Capítulos (Ciencias de la Computación e Inteligencia Artificial)
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Capítulo de Libro Coupling Between Messenger RNA Synthesis and Degradation during Genome Expression(Fidetia, 2015) Chávez de Diego, Sebastián; Pérez Aguado, David; Chávez de Diego, María José; Romero Campero, Francisco José; Universidad de Sevilla. Departamento de Genética; Universidad de Sevilla. Departamento de Matemática Aplicada I (ETSII); Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Junta de AndalucíaGenome expression involves the synthesis of messenger RNA (mRNA), a short lived molecule whose translation directs the synthesis of cellular proteins and that is subject to degradation after the translation process. Up to the date, mRNA synthesis and degradation has been considered as a linear phenomenon in which the above steps occur subsequently without a regulatory interconnection. However, gene expression can be studied as a global system in which all their stages are coupled and interconnected by regulatory mechanisms. We have contributed to demonstrate that the machineries of mRNA synthesis and degradation physically and functionally interact in the cell nucleus. We have proposed that it allows the cross-regulation of transcription with mRNA degradation and vice versa, giving rise to a circular system, which would explain the large robustness observed in gene expression (Haimovich et al, 2013).Capítulo de Libro Cellular solutions to some numerical NP-complete problems: A prolog implementation(Idea Group Inc., 2005) Cordón Franco, Andrés; Gutiérrez Naranjo, Miguel Ángel; Pérez Jiménez, Mario de Jesús; Riscos Núñez, Agustín; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Gheorghe, MarianThis chapter is devoted to the study of numerical NP-complete problems in the framework of cellular systems with membranes, also called P systems (Pǎun, 1998). The chapter presents efficient solutions to the subset sum and the knapsack problems. These solutions are obtained via families of P systems with the capability of generating an exponential working space in polynomial time. A simulation tool for P systems, written in Prolog, is also described. As an illustration of the use of this tool, the chapter includes a session in the Prolog simulator implementing an algorithm to solve one of the above problems.Capítulo de Libro Characterizing tractability by cell-like membrane systems(WORLD SCIENTIFIC PUBL CO PTE LTD, 2006) Gutiérrez Naranjo, Miguel Ángel; Pérez Jiménez, Mario de Jesús; Riscos Núñez, Agustín; Romero Campero, Francisco José; Romero Jiménez, Álvaro; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia ArtificialIn this paper we present a polynomial complexity class in the framework of membrane computing. In this context, and using accepting transition P systems, we provide a characterization of the standard computational class P of problems solvable in polynomial time by deterministic Turing machines.Capítulo de Libro Asynchronous Spiking neural P systems with structural plasticity(Springer, 2015) Cabarle, Francis George C.; Adorna, Henry N.; Pérez Jiménez, Mario de Jesús; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Calude, Cristian S.; Dinneen, Michael J.; Ministerio de Economía y Competitividad (MINECO). España; Universidad de Sevilla. TIC193 : Computación NaturalSpiking neural P (in short, SNP) systems are computing devices inspired by biological spiking neurons. In this work we consider SNP systems with structural plasticity (in short, SNPSP systems) working in the asynchronous (in short, asyn mode). SNPSP systems represent a class of SNP systems that have dynamic synapses, i.e. neurons can use plasticity rules to create or remove synapses. We prove that for asyn mode, bounded SNPSP systems (where any neuron produces at most one spike each step) are not universal, while unbounded SNPSP systems with weighted synapses (a weight associated with each synapse allows a neuron to produce more than one spike each step) are universal. The latter systems are similar to SNP systems with extended rules in asyn mode (known to be universal) while the former are similar to SNP systems with standard rules only in asyn mode (conjectured not to be universal). Our results thus provide support to the conjecture of the still open problem.Capítulo de Libro Implementing Enzymatic Numerical P Systems for AI Applications by Means of Graphic Processing Units(Springer, 2013) García Quismondo, Manuel; Macías Ramos, Luis Felipe; Pérez Jiménez, Mario de