Simulating FRSN P Systems with Real Numbers in P-Lingua on sequential and CUDA platforms

Fuzzy Reasoning Spiking Neural P systems (FRSN P systems, for short) is a variant of Spiking Neural P systems incorporating fuzzy logic elements that make it suitable to model fuzzy diagnosis knowledge and reasoning required for fault diagnosis applications. In this sense, several FRSN P system variants have been proposed, dealing with real numbers, trapezoidal numbers, weights, etc. The model incorporating real numbers was the first introduced [13], presenting promising applications in the field of fault diagnosis of electrical systems. For this variant, a matrix-based algorithm was provided which, when executed on parallel computing platforms, fully exploits the model maximally parallel capacities. In this paper we introduce a P-Lingua framework extension to parse and simulate FRSN P systems with real numbers. Two simulators, implementing a variant of the original matrix-based simulation algorithm, are provided: a sequential one (written in Java), intended to run on traditional CPUs, and a parallel one, intended to run on CUDAenabled devices.Ministerio de Economía y Competitividad TIN2012-3743

Spiking Neural P Systems with Functional Astrocytes

Spiking Neural P Systems (SN P Systems, for short) is a developing field within the universe of P Systems. New variants arise constantly as the study of their properties, such as computational completeness and computational efficiency, grows. Variants frequently incorporate new ingredients into the original model inspired by real neurophysiological structure of the brain. A singular element present within that structure is the astrocyte. Astrocytes, also known collectively as astroglia, are characteristic star-shaped glial cells in the brain and spinal cord. In this paper, a new variant of Spiking Neural P Systems incorporating astrocytes is introduced. These astrocytes are modelled as computing devices capable of performing function computation in a single computation step. In order to experimentally study the action of Spiking Neural P Systems with astrocytes, it is necessary to develop software providing the required simulation tools. Within this trend, P– Lingua offers a standard language for the definition of P Systems. Part of the same software project, pLinguaCore library provides particular implementations of parsers and simulators for the models specified in P–Lingua. Along with the new SN P System variant with astrocytes, an extension of the P–Lingua language allowing definition of these systems is presented in this paper, as well as an upgrade of pLinguaCore, including a parser and a simulator that supports the aforementioned variant.Ministerio de Ciencia e Innovación TIN2009–13192Junta de Andalucía P08-TIC-0420

Parallel simulation of Population Dynamics P systems: updates and roadmap

Population Dynamics P systems are a type of multienvironment P systems that serve as a formal modeling framework for real ecosystems. The accurate simulation of these probabilisticmodels, e.g. with Direct distribution based on Consistent Blocks Algorithm, entails large run times. Hence, parallel platforms such as GPUs have been employed to speedup the simulation. In 2012, the first GPU simulator of PDP systems was presented. However, it was able to run only randomly generated PDP systems. In this paper, we present current updates made on this simulator, involving an input modu le for binary files and an output module for CSV files. Finally, the simulator has been experimentally validated with a real ecosystem model, and its performance has been tested with two high-end GPUs: Tesla C1060 and K40.Ministerio de Economía y Competitividad TIN2012-37434Junta de Andalucía P08-TIC-0420

Membrane fission versus cell division: When membrane proliferation is not enough

Cell division is a process that produces two or more cells from one cell by replicating the original chromosomes so that each daughter cell gets a copy of them. Membrane fission is a process by which a biological membrane is split into two new ones in suchamanner that the contents of the initial membrane get distributedor separated among the new membranes. Inspired by these biological phenomena, new kinds of models we reconsidered in the discipline of Membrane Computing, in the context of P systems with active membranes, and tissue P systems that use symport/antiport rules, respectively. This paper combines the two approaches: cell-like P systems with symport/antiport rules and membrane separation are studied, from a computational complexity perspective.Specifically, the role of the environment in the context of cell-like P systems withmembrane separation is established, and additional borderlines between tractability and NP-hardness are summarized.Ministerio de Economía y Competitividad TIN2012- 3743

Parallel Simulation of PDP Systems: Updates and Roadmap

PDP systems are a type of multienvironment P systems, which serve as a formal modeling framework for Population Dynamics. The accurate simulation of these probabilistic models entails large run times. Hence, parallel platforms such as GPUs has been employed to speedup the simulation. In 2012 [14], the rst GPU simulator of PDP systems was presented. In this paper, we present current updates made on this simulator, and future developments to consider.Ministerio de Economía y Competitividad TIN2012-3743

