Among Sturmian words, some of them are morphic, i.e. fixed point of a non-identical morphism on words. Berstel and Séébold (1993) have shown that if a characteristic Sturmian word is morphic, then it can be extended by the left with one or two letters in such a way that it remains morphic and Sturmian. Yasutomi (1997) has proved that these were the sole possible additions and that, if we cut the first letters of such a word, it didn't remain morphic. In this paper, we give an elementary and combinatorial proof of this result.

We investigate the intersection of two finitely generated submonoids of the free monoid on a finite alphabet. To this purpose, we consider automata that recognize such submonoids and we study the product automata recognizing their intersection. By using automata methods we obtain a new proof of a result of Karhumäki on the characterization of the intersection of two submonoids of rank two, in the case of prefix (or suffix) generators. In a more general setting, for an arbitrary number of generators, we prove that if H and K are two finitely generated submonoids generated by prefix sets such that the product automaton associated to $H \cap K$ has a given special property then $\widetilde{rk}(H \cap K) \leq \widetilde{rk}(H) \widetilde{rk}(K)$ where $\widetilde{rk}(L)=\max(0,rk(L)-1)$ for any submonoid L.

The problem of assessing the reliability of clusters patients identified by clustering algorithms is crucial to estimate the significance of subclasses of diseases detectable at bio-molecular level, and more in general to support bio-medical discovery of patterns in gene expression data. In this paper we present an experimental analysis of the reliability of clusters discovered in lung tumor patients using DNA microarray data. In particular we investigate if subclasses of lung adenocarcinoma can be detected with high reliability at bio-molecular level. To this end we apply cluster validity measures based on random projections recently proposed by Bertoni and coworkers. The results show that at least two subclasses of lung adenocarcinoma can be detected with relatively high reliability, confirming and extending previous findings reported in the literature.

A morphism f is k-power-free if and only if f(w) is k-power-free whenever w is a k-power-free word.A morphism f is k-power-free up to m if and onlyif f(w) isk-power-free whenever w is a k-power-free word of length at most m.Given an integer k ≥ 2,we prove that a binary morphism is k-power-freeif and only if it is k-power-free up to k 2.This bound becomes linear for primitive morphisms:a binary primitive morphism is k-power-freeif and only if it is k-power-free up to 2k+1

A subgraph H of a graph G is conformal if G - V(H) has a perfect matching. An orientation D of G is Pfaffian if, for every conformal even circuit C, the number of edges of C whose directions in D agree with any prescribed sense of orientation of C is odd. A graph is Pfaffian if it has a Pfaffian orientation. Not every graph is Pfaffian. However, if G has a Pfaffian orientation D, then the determinant of the adjacency matrix of D is the square of the number of perfect matchings of G. (See the book by Lovász and Plummer [Matching Theory. Annals of Discrete Mathematics, vol. 9. Elsevier Science (1986), Chap. 8.] A matching covered graph is a nontrivial connected graph in which every edge is in some perfect matching. The study of Pfaffian orientations of graphs can be naturally reduced to matching covered graphs. The properties of matching covered graphs are thus helpful in understanding Pfaffian orientations of graphs. For example, say that two orientations of a graph are similar if one can be obtained from the other by reversing the orientations of all the edges in a cut of the graph. Using one of the theorems we proved in [M.H. de Carvalho, C.L. Lucchesi and U.S.R. Murty, Optimal ear decompositions of matching covered graphs. J. Combinat. Theory B85 (2002) 59–93] concerning optimal ear decompositions, we show that if a matching covered graph is Pfaffian then the number of dissimilar Pfaffian orientations of G is 2b(G), where b(G) is the number of “bricks” of G. In particular, any two Pfaffian orientations of a bipartite graph are similar. We deduce that the problem of determining whether or not a graph is Pfaffian is as difficult as the problem of determining whether or not a given orientation is Pfaffian, a result first proved by Vazirani and Yanakakis [Pfaffian orientation of graphs, 0,1 permanents, and even cycles in digraphs. Discrete Appl. Math.25 (1989) 179–180]. We establish a simple property of minimal graphs without a Pfaffian orientation and use it to give an alternative proof of the characterization of Pfaffian bipartite graphs due to Little [ A characterization of convertible (0,1)-matrices. J. Combinat. Theory B18 (1975) 187–208] .