Jesús; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Kelemen, Jozef; Romportl, Jan; Zackova, Eva; Ministerio de Ciencia e Innovación (MICIN). España; Junta de Andalucía; Ministerio de Educación y Ciencia (MEC). España; Universidad de Sevilla. TIC193: Computación NaturalA P system represents a distributed and parallel computing model in which basic data structures are, for instance, multisets and strings. Enzymatic Numerical P Systems (ENPS) are a type of P systems whose basic data structures are sets of numerical variables. Separately, GPGPU (general-purpose computing on graphics processing units) is a novel technological paradigm which focuses on the development of tools for graphic cards to solve general purpose problems. This paper proposes an ENPS simulator based on GPUs and presents general concepts about its design and some future ideas and perspectives.Capítulo de Libro Infobiotics Workbench: A P Systems Based Tool for Systems and Synthetic Biology(Springer, 2014) Blakes, Jonathan; Twycross, Jamie; Konur, Savas; Romero Campero, Francisco José; Krasnogor, Natalio; Gheorghe, Marian; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Frisco, Pierluigi; Gheorghe, Marian; Pérez Jiménez, Mario de Jesús; Ministerio de Ciencia e Innovación (MICIN). España; Junta de AndalucíaThis chapter gives an overview of an integrated software suite, the Infobiotics Workbench, which is based on a novel spatial discrete-stochastic P systems modelling framework. The Workbench incorporates three important features, simulation, model checking and optimisation. Its capability for building, analysing and optimising large spatially discrete and stochastic models of multicellular systems makes it a useful, coherent and comprehensive in silico tool in systems and synthetic biology research.Capítulo de Libro Evolution of the Flowering Pathways(Springer, 2016) Lucas Reina, Eva; Ortiz Marchena, M Isabel; Romero Campero, Francisco José; Calonje, Myriam; Romero, José M.; Valverde, Federico; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Lüttge, Ulrich; Cánovas, Francisco M.; Matyssek, RainerFlowering plants are some of the most successful organisms on Earth, particularly those used in agriculture due to the widespread distribution produced by farming activities. The correct moment of the year to flower is a crucial decision as it strongly compromises the success of the progeny and is thus strictly controlled. Crops have been artificially selected to flower in those conditions better adapted for human production, and many genes related to flowering time are selected as targets for breeding programs. These characteristics reflect a complex regulatory pathway that has to respond both to predictable and unexpected changes in the environment. This plasticity confers the flowering plants with a genetic toolkit to adapt to varied habitats and changing environmental conditions. Recent advances in massive acquisition of data from many different species belonging to the green eukaryotic lineage allow us to make an evolutionary approach to the main mechanisms that influence the floral transition and how flowers are formed in modern plants. This work will review some of these aspects from the floral transition to the floral organogenesis.Capítulo de Libro On the Velocity Update in Multi-Objective Particle Swarm Optimizers(Springer, 2010) Durillo, Juan J.; Nebro, Antonio J.; García Nieto, José Manuel; Alba, Enrique; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Coello Coello, Carlos A.; Dhaenens, Clarisse; Jourdan, Laetitia; Ministerio de Ciencia e Innovación (MICIN). España; Junta de AndalucíaSince its appearance, Particle Swarm Optimization (PSO) has become a very popular technique for solving optimization problems because of both its simplicity and its fast convergence properties. In the last few years there has been a variety of proposals for extending it to handle with multiples objectives. Although many of them keep the same properties of the original algorithm, they face difficulties when tackling the optimization of some multi-modal problems, i.e., those having more than one suboptimal front of solutions. Recent studies have shown that this disadvantage could be related to the velocity of the particles: uncontrolled high velocities may have no effect in particles movements. While many of the contributions on the specialized literature have focused on the selection of the leaders of the swarm, studies about different schemes for controlling the velocity of the particles are scarce in the multi-objective domain. In this