BWMC2011. Brainstorming Week On Membrane Computing (9th. 2011. Sevilla)

URI permanente para esta colecciónhttps://hdl.handle.net/11441/34361

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Ninth Brainstorming Week on Membrane Computing, Sevilla, January 31 - February 4, 2011 : RGNC REPORT 1/2011
(Fénix Editora, 2011) Martínez del Amor, Miguel Ángel; Paun, Gheorghe; Pérez Hurtado de Mendoza, Ignacio; Romero Campero, Francisco José; Valencia Cabrera, Luis; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Research Group on Natural Computing; Universidad de Sevilla. TIC193: Computación Natural
Linear Time Solution to Prime Factorization by Tissue P Systems with Cell Division
(Fénix Editora, 2011) Zhang, Xingyi; Niu, Yunyun; Pan, Linqiang; Pérez Jiménez, Mario de Jesús; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Ministerio de Ciencia e Innovación (MICIN). España; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación Natural
Prime factorization is useful and crucial for public-key cryptography, and its application in public-key cryptography is possible only because prime factorization has been presumed to be difficult. A polynomial-time algorithm for prime factorization on a quantum computer is given by P. W. Shor in 1997. In this work, a linear-time solution for prime factorization is given on a kind of biochemical computational devices - tissue P systems with cell division, instead of physical computational devices.
Integer Linear Programming for Tissue-like P Systems
(Fénix Editora, 2011) Reina Molina, Raúl; Díaz Pernil, Daniel; Gutiérrez Naranjo, Miguel Ángel; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. Departamento de Matemática Aplicada I (ETSII); Universidad de Sevilla. TIC193: Computación Natural; Universidad de Sevilla. FQM296: Topología Computacional y Matemática Aplicada
In this paper we report a work-in-progress whose final target is the implementation of tissue-like P system in a cluster of computers which solves some instances of the segmentation problem in 2D Digital Imagery. We focus on the theoretical aspects and the problem of choosing a maximal number of application of rules by using Integer Linear Programming techniques. This study is on the basis of a future distribution of the parallel work among the processors.
Elementary Active Membranes Have the Power of Counting
(Fénix Editora, 2011) Porreca, Antonio E.; Leporati, Alberto; Mauri, Giancarlo; Zandron, Claudio
We prove that uniform families of P systems with active membranes operat- ing in polynomial time can solve the whole class of PP decision problems, without using nonelementary membrane division or dissolution rules. This result also holds for families having a stricter uniformity condition than the usual one.
Smoothing Problem in 2D Images with Tissue-like P Systems and Parallel Implementation
(Fénix Editora, 2011) Peña Cantillana, Francisco; Díaz Pernil, Daniel; Christinal, Hepzibah A.; Gutiérrez Naranjo, Miguel Ángel; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. Departamento de Matemática Aplicada I (ETSII); Universidad de Sevilla. TIC193: Computación Natural; Universidad de Sevilla. FQM296: Topología Computacional y Matemática Aplicada
Smoothing is often used in Digital Imagery to reduce noise within an image. In this paper we present a Membrane Computing algorithm for smoothing 2D images in the framework of tissue-like P systems. The algorithm has been implemented by using a novel device architecture called CUDATM, (Compute Unified Device Architecture). We present some examples, compare the obtained time and present some research lines for the future.
Towards Bridging Two Cell-Inspired Models: P Systems and R Systems
(Fénix Editora, 2011) Paun, Gheorghe; Pérez Jiménez, Mario de Jesús; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación Natural
We examine, from the point of view of membrane computing, the two basic assumptions of reaction systems, the "threshold" and "no permanence" ones. In certain circumstances (e.g., defining the successful computations by local halting), the second assumption can be incorporated in a transition P system or in a symport/antiport P system without losing the universality. The case of the first postulate remains open: the reaction systems deal, deterministically, with finite sets of symbols, which is not of much interest for computing; three ways to introduce nondeterminism are suggested and left as research topics.
dP Automata versus Right-Linear Simple Matrix Grammars
(Fénix Editora, 2011) Paun, Gheorghe; Pérez Jiménez, Mario de Jesús; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación Natural
We consider dP automata with the input string distributed in an arbitrary (hence not necessary balanced) way, and we investigate their language accepting power, both in the case when a bound there is on the number of objects present inside the system and in the general case. The relation with right-linear simple matrix grammars is useful in this respect. Some research topics and open problems are also formulated.
