Grammars with two-sided contexts

In a recent paper (M. Barash, A. Okhotin, "Defining contexts in context-free grammars", LATA 2012), the authors introduced an extension of the context-free grammars equipped with an operator for referring to the left context of the substring being defined. This paper proposes a more general model, in which context specifications may be two-sided, that is, both the left and the right contexts can be specified by the corresponding operators. The paper gives the definitions and establishes the basic theory of such grammars, leading to a normal form and a parsing algorithm working in time O(n^4), where n is the length of the input string.Comment: In Proceedings AFL 2014, arXiv:1405.527

Complexity and modeling power of insertion-deletion systems

SISTEMAS DE INSERCIÓN Y BORRADO: COMPLEJIDAD Y CAPACIDAD DE MODELADO El objetivo central de la tesis es el estudio de los sistemas de inserción y borrado y su capacidad computacional. Más concretamente, estudiamos algunos modelos de generación de lenguaje que usan operaciones de reescritura de dos cadenas. También consideramos una variante distribuida de los sistemas de inserción y borrado en el sentido de que las reglas se separan entre un número finito de nodos de un grafo. Estos sistemas se denominan sistemas controlados mediante grafo, y aparecen en muchas áreas de la Informática, jugando un papel muy importante en los lenguajes formales, la lingüística y la bio-informática. Estudiamos la decidibilidad/ universalidad de nuestros modelos mediante la variación de los parámetros de tamaño del vector. Concretamente, damos respuesta a la cuestión más importante concerniente a la expresividad de la capacidad computacional: si nuestro modelo es equivalente a una máquina de Turing o no. Abordamos sistemáticamente las cuestiones sobre los tamaños mínimos de los sistemas con y sin control de grafo.COMPLEXITY AND MODELING POWER OF INSERTION-DELETION SYSTEMS The central object of the thesis are insertion-deletion systems and their computational power. More specifically, we study language generating models that use two string rewriting operations: contextual insertion and contextual deletion, and their extensions. We also consider a distributed variant of insertion-deletion systems in the sense that rules are separated among a finite number of nodes of a graph. Such systems are refereed as graph-controlled systems. These systems appear in many areas of Computer Science and they play an important role in formal languages, linguistics, and bio-informatics. We vary the parameters of the vector of size of insertion-deletion systems and we study decidability/universality of obtained models. More precisely, we answer the most important questions regarding the expressiveness of the computational model: whether our model is Turing equivalent or not. We systematically approach the questions about the minimal sizes of the insertiondeletion systems with and without the graph-control

On the Power of Insertion P Systems of Small Size

In this article we investigate insertion systems of small size in the framework of P systems. We consider P systems with insertion rules having one symbol context and we show that they have the computational power of matrix grammars. If contexts of length two are permitted, then any recursively enumerable language can be generated. In both cases an inverse morphism and a weak coding were applied to the output of the corresponding P systems

Dynamic Network Notation: A Graphical Modeling Language to Support the Visualization and Management of Network Effects in Service Platforms

Service platforms have moved into the center of interest in both academic research and the IT industry due to their economic and technical impact. These multitenant platforms provide own or third party software as metered, on-demand services. Corresponding service offers exhibit network effects. The present work introduces a graphical modeling language to support service platform design with focus on the exploitation of these network effects

Merkityn kaksoisnegaation sovellukset

Nested complementation plays an important role in expressing counter- i.e. star-free and first-order definable languages and their hierarchies. In addition, methods that compile phonological rules into finite-state networks use double-nested complementation or "double negation". This paper reviews how the double-nested complementation extends to a relatively new operation, generalized restriction (GR), coined by the author. ... The paper demonstrates that the GR operation has an interesting potential in expressing regular languages, various kinds of grammars, bimorphisms and relations. This motivates a further study of optimized implementation of the operation.Non peer reviewe

Context-driven discovery of gene cassettes in mobile integrons using a computational grammar

<p>Abstract</p> <p>Background</p> <p>Gene discovery algorithms typically examine sequence data for low level patterns. A novel method to computationally discover higher order DNA structures is presented, using a context sensitive grammar. The algorithm was applied to the discovery of gene cassettes associated with integrons. The discovery and annotation of antibiotic resistance genes in such cassettes is essential for effective monitoring of antibiotic resistance patterns and formulation of public health antibiotic prescription policies.</p> <p>Results</p> <p>We discovered two new putative gene cassettes using the method, from 276 integron features and 978 GenBank sequences. The system achieved <it>κ </it>= 0.972 annotation agreement with an expert gold standard of 300 sequences. In rediscovery experiments, we deleted 789,196 cassette instances over 2030 experiments and correctly relabelled 85.6% (<it>α </it>≥ 95%, <it>E </it>≤ 1%, mean sensitivity = 0.86, specificity = 1, F-score = 0.93), with no false positives.</p> <p>Error analysis demonstrated that for 72,338 missed deletions, two adjacent deleted cassettes were labeled as a single cassette, increasing performance to 94.8% (mean sensitivity = 0.92, specificity = 1, F-score = 0.96).</p> <p>Conclusion</p> <p>Using grammars we were able to represent heuristic background knowledge about large and complex structures in DNA. Importantly, we were also able to use the context embedded in the model to discover new putative antibiotic resistance gene cassettes. The method is complementary to existing automatic annotation systems which operate at the sequence level.</p