The aim of this paper is to evaluate the growth orderof the complexity function (in rectangles)for two-dimensional sequencesgenerated by a linear cellular automatonwith coefficients in $\mathbb{Z}/l \mathbb{Z}$ , and polynomial initial condition.We prove that the complexity functionis quadratic when l is a prime and that it increases with respect to the number of distinct prime factors of l.

The first-value operator assigns to any sequence of partial functions of the same type a new such function. Its domain is the union of the domains of the sequence functions, and its value at any point is just the value of the first function in the sequence which is defined at that point. In this paper, the first-value operator is applied to establish hierarchies of classes of functions under various settings. For effective sequences of computable discrete functions, we obtain a hierarchy connected with Ershov's one within $\Delta^{0}_2$. The non-effective version over real functions is connected with the degrees of discontinuity and yields a hierarchy related to Hausdorff's difference hierarchy in the Borel class $\Delta^{B}_2$. Finally, the effective version over approximately computable real functions forms a hierarchy which provides a useful tool in computable analysis.

The study of inductive and coinductive types (like finite lists and streams, respectively) is usually conducted within the framework of category theory, which to all intents and purposes is a theory of sets and functions between sets. Allegory theory, an extension of category theory due to Freyd, is better suited to modelling relations between sets as opposed to functions between sets. The question thus arises of how to extend the standard categorical results on the existence of final objects in categories (for example, coalgebras and products) to their existence in allegories. The motivation is to streamline current work on generic programming, in which the use of a relational theory rather than a functional theory has proved to be desirable. In this paper, we define the notion of a relational final dialgebra and prove, for an important class of dialgebras, that a relational final dialgebra exists in an allegory if and only if a final dialgebra exists in the underlying category of maps. Instances subsumed by the class we consider include coalgebras and products. An important lemma expresses bisimulations in allegorical terms and proves this equivalent to Aczel and Mendler's categorical definition.

Algebraic systems of equations define functions using recursion where parameter passing is permitted. This generalizes the notion of a rational system of equations where parameter passing is prohibited. It has been known for some time that algebraic systems in Greibach Normal Form have unique solutions. This paper presents a categorical approach to algebraic systems of equations which generalizes the traditional approach in two ways i) we define algebraic equations for locally finitely presentable categories rather than just Set; and ii) we define algebraic equations to allow right-hand sides which need not consist of finite terms. We show these generalized algebraic systems of equations have unique solutions by replacing the traditional metric-theoretic arguments with coalgebraic arguments.

This paper investigates one possible model of reversible computations, animportant paradigm in the context of quantum computing. Introduced byBennett, a reversible pebble game is anabstraction of reversible computation that allows to examine the space andtime complexity of various classes of problems. We present a techniquefor proving lower and upper bounds on time and space complexity for severaltypes of graphs. Using this technique we show that the time needed toachieve optimal space for chain topology is Ω(nlgn) for infinitelymany n and we discusstime-space trade-offs for chain. Further we show a tight optimalspace bound for the binary tree of height h of the form h + Θ(lg*h)and discuss space complexity for the butterfly. These results give anevidence that reversible computations need more resources than standardcomputations. We also show an upper bound on time and space complexity ofthe reversible pebble game based on the time and space complexity of thestandard pebble game, regardless of the topology of the graph.

We show that the size of a Las Vegas automaton and the size of a complete, minimal deterministic automaton accepting a regular language are polynomially related. More precisely, we show that if a regular language L is accepted by a Las Vegas automaton having r states such that the probability for a definite answer to occur is at least p, then r ≥ np, where n is the number of the states of the minimal deterministic automaton accepting L. Earlier this result has been obtained in [2] by using a reduction to one-way Las Vegas communication protocols, but here we give a direct proof based on information theory.