Limits on Efficient Computation in P Systems with Symport/Antiport Rules

Classical membrane systems with symport/antiport rules observe the con- servation law, in the sense that they compute by changing the places of objects with respect to the membranes, and not by changing the objects themselves. In these systems the environment plays an active role because the systems not only send objects to the environment, but also bring objects from the environment. In the initial configuration of a system, there is a special alphabet whose elements appear in an arbitrary large number of copies. The ability of these computing devices with infinite copies of some objects has been widely exploited in the design of efficient solutions to computationally hard problems. This paper deals with computational aspects of P systems with symport/antiport rules and membrane division rules or membrane separation rules. Specifically, we study the limitations of such P systems when the only communication rules allowed have length 1.Ministerio de Ciencia e Innovación TIN2012-3743

On Efficiency of P Systems with Symport/Antiport and Membrane Division

Classical membrane systems with symport/antiport rules observe the con- servation law, in the sense that they compute by changing the places of objects with respect to the membranes, and not by changing the objects themselves. In these systems the environment plays an active role because the systems not only send objects to the environment, but also bring objects from the environment. In the initial configuration of a system, there is a special alphabet whose elements appear in an arbitrary large number of copies. The ability of these computing devices to have infinite copies of some objects has been widely exploited in the design of efficient solutions to computationally hard problems. This paper deals with computational aspects of P systems with symport/antiport and membrane division rules where there is not an environment having the property mentioned above. Specifically, we establish the relationships between the polynomial complexity class associated with P systems with symport/antiport, membrane division rules, and with or without environment. As a consequence, we prove that the role of the environment is irrelevant in order to solve NP–complete problems in an efficient way.Ministerio de Ciencia e Innovación TIN2012-3743

Minimal Cooperation in P Systems with Symport/Antiport: A Complexity Approach

Membrane systems with symport/antiport rules compute by just moving objects among membranes, and not by changing the objects themselves. In these systems the environment plays an active role because, not only it receives objects from the system, but it also sends objects into the system. Actually, in this framework it is commonly assumed that an arbitrarily large number of copies of some objects are initially available in the environment. This special feature has been widely exploited for the design of e cient solutions to computationally hard problems in the framework of tissue like P systems able to create an exponential workspace in polynomial time (e.g. via cell division or cell separation rules). This paper deals with cell-like P systems which use symport/antiport rules as communication rules, and the role played by the minimal cooperation is studied from a computational complexity point of view. Speci cally, the limitations on the e ciency of P systems with membrane separation whose symport/antiport rules involve at most two objects are established. In addition, a polynomial time solution to HAM-CYCLE problem, a well known NP-complete problem, by using a family of such kind of P systems with membrane division, is provided. Therefore, in the framework of cell-like P systems with minimal cooperation in communication rules, passing from membrane separation to membrane division amounts to passing from tractability to NP{hardness.Ministerio de Economía y Competitividad TIN2012-3743

Computational Efficiency of P Systems with Symport/Antiport Rules and Membrane Separation

Membrane ssion is a process by which a biological membrane is split into two new ones in such a way that the contents of the initial membrane is separated and distributed between the new membranes. Inspired by this biological phenomenon, membrane separation rules were considered in membrane computing. In this paper we deal with celllike P systems with membrane separation rules that use symport/antiport rules (such systems compute by changing the places of objects with respect to the membranes, and not by changing the objects themselves) as communication rules. Speci cally we study a lower bound on the length of communication rules with respect to the computational e ciency of such kind of membrane systems; that is, their ability to solve computationally hard problems in polynomial time by trading space for time. The main result of this paper is the following: communication rules involving at most three objects is enough to achieve the computational e ciency of P systems with membrane separation. Thus, a polynomial time solution to SAT problem is provided in this computing framework. It is known that only problems in P can be solved in polynomial time by using minimal cooperation in communication rules and membrane separation, so the lower bound of the e ciency obtained is an optimal bound.Ministerio de Economía y Competitividad TIN2012-3743

The role of the direction in tissue P systems with cell separation

Tissue P systems with cell separation where the communication among cells is performed by means of symport and antiport rules are able to efficiently solve computationally hard problems in a feasible time by a space-time trade off. Symport and antiport rules formally capture the cases where a number of chemical substances pass through a membrane at the same time, with the help of each other, either in the same direction (symport) or in opposite directions (antiport). The present paper investigates the role of the direction in communication rules from a computational complexity point of view. More precisely, the efficiency of tissue P systems with cell separation is analyzed in the case when their communication rules are all of the same type: either symport rules or antiport rules. The main result is that in the framework of tissue P systems with cell separation, passing from using only symport rules to using only antiport rules amounts to passing from non-efficiency to efficiency, assuming that P ≠ NP.Ministerio de Economía y Competitividad TIN2012-37434Junta de Andalucía P08 – TIC 0420