research Article

Abstract: The simple intramolecular model for gene assembly in ciliates consists of three molecular operations based on local DNA manipulations. It was shown to predict correctly the assembly of all currently known ciliate gene patterns. Mathematical models in terms of signed permutations and signed strings proved limited in capturing some of the combinatorial details of the simple gene assembly process. A different formalization in terms of overlap-inclusion graphs, recently introduced by Brijder and Hoogeboom, proved well-suited to describe two of the three operations of the model and their combinatorial properties. We introduce in this paper an extension of the framework of …Brijder and Hoogeboom in terms of directed overlap-inclusion graphs where more of the linear structure of the ciliate genes is described. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. Show more

Keywords: Directed overlap-inclusion graphs, gene assembly in Ciliates, simple operations

DOI: 10.3233/FI-2011-526

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 29-44, 2011

Authors: Ballier, Alexis | Guillon, Pierre | Kari, Jarkko

Article Type: Research Article

Abstract: We construct a cellular automaton (CA) with a sofic and mixing limit set and then construct a stable CA with the same limit set, showing there exist subshifts that can be limit sets of both stable and unstable CAs, answering a question raised by A. Maass.

DOI: 10.3233/FI-2011-527

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 45-57, 2011

Authors: Böckenhauer, Hans-Joachim | Hromkovič, Juraj | Sprock, Andreas

Article Type: Research Article

Abstract: In reoptimization, we consider the following scenario: Given an instance of a hard optimization problem together with an optimal solution for it, we want to solve a locally modified instance of the problem. It has recently been shown for several hard optimization problems that their corresponding reoptimization variants remain 𝒩𝒫-hard or even hard to approximate whereas they often admit improved approximation ratios. In this paper, we investigate a generalization of the reoptimization concept where we are given not only one optimal solution but multiple optimal solutions for an instance. We prove, for some variants of the Steiner tree problem and …the traveling salesman problem, that the known reoptimization hardness results carry over to this generalized setting. Moreover, we consider the performance of local search strategies on reoptimization problems. We show that local search does not work for solving TSP reoptimization, even in the presence of multiple solutions. Show more

Keywords: Reoptimization, Steinertree, TSP, Multiple Given Solution, Hardness

DOI: 10.3233/FI-2011-528

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 59-76, 2011

Authors: Bonizzoni, Paola | Ferretti, Claudio | Mary, A. Roslin Sagaya | Mauri, Giancarlo

Article Type: Research Article

Abstract: We propose a new formalism for generating picture languages based on an assembly mechanism of tiles that uses rules having a context and a replacement site. More precisely, a picture language will be generated from a finite set of initial pictures by iteratively applying rewriting rules from a given finite set of rules, called a tiling rule system (TRuS system). We prove that the TRuS systems have a greater generative capacity than the tiling systems of Giammarresi and Restivo. This is due mainly to the use of the notion of replacement site, but we further characterize the difference between these …systems by comparing them to Wang systems. Show more

DOI: 10.3233/FI-2011-529

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 77-93, 2011

Authors: Cui, Cewei | Dang, Zhe | Fischer, Thomas R.

Article Type: Research Article

Abstract: We introduce (finite and infinite) typical paths of a graph and prove that the typical paths carry all information with probability 1, asymptotically. An automata-theoretic characterization of the typical paths is shown: finite typical paths can be accepted by reversal-bounded multicounter automata and infinite typical paths can be accepted by counting Büchi automata (a generalization of reversal-bounded multicounter automata running on ω-words). We take a statechart example to show how to generate typical paths from a graph using SPIN model checker. The results are useful in automata theory since one can identify an information-concentrated-core of a regular language such that …only words in the information-concentrated-core carry nontrivial information. When the graph is used to specify the system under test, the results are also useful in software testing by providing an information-theoretic approach to select test cases that carry nontrivial information of the system specification. Show more

Keywords: graph, entropy, path

DOI: 10.3233/FI-2011-530

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 95-109, 2011

Authors: Eğecioğlu, Ömer | Hegedüs, Lászl´ | Nagy, Benedek

Article Type: Research Article

Abstract: We consider stateless counter machines which mix the features of one-head counter machines and a special type of two-head Watson-Crick automata (WK-automata). Our Watson-Crick counter machines are biologically motivated. They have two heads that read the input starting from the two extremes. The reading process is finished when there are no more symbols between the heads, i.e., every letter of the input is processed by either head. Depending on whether the heads are required to advance at each move, we distinguish between realtime and non-realtime machines. If every counter makes at most k alternations between nondecreasing and decreasing modes in …every computation, then the machine is k-reversal. It is reversal bounded if it is k-reversal for some k. In this paper we concentrate on the properties of both deterministic and nondeterministic stateless WK-automata with reversal bounded counters. Show more