Well-Tempered P Systems: Towards a Membrane Computing Environment for Music Composition
(Fénix Editora, 2011) Obtulowicz, Adam
A proposal of designing a membrane computing environment for music composition is outlined.
On a Contribution of Membrane Computing to a Cultural Synthesis of Computer Science, Mathematics, and Biological Sciences
(Fénix Editora, 2011) Obtulowicz, Adam
Some topic contribution of membrane computing to a cultural synthesis of computer science, mathematics and biological sciences is presented.
BFS Solution for Disjoint Paths in P Systems
(Fénix Editora, 2011) Nicolescu, Radu; Wu, Huiling
This paper continues the research on determining a maximum cardinality set of edge- and node-disjoint paths between a source cell and a target cell in P systems. We review the previous solution, based on depth-fi rst search (DFS), and we propose a faster solution, based on breadth-fi rst search (BFS), which leverages the parallel and distributed characteristics of P systems. The runtime complexity shows that, our BFS- based solution performs better than the DFS-based solution, in terms of P steps.
MP Modeling of Glucose-Insulin Interactions in the Intravenous Glucose Tolerance Test
(Fénix Editora, 2011) Manca, Vincenzo; Marchetti, Luca; Pagliarini, Roberto
The Intra Venous Glucose Tolerance Test (IVGTT) is an experimental pro- cedure in which a challenge bolus of glucose is administered intra-venously and plasma glucose and insulin concentrations are then frequently sampled. An open problem is to construct a model representing simultaneously the entire control system. In the last three decades, several models appeared in the literature. One of the mostly used one is known as the minimal model, which has been challenged by the dynamical model. However, both the models have not escape from criticisms and drawbacks. In this paper we apply Metabolic P systems theory for developing new physiologically based models of the glucose-insulin system which can be applied to the Intra Venous Glucose Tolerance Test. We considered ten data-sets obtained from literature and for each of them we found an MP model which ts the data and explains the regulations of the dynamics. Finally, further analysis are planned in order to de ne common patterns which explain, in general, the action of the glucose-insulin control system.
Towards Automated Verification of P Systems Using Spin
(Fénix Editora, 2011) Lefticaru, Raluca; Tudose, Cristina; Ipate, Florentin
This paper presents an approach to P systems verification using the Spin model checker. A tool which implements the proposed approach has been developed and can automatically transform P system specifications from P-Lingua into Promela, the language accepted by the well known model checker Spin. The properties expected for the P system are specified using some patterns, representing high level descriptions of frequently asked questions, formulated in natural language. These properties are automatically translated into LTL specifications for the Promela model and the Spin model checker is run against them. In case a counterexample is received, the Spin trace is decoded and expressed as a P system computation. The tool has been tested on a number of examples and the results obtained are presented in the paper.
Forward and Backward Chaining with P Systems
(Fénix Editora, 2011) Ivanov, Sergiu; Alhazov, Artiom; Rogozhin, Vladimir; Gutiérrez Naranjo, Miguel Ángel; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Ministerio de Ciencia e Innovación (MICIN). España; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación Natural
On the one hand, one of the concepts which lies at the basis of membrane computing is the multiset rewriting rule. On the other hand, the paradigm of rules is profusely used in computer science for representing and dealing with knowledge. Therefore, it makes much scene to establish a "bridge" between these domains, for instance, by designing P systems reproducing forward and backward chaining which can be used as tools for reasoning in propositional logic. Our work shows again, how powerful and intuitive the formalism of membrane computing is and how it can be used to represent concepts and notions from totally unrelated areas.
Modeling, Verification and Testing of P Systems Using Rodin and ProB
(Fénix Editora, 2011) Ipate, Florentin; Turcanu, Adrian
In this paper we present an approach to modelling, verification and testing for cell-like P-systems based on Event-B and the Rodin platform. We present a general framework for modelling P systems using Event-B, which we then use to implement two P-system models in the Rodin platform. For each of the two models, we use the associated Pro-B model checker to verify properties and we present some of the results obtained
Spiking Neural dP Systems
(Fénix Editora, 2011) Ionescu, Mihai; Paun, Gheorghe; Pérez Jiménez, Mario de Jesús; Yokomori, Takashi; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación Natural
We bring together two topics recently introduced in membrane computing, the much investigated spiking neural P systems (in short, SN P systems), inspired from the way the neurons communicate through spikes, and the dP systems (distributed P systems, with components which "read" strings from the environment and then cooperate in accepting their concatenation). The goal is to introduce SN dP systems, and to this aim we first introduce SN P systems with the possibility to input, at their request, spikes from the environment; this is done by so-called request rules. A preliminary investigation of the obtained SN dP systems (they can also be called automata) is carried out. As expected, request rules are useful, while the distribution in terms of dP systems can handle languages which cannot be generated by usual SN P systems. We always work with extended SN P systems; the non-extended case, as well as several other natural questions remain open.
