First Steps Towards a Geometry of Computation

We introduce a geometrical setting which seems promising for the study of computation in multiset rewriting systems, but could also be applied to register machines and other models of computation. This approach will be applied here to membrane systems (also known as P systems) without dynamical membrane creation. We discuss the role of maximum parallelism and further simplify our model by considering only one membrane and sequential application of rules, thereby arriving at asynchronous multiset rewriting systems (AMR systems). Considering only one membrane is no restriction, as each static membrane system has an equivalent AMR system. It is further shown that AMR systems without a priority relation on the rules are equivalent to Petri Nets. For these systems we introduce the notion of asymptotically exact computation, which allows for stochastic appearance checking in a priori bounded (for some complexity measure) computations. The geometrical analogy in the lattice Nd0 ; d 2 N, is developed, in which a computation corresponds to a trajectory of a random walk on the directed graph induced by the possible rule applications. Eventually this leads to symbolic dynamics on the partition generated by shifted positive cones C+ p , p 2 Nd0 , which are associated with the rewriting rules, and their intersections. Complexity measures are introduced and we consider non-halting, loop-free computations and the conditions imposed on the rewriting rules. Eventually, two models of information processing, control by demand and control by availability are discussed and we end with a discussion of possible future developments

A Logic Programming Approach to Reaction Systems

Reaction systems (RS) are a computational framework inspired by the functioning of living cells, suitable to model the main mechanisms of biochemical reactions. RS have shown to be useful also for computer science applications, e.g. to model circuits or transition systems. Since their introduction about 10 years ago, RS matured into a fruitful and dynamically evolving research area. They have become a popular novel model of interactive computation. RS can be seen as a rewriting system interacting with the environment represented by the context. RS pose some problems of implementation, as it is a relatively recent computation model, and several extensions of the basic model have been designed. In this paper we present some preliminary work on how to implement this formalism in a logic programming language (Prolog). To the best of our knowledge this is the first approach to RS in logic programming. Our prototypical implementation does not aim to be highly performing, but has the advantage of being high level and easily modifiable. So it is suitable as a rapid prototyping tool for implementing several extensions of reaction systems in the literature as well as new ones. We also make a preliminary implementation of a kind of memoization mechanism for stopping potentially infinite and repetitive computations. Then we show how to implement in our interpreter an extension of RS for modeling a nondeterministic context and interaction between components of a (biological) system. We then present an extension of the interpreter for implementing the recently introduced networks of RS

Rule-based Methodologies for the Specification and Analysis of Complex Computing Systems

Desde los orígenes del hardware y el software hasta la época actual, la complejidad de los sistemas de cálculo ha supuesto un problema al cual informáticos, ingenieros y programadores han tenido que enfrentarse. Como resultado de este esfuerzo han surgido y madurado importantes áreas de investigación. En esta disertación abordamos algunas de las líneas de investigación actuales relacionada con el análisis y la verificación de sistemas de computación complejos utilizando métodos formales y lenguajes de dominio específico. En esta tesis nos centramos en los sistemas distribuidos, con un especial interés por los sistemas Web y los sistemas biológicos. La primera parte de la tesis está dedicada a aspectos de seguridad y técnicas relacionadas, concretamente la certificación del software. En primer lugar estudiamos sistemas de control de acceso a recursos y proponemos un lenguaje para especificar políticas de control de acceso que están fuertemente asociadas a bases de conocimiento y que proporcionan una descripción sensible a la semántica de los recursos o elementos a los que se accede. También hemos desarrollado un marco novedoso de trabajo para la Code-Carrying Theory, una metodología para la certificación del software cuyo objetivo es asegurar el envío seguro de código en un entorno distribuido. Nuestro marco de trabajo está basado en un sistema de transformación de teorías de reescritura mediante operaciones de plegado/desplegado. La segunda parte de esta tesis se concentra en el análisis y la verificación de sistemas Web y sistemas biológicos. Proponemos un lenguaje para el filtrado de información que permite la recuperación de informaciones en grandes almacenes de datos. Dicho lenguaje utiliza información semántica obtenida a partir de ontologías remotas para re nar el proceso de filtrado. También estudiamos métodos de validación para comprobar la consistencia de contenidos web con respecto a propiedades sintácticas y semánticas. Otra de nuestras contribuciones es la propuesta de un lenguaje que permite definir y comprobar automáticamente restricciones semánticas y sintácticas en el contenido estático de un sistema Web. Finalmente, también consideramos los sistemas biológicos y nos centramos en un formalismo basado en lógica de reescritura para el modelado y el análisis de aspectos cuantitativos de los procesos biológicos. Para evaluar la efectividad de todas las metodologías propuestas, hemos prestado especial atención al desarrollo de prototipos que se han implementado utilizando lenguajes basados en reglas.Baggi ., M. (2010). Rule-based Methodologies for the Specification and Analysis of Complex Computing Systems [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/8964Palanci

Membrane Computing as a Modeling Framework. Cellular Systems Case Studies

Membrane computing is a branch of natural computing aiming to abstract computing models from the structure and functioning of the living cell, and from the way cells cooperate in tissues, organs, or other populations of cells. This research area developed very fast, both at the theoretical level and in what concerns the applications. After a very short description of the domain, we mention here the main areas where membrane computing was used as a framework for devising models (biology and bio-medicine, linguistics, economics, computer science, etc.), then we discuss in a certain detail the possibility of using membrane computing as a high level computational modeling framework for addressing structural and dynamical aspects of cellular systems. We close with a comprehensive bibliography of membrane computing applications