DOI: 10.3233/FI-2011-531

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 111-123, 2011

Authors: Eisman, Gerry | Ravikumar, Bala

Article Type: Research Article

Abstract: Approximate computation is a central concept in algorithms and computation theory. Our notion of approximation is that the algorithm performs correctly on most of the inputs. We propose some finite automata models to study the question of how well a finite automaton can approximately recognize a non-regular language. On the one hand, we show that there are natural problems for which a DFA can correctly solve almost all the instances, but not all instances. An example of such a problem is a decision question about the number of digits in the square of a given integer. On the other hand, …we show that some languages (such as Lmajority = {x ∈ (0 + 1)* | x has more 1′s than 0′s }) can't be approximated by any regular language in a strong sense. We also show that there are problems that are intermediate (between the extremes stated above) in terms of how we well a regular language can approximate it. An example of such a problem is a decision question about the number of digits in the product of two integers. We also present results comparing different models of approximation. Show more

Keywords: finite automata, approximation, majority language, squaring

DOI: 10.3233/FI-2011-532

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 125-142, 2011

Authors: Gao, Yuan | Salomaa, Kai | Yu, Sheng

Article Type: Research Article

Abstract: We consider the transition complexity of regular languages based on the incomplete deterministic finite automata. We establish tight bounds for the transition complexity of Boolean operations, in the case of union the upper and lower bounds differ by a multiplicative constant two. We show that the transition complexity results for union and complementation are very different from the state complexity results for the same operations. However, for intersection, the transition complexity bounds turn out to be similar to the corresponding bounds for state complexity.

Keywords: transition complexity, deterministic finite automaton, incomplete automaton, regular languages, Boolean operations

DOI: 10.3233/FI-2011-533

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 143-158, 2011

Authors: Holzer, Markus | Klein, Andreas | Kutrib, Martin | Ruepp, Oliver

Article Type: Research Article

Abstract: We show that the popular pencil puzzle NURIKABE is intractable from the computational complexity point of view, that is, it is NP-complete, even when the involved numbers are 1 and 2 only. To this end, we show how to simulate Boolean gates by the puzzle under consideration. Moreover, we also study some NURIKABE variants, which remain NP-complete, too.

DOI: 10.3233/FI-2011-534

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 159-174, 2011

Authors: Honkala, Juha

Article Type: Research Article

Abstract: We study the DT0L sequence equivalence problem for marked morphisms. We show that to decide this problem it is enough to consider initial terms involving at most 2n morphisms where n is the cardinality of the underlying alphabet.

Keywords: DT0L system, DT0L sequence equivalence problem, marked morphism, decidability

DOI: 10.3233/FI-2011-535

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 175-182, 2011

Authors: Ilie, Lucian | Smyth, William F.

Article Type: Research Article

Abstract: Unique substrings appear scattered in the stringology literature and have important applications in bioinformatics. In this paper we initiate a study of minimum unique substrings in a given string; that is, substrings that occur exactly once while all their substrings are repeats. We discover a strong duality between minimum unique substrings and maximum repeats which, in particular, allows fast computation of one from the other. We give several optimal algorithms, some of which are very simple and efficient. Their combinatorial properties are investigated and a number of open problems are proposed.

DOI: 10.3233/FI-2011-536

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 183-195, 2011

Authors: Karhumäki, Juhani | Saarela, Aleksi

Article Type: Research Article

Abstract: We show by a simple reduction that the unique decipherability problem in the language monoid of regular languages over a non-unary alphabet is undecidable.

DOI: 10.3233/FI-2011-537

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 197-200, 2011

Authors: Kari, Lila | Seki, Shinnosuke | Kopecki, Steffen

Article Type: Research Article

Abstract: Hairpin completion is an abstract operation modeling a DNA bio-operation which receives as input a DNA strand w = xαy\bar{α}, and outputs w' = xαy\bar{α}\bar{x}, where \bar{x} denotes the Watson-Crick complement of x. In this paper, we focus on the problem of finding conditions under which the iterated hairpin completion of a given word is regular. According to the numbers of words α and \bar{α} that initiate hairpin completion and how they are scattered, we classify the set of all words w. For some basic classes of words w containing small numbers of occurrences of α and \bar{α}, we prove …that the iterated hairpin completion of w is regular. For other classes with higher numbers of occurrences of α and \bar{α}, we prove a necessary and sufficient condition for the iterated hairpin completion of a word in these classes to be regular. Show more

Keywords: combinatorics on words, commutativity of words, DNA computing, iterated hairpin completion, regularity test, single-primer hairpin completion