Spiking Neural P Systems with Several Types of Spikes
(Fénix Editora, 2011) Ionescu, Mihai; Paun, Gheorghe; Pérez Jiménez, Mario de Jesús; Rodríguez Patón, Alfonso; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación Natural
With a motivation related to gene expression, where enzymes act in series, somewhat similar to the train spikes traveling along the axons of neurons, we consider an extension of spiking neural P systems, where several types of "spikes" are allowed. The power of the obtained spiking neural P systems is investigated and the modeling of gene expression in these terms is discussed. Some further extensions are mentioned, such as considering a process of decay in time of the spikes.
Notes About Spiking Neural P Systems
(Fénix Editora, 2011) Ionescu, Mihai; Paun, Gheorghe; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación Natural
Spiking neural P systems (SN P systems, for short) are much investigated in the last years in membrane computing, but still many open problems and research topics are open in this area. Here, we first recall two such problems (both related to neural biology) from. One of them asks to build an SN P system able to store a number, and to provide it to a reader without losing it, so that the number is available for a further reading. We build here such a memory module and we discuss its extension to model/implement more general operations, specific to (simple) data bases. Then, we formulate another research issue, concerning pattern recognition in terms of SN P systems. In the context, we define a recent version of SN P systems, enlarged with rules able to request spikes from the environment; based on this version, so-called SN dP systems were recently introduced, extending to neural P systems the idea of a distributed dP automaton. Some details about such devices are also given, as a further invitation to the reader to this area of research.
Implementing Local Search with Membrane Computing
(Fénix Editora, 2011) Gutiérrez Naranjo, Miguel Ángel; Pérez Jiménez, Mario de Jesús; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Ministerio de Ciencia e Innovación (MICIN). España; Junta de Andalucía; Universidad de Sevilla. TIC193: Computación Natural
Local search is currently one of the most used methods for finding solution in real-life problems. In this paper we present an implementation of local search with Membrane Computing techniques applied to the N-queens problem as a case study. A CLIPS program inspired in the Membrane Computing design has been implemented and several experiments have been performed.
Toward a Self-replicating Metabolic P System
(Fénix Editora, 2011) Franco, Giuditta; Manca, Vincenzo
This work concerns the synthesis of a "minimal cell' by means of a P system, which is a distributed rewriting system inspired by the structure and the functioning of the biological cell. Specifically, we aim to define a dynamical system which exhibits a steady metabolic evolution, resulting in self-maintenance and self-reproduction. Metabolic P systems represent a class of P systems particularly promising to model a minimal cell in discrete terms, since they have already successfully modeled several metabolisms. The main further step is thus to find a simple way to obtain Metabolic P system self-replication. This paper deals with ideas presented at the BWMC11 (held in Seville, Feb 2011) and opens a new trend in membrane computing, based on computational synthetic biology oriented applications of P systems modeling. The framework is here outlined, and some problems to tackle the synthesis of a minimal cell are discussed. Moreover, an overview of literature and a list of appealing research directions is given, along with several references.
Using Central Nodes to Improve P System Synchronization
(Fénix Editora, 2011) Dinneen, Michael J.; Kim, Yun-Bum; Nicolescu, Radu
We present an improved solution for the Firing Squad Synchronization Problem (FSSP) for digraph-based P systems. We improve our previous FSSP algorithm by allowing the general to delegate a more central cell in the P system to send the nal command to synchronize. With e being the eccentricity of the general and r denoting the radius of the underlying digraph, our new algorithm guarantees to synchronize all cells of the system, between e + 2r + 3 steps (for all trees structures and many digraphs) and up to 3e + 7 steps, in the worst case for any digraph. Empirical results show our new algorithm for tree-based P systems yields at least 20% reduction in the number of steps needed to synchronize over the previous best-known algorithm.

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