We study some arithmetical and combinatorial properties of β-integers for β being the larger root of the equation x2 = mx - n,m,n ∈ ℵ, m ≥ n +2 ≥ 3. We determine with the accuracy of ± 1 the maximal number of β-fractional positions, which may arise as a result of addition of two β-integers. For the infinite word uβ> coding distances between the consecutive β-integers, we determine precisely also the balance. The word uβ> is the only fixed point of the morphism A → Am-1B and B → Am-n-1B. In the case n = 1, the corresponding infinite word uβ> is sturmian, and, therefore, 1-balanced. On the simplest non-sturmian example with n≥ 2, we illustrate how closely the balance and the arithmetical properties of β-integers are related.

We introduce and investigate string assembling systems which form a computational model that generates strings from copies out of a finite set of assembly units. The underlying mechanism is based on piecewise assembly of a double-stranded sequence of symbols, where the upper and lower strand have to match. The generation is additionally controlled by the requirement that the first symbol of a unit has to be the same as the last symbol of the strand generated so far, as well as by the distinction of assembly units that may appear at the beginning, during, and at the end of the assembling process. We start to explore the generative capacity of string assembling systems. In particular, we prove that any such system can be simulated by some nondeterministic one-way two-head finite automaton, while the stateless version of the two-head finite automaton marks to some extent a lower bound for the generative capacity. Moreover, we obtain several incomparability and undecidability results as well as (non-)closure properties, and present questions for further investigations.

In this paper, we define the notion of biRFSA which is a residual finate stateautomaton (RFSA) whose the reverse is also an RFSA. The languages recognized bysuch automata are called biRFSA languages. We prove that the canonical RFSA of abiRFSA language is a minimal NFA for this language and that each minimalNFA for this language is a sub-automaton of the canonical RFSA. This leadsto a characterization of the family of biRFSA languages.In the second part of this paper, we define the family of biseparable automata. We prove that every biseparable NFA is uniquely minimal among all NFAs recognizinga same language, improving the result of H. Tamm and E. Ukkonen for bideterministic automata.

Digital trees or tries are a general purpose flexible data structure that implements dictionaries built on words. The present paper is focussed on the average-case analysis of an important parameter of this tree-structure, i.e., the stack-size. The stack-size of a tree is the memory needed by a storage-optimal preorder traversal. The analysis is carried out under a general model in which words are produced by a source (in the information-theoretic sense) that emits symbols. Under some natural assumptions that encompass all commonly used data models (and more), we obtain a precise average-case and probabilistic analysis of stack-size. Furthermore, we study the dependency between the stack-size and the ordering on symbols in the alphabet: we establish that, when the source emits independent symbols, the optimal ordering arises when the most probable symbol is the last one in this order.

In this paper we investigate how it is possible to recover an automaton from a rational expression that has been computed from that automaton. The notion of derived term of an expression, introduced by Antimirov, appears to be instrumental in this problem. The second important ingredient is the co-minimization of an automaton, a dual and generalized Moore algorithm on non-deterministic automata.
We show here that if an automaton is then sufficiently “decorated”, the combination of these two algorithms gives the desired result. Reducing the amount of “decoration” is still the object of ongoing investigation.

We present a new incremental algorithm for minimising deterministic finite automata. Itruns in quadratic time for any practical application and may be halted at any point,returning a partially minimised automaton. Hence, the algorithm may be applied to a givenautomaton at the same time as it is processing a string for acceptance. We also includesome experimental comparative results.

This paper discusses context-free rewriting systems inwhich there exist two disjoint finite sets of rules, and a symbol, referred to as a condition of applicability, is attached to each rule in either of these two sets. In one set, a rule with a symbol attached to it is applicable if the attached symbol occurs in the current rewritten string while in the other set, such a rule is applicable if the attached symbol does not occur there. The present paper demonstrates that these rewriting systems are computationally complete. From this main result, the paper derives several consequences and solves several open problems.

We say that two languages X and Y are conjugates if they satisfy the conjugacy equationXZ = ZY for some language Z. We study several problems associated with this equation. For example, we characterize all sets which are conjugated via a two-element biprefix set Z, as well as all two-element sets which are conjugates.

We proceed our work on iterated transductions by studying the closure underunion and composition of some classes of iterated functions. Weanalyze this closure for the classes of length-preservingrational functions, length-preserving subsequential functions andlength-preserving sequential functions with terminal states. All the classes weobtain are equal. We also study the connection with deterministiccontext-sensitive languages.