DOI: 10.3233/FI-2011-538

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 201-215, 2011

Authors: Kleijn, Jetty | Koutny, Maciej

Article Type: Research Article

Abstract: In membrane systems, biochemical reactions taking place in the compartments of a cell are abstracted to evolution rules that specify which and how many objects are consumed and produced. The recently proposed reaction systems also investigate processes carried by biochemical reactions, but the resulting computational model is remarkably different. A key difference is that in reaction systems, biochemical reactions are modeled using a qualitative rather than a quantitative approach. In this paper, we introduce so-called set membrane systems, a variant of membrane systems with qualitative evolution rules inspired by reaction systems. We then relate set membrane systems to Petri nets …which leads to a new class of Petri nets: set-nets with localities. This Petri net model provides a faithful match with the operational semantics of set membrane systems. Show more

Keywords: membrane system, reaction system, biochemistry, natural computing, Petri net, set-net, locality, inhibitor, promoter

DOI: 10.3233/FI-2011-539

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 217-230, 2011

Authors: Kunc, Michal | Okhotin, Alexander

Article Type: Research Article

Abstract: The number of states in a two-way nondeterministic finite automaton (2NFA) needed to represent intersection of languages given by an m-state 2NFA and an n-state 2NFA is shown to be at least m+n and at most m+n+1. For the union operation, the number of states is exactly m+n. The lower bound is established for languages over a one-letter alphabet. The key point of the argument is the following number-theoretic lemma: for all m, n ≥ 2 with m, n ≠ 6 (and with finitely many other exceptions), there exist partitions m = p1 +. . .+ pk and …n = q1 +. . .+ql , where all numbers p1 , . . . , pk , q1 , . . . , ql ≥ 2 are powers of pairwise distinct primes. For completeness, an analogous statement about partitions of any two numbers m, n ∉ {4, 6} (with a few more exceptions) into sums of pairwise distinct primes is established as well. Show more

Keywords: Finite automata, two-way automata, state complexity, partitions into sums of primes

DOI: 10.3233/FI-2011-540

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 231-239, 2011

Authors: Morita, Kenichi

Article Type: Research Article

Abstract: A two-way reversible multi-head finite automaton (RMFA) is introduced as a simple model of reversible computing, and its language accepting capability is studied. We show that various non-regular context-free languages, and non-context-free context-sensitive languages are accepted by RMFAs with a few heads. For example, we give an RMFA with three heads that accepts the language consisting of all words whose length is a prime number. A construction method of a garbage-less RMFA from a given RFMA is also shown.

Keywords: reversible computing, multi-head finite automaton, language recognition

DOI: 10.3233/FI-2011-541

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 241-254, 2011

Authors: Okubo, Fumiya | Yokomori, Takashi

Article Type: Research Article

Abstract: Hairpin completion and its variant called bounded hairpin completion are operations on formal languages, inspired by a hairpin formation in molecular biology. Another variant called hairpin lengthening has been recently introduced, and the related closure properties and algorithmic problems concerning several families of languages have been studied. In this paper, we introduce a new operation of this kind, called hairpin incompletion which is not only an extension of bounded hairpin completion, but also a restricted (bounded) variant of hairpin lengthening. Further, the hairpin incompletion operation provides a formal language theoretic framework that models a bio-molecular technique nowadays known as Whiplash …PCR. We study the closure properties of language families under both the operation and its iterated version. We show that a family of languages closed under intersection with regular sets, concatenation with regular sets, and finite union is closed under one-sided iterated hairpin incompletion, and that a family of languages containing all linear languages and closed under circular permutation, left derivative and substitution is also closed under iterated hairpin incompletion. Show more

DOI: 10.3233/FI-2011-542

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 255-269, 2011

Authors: Pan, Linqiang | Wang, Jun | Hoogeboom, Hendrik Jan

Article Type: Research Article

Abstract: In a biological system, if a long enough time interval is given, an enabled chemical reaction will finish its reaction in the given time interval. With this motivation, it is natural to impose a bound on the time interval when an enabled spiking rule in a spiking neural P system (SN P system, for short) remains unused. In this work, a new working mode of SN P systems is defined, which is called limited asynchronous mode. In an SN P system working in limited asynchronous mode, if a rule is enabled at some step, this rule is not obligatorily used. …From this step on, if the unused rule may be used later, it should be used in the given time interval. If further spikes make the rule non-applicable, then the computation continues in the new circumstances. The computation result of a computation in an SN P system working in limited asynchronous mode is defined as the total number of spikes sent into the environment by the system. It is proved that limited asynchronous SN P systems with standard spiking rules are universal. If the number of spikes present in each neuron of a limited asynchronous SN P system with standard spiking rules is bounded during a computation, then the power of a limited asynchronous SN P system with standard spiking rules falls drastically, and we get a characterization of semilinear sets of numbers. Show more

Keywords: Membrane computing, Spiking neural P system, Asynchronous mode, Turing Computability

DOI: 10.3233/FI-2011-543

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 271-293, 2011

Authors: Pérez-Jiménez, Mario J. | Riscos-Núñez, Agustín | Rius-Font, Miquel | Romero-Campero, Francisco J.