Twenty years of rewriting logic

AbstractRewriting logic is a simple computational logic that can naturally express both concurrent computation and logical deduction with great generality. This paper provides a gentle, intuitive introduction to its main ideas, as well as a survey of the work that many researchers have carried out over the last twenty years in advancing: (i) its foundations; (ii) its semantic framework and logical framework uses; (iii) its language implementations and its formal tools; and (iv) its many applications to automated deduction, software and hardware specification and verification, security, real-time and cyber-physical systems, probabilistic systems, bioinformatics and chemical systems

Basic completion strategies as another application of the Maude strategy language

The two levels of data and actions on those data provided by the separation between equations and rules in rewriting logic are completed by a third level of strategies to control the application of those actions. This level is implemented on top of Maude as a strategy language, which has been successfully used in a wide range of applications. First we summarize the Maude strategy language design and review some of its applications; then, we describe a new case study, namely the description of completion procedures as transition rules + control, as proposed by Lescanne.Comment: In Proceedings WRS 2011, arXiv:1204.531

Communication in membrana Systems with symbol Objects.

Esta tesis está dedicada a los sistemas de membranas con objetos-símbolo como marco teórico de los sistemas paralelos y distribuidos de procesamiento de multiconjuntos.Una computación de parada puede aceptar, generar o procesar un número, un vector o una palabra; por tanto el sistema define globalmente (a través de los resultados de todas sus computaciones) un conjunto de números, de vectores, de palabras (es decir, un lenguaje), o bien una función. En esta tesis estudiamos la capacidad de estos sistemas para resolver problemas particulares, así como su potencia computacional. Por ejemplo, las familias de lenguajes definidas por diversas clases de estos sistemas se comparan con las familias clásicas, esto es, lenguajes regulares, independientes del contexto, generados por sistemas 0L tabulados extendidos, generados por gramáticas matriciales sin chequeo de apariciones, recursivamente enumerables, etc. Se prestará especial atención a la comunicación de objetos entre regiones y a las distintas formas de cooperación entre ellos.Se pretende (Sección 3.4) realizar una formalización los sistemas de membranas y construir una herramienta tipo software para la variante que usa cooperación no distribuida, el navegador de configuraciones, es decir, un simulador, en el cual el usuario selecciona la siguiente configuración entre todas las posibles, estando permitido volver hacia atrás. Se considerarán diversos modelos distribuidos. En el modelo de evolución y comunicación (Capítulo 4) separamos las reglas tipo-reescritura y las reglas de transporte (llamadas symport y antiport). Los sistemas de bombeo de protones (proton pumping, Secciones 4.8, 4.9) constituyen una variante de los sistemas de evolución y comunicación con un modo restrictivo de cooperación. Un modelo especial de computación con membranas es el modelo puramente comunicativo, en el cual los objetos traspasan juntos una membrana. Estudiamos la potencia computacional de las sistemas de membranas con symport/antiport de 2 o 3 objetos (Capítulo 5) y la potencia computacional de las sistemas de membranas con alfabeto limitado (Capítulo 6).El determinismo (Secciones 4.7, 5.5, etc.) es una característica especial (restrictiva) de los sistemas computacionales. Se pondrá especial énfasis en analizar si esta restricción reduce o no la potencia computacional de los mismos. Los resultados obtenidos para sistemas de bombeo del protones están transferidos (Sección 7.3) a sistemas con catalizadores bistabiles. Unos ejemplos de aplicación concreta de los sistemas de membranas (Secciones 7.1, 7.2) son la resolución de problemas NP-completos en tiempo polinomial y la resolución de problemas de ordenación.This thesis deals with membrane systems with symbol objects as a theoretical framework of distributed parallel multiset processing systems.A halting computation can accept, generate or process a number, a vector or a word, so the system globally defines (by the results of all its computations) a set of numbers or a set of vectors or a set of words, (i.e., a language), or a function. The ability of these systems to solve particular problems is investigated, as well as their computational power, e.g., the language families defined by different classes of these systems are compared to the classical ones, i.e., regular, context-free, languages generated by extended tabled 0L systems, languages generated by matrix grammars without appearance checking, recursively enumerable languages, etc. Special attention is paid to communication of objects between the regions and to the ways of cooperation between the objects.An attempt to formalize the membrane systems is made (Section 3.4), and a software tool is constructed for the non-distributed cooperative variant, the configuration browser, i.e., a simulator, where the user chooses the next configuration among the possible ones and can go back. Different distributed models are considered. In the evolution-communication model (Chapter 4) rewriting-like rules are separated from transport rules. Proton pumping systems (Sections 4.8, 4.9) are a variant of the evolution-communication systems with a restricted way of cooperation. A special membrane computing model is a purely communicative one: the objects are moved together through a membrane. We study the computational power of membrane systems with symport/antiport of 2 or 3 objects (Chapter 5) and the computational power of membrane systems with a limited alphabet (Chapter 6).Determinism (Sections 4.7, 5.5, etc.) is a special property of computational systems; the question of whether this restriction reduces the computational power is addressed. The results on proton pumping systems can be carried over (Section 7.3) to the systems with bi-stable catalysts. Some particular examples of membrane systems applications are solving NP-complete problems in polynomial time, and solving the sorting problem

Formal methods for modeling and analysis of hybrid systems

A technique based on the use of a quantifier elimination decision procedure for real closed fields and simple theorem proving to construct a series of successively finer qualitative abstractions of hybrid automata is taught. The resulting abstractions are always discrete transition systems which can then be used by any traditional analysis tool. The constructed abstractions are conservative and can be used to establish safety properties of the original system. The technique works on linear and non-linear polynomial hybrid systems: the guards on discrete transitions and the continuous flows in all modes can be specified using arbitrary polynomial expressions over the continuous variables. An exemplar tool in the SAL environment built over the theorem prover PVS is detailed. The technique scales well to large and complex hybrid systems