Fundamenta Informaticae - Volume 136, issue 3

Authors: Pan, Linqiang | Păun, Gheorghe | Pérez-Jiménez, Mario J.

Article Type: Other

DOI: 10.3233/FI-2015-1150

Citation: Fundamenta Informaticae, vol. 136, no. 3, pp. i-i, 2015

Authors: He, Juanjuan | Zhang, Kai

Article Type: Research Article

Abstract: The multiobjective multiple traveling salesman problem (MmTSP), in which multiple salesmen and objectives are involved in a route, is known to be NP-hard. The MmTSP is more appropriate for real-life applications than the classical traveling salesman problem (TSP), however it has not received the same amount of attention. Due to the high complexity of the MmTSP, a promising algorithm for solving it must be based on a global search procedure. This paper proposes a hybrid global search algorithm, that belongs to the membrane computing framework. The search behavior of the algorithm is enhanced by a communication mechanism. The multichromosome representation …is considered to reduce the excess runtime. The effectiveness of the proposed algorithm is tested on the MmTSP with disparately-scaled objective functions, salesmen and problem sizes. The experimental results are compared with the NSGA-II and several evolutionary strategies with decomposition, including simulated annealing algorithm, hill climbing method, pure evolutionary algorithm, and genetic algorithm. Show more

Keywords: Evolutionary multiobjective optimization, Membrane computing, Multiobjective multiple traveling salesman problem

DOI: 10.3233/FI-2015-1151

Citation: Fundamenta Informaticae, vol. 136, no. 3, pp. 199-208, 2015

Authors: Juayong, Richelle Ann B. | Adorna, Henry N.

Article Type: Research Article

Abstract: This paper explores the relation of computations in Evolution-Communication P systems with energy (ECPe systems) and non-cooperative Transition P systems without dissolution (TP systems). We have shown that for every non-cooperative TP system, we can construct an ECPe system that, (i) generates the same language, and (ii) each halting computation that takes τ steps in the TP system can be simulated in at most 3τ + 1 steps in its corresponding ECPe system.

Keywords: Membrane computing, Evolution-Communication P systems with Energy, Transition P systems

DOI: 10.3233/FI-2015-1152

Citation: Fundamenta Informaticae, vol. 136, no. 3, pp. 209-217, 2015

Authors: Kong, Yuan | Shi, Xiaolong | Xu, Jinbang | Huang, Xinquan

Article Type: Research Article

Abstract: Spiking neural P systems with astrocytes (SNPA systems, for short) are a class of distributed parallel computing devices inspired from the way neurons communicate by means of spikes. In this work, we investigate the reversibility in SNPA systems as well as the computational power of reversible SNPA systems. It is proved that reversible SNPA systems are universal, where the forgetting rules and the feature of delay in spiking rules are not used, and each neuron contains only one spiking rule. The result suggests that the astrocytes play a key role in the functioning of reversible SNPA systems.

Keywords: Spiking neural P system, astrocyte, reversible register machine, universality

DOI: 10.3233/FI-2015-1153

Citation: Fundamenta Informaticae, vol. 136, no. 3, pp. 219-230, 2015

Authors: Kong, Yuan | Zhang, Zheng | Liu, Yang

Article Type: Research Article

Abstract: Spiking neural P systems with astrocytes (SNPA systems, for short) are a class of distributed parallel computing devices inspired from the way spikes pass along the synapses between neurons. In this work, we investigate the computational power of SNPA systems as language generators. Specifically, representations of recursively enumerable languages and of regular languages are given by means of SNPA systems without forgetting rules. Furthermore, a simple finite language is produced which can be generated by SNPA systems, while it cannot be generated by usual spiking neural P systems. These results show that the astrocytes are a powerful ingredient for spiking …neural P systems as language generators. Show more