Article Type: Research Article

Abstract: In 1936 A. Turing showed the existence of a universal machine able to simulate any Turing machine given its description. In 1956, C. Shannon formulated for the first time the problem of finding the smallest possible universal Turing machine according to some critera to measure its size such as the number of states and symbols. Within the framework of Membrane Computing different studies have addressed this problem: small universal symport/antiport P systems (by considering the number of membranes, the weight of the rules and the number of objects as a measure of the size of the system), small universal splicing …P systems (by considering the number of rules as a measure of the size of the system), and small universal spiking neural P systems (by considering the number of neurons as a measure of the size of the system). In this paper the problem of determining the smallest possible efficient P system is explicitly formulated. Efficiency within the framework of Membrane Computing refers to the capability of solving computationally hard problems (i.e. problems such that classical electronic computer cannot solve instances of medium/large size in any reasonable amount of time) in polynomial time. A descriptive measure to define precisely the notion of small P system is presented in this paper. Show more

Keywords: Membrane Computing, Small universal P Systems, Small effcient P systems, SAT problem

DOI: 10.3233/FI-2011-544

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 295-308, 2011

Authors: Raghavan, Rama | Ramesh, H. | Gheorghe, Marian | Krishna, Shankara Narayanan

Article Type: Research Article

Abstract: Here we continue the study of bio-Turing machines introduced in [2] and further investigated in [17]. We introduce a restricted model of bio-Turing machine and we investigate its computational power, a hierarchy of languages accepted, and deterministic and nondeterministic variants. A comprehensive example illustrating the modelling power of the introduced machine ends the paper.

DOI: 10.3233/FI-2011-545

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 309-320, 2011

Authors: Tran, Nicholas

Article Type: Research Article

Abstract: This paper introduces and studies two notions of easy sets without hard subsets: i) 𝒞-hollow sets are defined to be sets in P that have no 𝒞 – P subsets for (presumably) superclasses 𝒞 of P such as NP, PSPACE, E, NE, RE, etc.; and ii) 𝒞-scant sets are defined to be sets in P that have no many-one 𝒞-complete subsets. These sets complement well-studied objects in complexity such as P-printable sets, immune sets and complexity cores. First, characterizations of 𝒞-hollow sets and 𝒞-scant sets are obtained in terms of universally easy sets, introduced and studied in [7] as an …automatic method for generating easy instances of intractable problems. Second, the following results regarding existence of 𝒞-hollow sets are obtained: infinite NP-hollow tally (equivalently, P-printable) sets exist iff some nondeterministic time complexity class equals its deterministic counterpart; in contrast, infinite E/NE/RE-hollow sets do not exist. Finally, it is shown that P-printable-immune sets in P are 𝒞-scant for E and NE. Show more

DOI: 10.3233/FI-2011-546

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 321-328, 2011

Authors: Verlan, Sergey | Margenstern, Maurice

Article Type: Research Article

Abstract: Splicing test tube systems are one of the first distributed computing models based on splicing. The model introduces (test) tubes where the splicing operation is applied, which are arranged in a communication network with filters that permits to redistribute the words between the tubes at each step. We show that the computational completeness can be achieved with two tubes when the communication graph does not have self-loops. We also construct a universal splicing test tube system with 2 tubes having 23 rules.

Keywords: Splicing, test tube systems, universality

DOI: 10.3233/FI-2011-547

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 329-342, 2011

Authors: Yen, Hsu-Chun

Article Type: Research Article

Abstract: Although randomization often increases the degree of flexibility in system design, analyzing system properties in the probabilistic framework introduces additional difficulties and challenges in comparison with their nonprobabilistic counterparts. In this paper, we focus on probabilistic versions of two problems frequently encountered in discrete event systems, namely, the reachability and forbidden-state problems. Our main concern is to see whether there exists a (or for every) non-blocking or fair control policy under which a given finite- or infinite-state system can be guided to reach (or avoid) a set of goal states with probability one. For finite-state systems, we devise algorithmic approaches …which result in polynomial time solutions to the two problems. For infinite-state systems modelled as Petri nets, the problems are undecidable in general. For the class of persistent Petri nets, we establish a valuation approach through which the convergence behavior of a system is characterized, which in turn yields solutions to the reachability and forbidden-state problems. Show more

Keywords: Forbidden-state avoidance, Petri net, probabilistic controlled transition system, reachability

DOI: 10.3233/FI-2011-548

Citation: Fundamenta Informaticae, vol. 110, no. 1-4, pp. 343-359, 2011