Keywords: Membrane computing, spiking neural P system, astrocyte

DOI: 10.3233/FI-2015-1154

Citation: Fundamenta Informaticae, vol. 136, no. 3, pp. 231-240, 2015

Authors: Li, Yanzhang | Zhou, Changjun | Zheng, Xuedong

Article Type: Research Article

Abstract: The protein structure folding is one of the most challenging problems in the field of bioinformatics. The main problem of protein structure prediction in the 3D toy model is to find the lowest energy conformation. Although many heuristic algorithms have been proposed to solve the protein structure prediction (PSP) problem, the existing algorithms are far from perfect since PSP is an NP-problem. In this paper, we proposed an artificial bee colony (ABC) algorithm based on the toy model to solve PSP problem. In order to improve the global convergence ability and convergence speed of the ABC algorithm, we adopt a …new search strategy by combining the global solution into the search equation. Experimental results illustrate that the suggested algorithm can get the lowest energy when the algorithm is applied to the Fibonacci sequences and to four real protein sequences which come from the Protein Data Bank (PDB). Compared with the results obtained by PSO, LPSO, PSO-TS, PGATS, our algorithm is more efficient. Show more

Keywords: Protein structure prediction, ABC algorithm, Fibonacci sequences

DOI: 10.3233/FI-2015-1155

Citation: Fundamenta Informaticae, vol. 136, no. 3, pp. 241-252, 2015

Authors: Macías-Ramos, Luis F. | Pérez-Jiménez, Mario J. | Song, Tao | Pan, Linqiang

Article Type: Research Article

Abstract: Spiking neural P systems (SN P systems for short) are a class of neural-like computing models in the framework of membrane computing. Inspired by the neurophysiological structure of the brain, SN P systems have been extended in various ways. P–Lingua is a standard language for the definition of P systems, where pLinguaCore library provides particular implementations of parsers and simulators for the models specified in P–Lingua. A support for simulating SN P systems in P–Lingua was introduced recently and soon expanded to cover further features of these systems. In this paper, we present an extension of P–Lingua related to asynchronous …SN P systems, in order to incorporate simulation capabilities for limited asynchronous SN P systems and asynchronous SN P systems with local synchronization. Show more

Keywords: Membrane computing, Spiking neural P system, Asynchronous mode, P-Lingua

DOI: 10.3233/FI-2015-1156

Citation: Fundamenta Informaticae, vol. 136, no. 3, pp. 253-267, 2015

Authors: Martínez-del-Amor, Miguel A. | García-Quismondo, Manuel | Macías-Ramos, Luis F. | Valencia-Cabrera, Luis | Riscos-Núñez, Agustin | Pérez-Jiménez, Mario J.

Article Type: Research Article

Abstract: P systems have been proven to be useful as modeling tools in many fields, such as Systems Biology and Ecological Modeling. For such applications, the acceleration of P system simulation is often desired, given the computational needs derived from these kinds of models. One promising solution is to implement the inherent parallelism of P systems on platforms with parallel architectures. In this respect, GPU computing proved to be an alternative to more classic approaches in Parallel Computing. It provides a low cost, and a manycore platform with a high level of parallelism. The GPU has been already employed to speedup …the simulation of P systems. In this paper, we look over the available parallel P systems simulators on the GPU, with special emphasis on those included in the PMCGPU project, and analyze some useful guidelines for future implementations and developments. Show more

Keywords: Membrane Computing, P systems, Parallel Computing, GPU computing, CUDA

DOI: 10.3233/FI-2015-1157

Citation: Fundamenta Informaticae, vol. 136, no. 3, pp. 269-284, 2015

Authors: Niu, Yunyun | Venkat, Ibrahim | Khader, Ahamad Tajudin | Subramanian, K.G.

Article Type: Research Article

Abstract: It is known that the Common Algorithmic Problem (CAP) has the nice property that several other NP-complete problems can be reduced to it in linear time. The decision version of this problem is known to be efficiently solved by a family of recognizer P systems with active membranes with three electrical charges working in the maximally parallel way. We here work with a variant of P systems with active membranes without polarizations and present a uniform solution to CAP in the minimally parallel mode.

Keywords: Membrane Computing, P System, Minimal Parallelism, Common Algorithmic Problem

DOI: 10.3233/FI-2015-1158

Citation: Fundamenta Informaticae, vol. 136, no. 3, pp. 285-296, 2015