work, we study different mechanisms in order to update the velocity of each particle with the idea of enhancing the search capabilities of multi-objective PSO algorithms. Our experiments show that some modifications help to over-coming the difficulties observed in previous proposals when dealing with hard optimization problems.Capítulo de Libro Applications of Membrane Computing(Springer, 2006) Ciobanu, Gabriel; Paun, Gheorghe; Pérez Jiménez, Mario de Jesús; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación NaturalCapítulo de Libro Membrane System-Based Models for Specifying Dynamical Population Systems(Springer, 2014) Colomer Cugat, M. Ángels; García Quismondo, Manuel; Macías Ramos, Luis Felipe; Martínez del Amor, Miguel Ángel; Pérez Hurtado de Mendoza, Ignacio; Pérez Jiménez, Mario de Jesús; Riscos Núñez, Agustín; Valencia Cabrera, Luis; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Frisco, Pierluigi; Gheorghe, Marian; Pérez Jiménez, Mario de Jesús; Junta de Andalucía; Ministerio de Economía y Competitividad (MINECO). España; Universidad de Sevilla. TIC193: Computación NaturalPopulation Dynamics P systems (PDP systems, in short) provide a new formal bio-inspired modelling framework, which has been successfully used for modelling population dynamics on real ecosystems. The semantics of these systems is captured by the Direct distribution based on Consistent Blocks Algorithm (DCBA), which has been engineered into software simulation tools. In particular, MeCoSim (Membrane Computing Simulator) is a GUI developed in the framework of P-Lingua that can be used as a simulation environment for running virtual experiments. The parameters of each scenario to be simulated can be easily adjusted in a visual way, as well as the settings for the desired output format, thus facilitating the validation of the designed models against real data. The simulation of PDP systems is data intensive for large models. Therefore, the development of efficient simulators for this field is needed. In fact, the computational power of GPUs is currently being used to accelerate simulations of PDP systems. We illustrate the modelling framework presented with a case study concerning pandemics.Capítulo de Libro Formal Verification of Programs in Molecular Models with Random Access Memory(Fénix Editorial, 2005) Pérez Jiménez, Mario de Jesús; Sancho Caparrini, Fernando; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Pérez Jiménez, Mario de Jesús; Romero Jiménez, Álvaro; Sancho Caparrini, Fernando; Ministerio de Ciencia Y Tecnología (MCYT). España; Universidad de Sevilla. TIC193: Computación NaturalFormal verification of molecular programs is a first step towards their automatic processing by means of reasoning systems (ACL2, PVS, etc). In this paper a systematic method to establish verifications of these programs within molecular models with memory, that is, molecular computing models where some operations modifying the inner structure of molecules exist, is proposed. The method presented in this work is applied to relevant problems for the design of molecular programs solving some well-known numerical NP-complete problems: the Generating Cover Families problem, the Set Covering problem and the Minimal Set Cover Selection Problem.Capítulo de Libro Skeletonizing Digital Images with Cellular Automata(Springer, 2014) Díaz Pernil, Daniel; Peña Cantillana, Francisco; 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); Rosin, Paul; Adamatzky, Andrew; Sun, Xianfang; Ministerio de Economía y Competitividad (MINECO). España; Universidad de Sevilla. TIC193: Computación Natural; Universidad de Sevilla. FQM296: Topología Computacional y Matemática AplicadaThe skeletonization of an image consists of converting the initial image into a more compact representation. In general, the skeleton preserves the basic struc-ture and, in some sense, keeps the meaning. The most important features concerning a shape are its topology (represented by connected components, holes, etc.) and its geometry (elongated parts, ramifications, etc.), thus they must be preserved. Skele-tonization is usually considered as a pre-processing step in pattern recognition algo-rithms, but its study is also interesting by itself for the analysis of line-based images such as texts, line drawings, human fingerprints classification or cartography. Since the introduction of the concept by Blum in 1962 under the name of medial axis transform, many algorithms have been published in this topic and there are many different approaches to the problem, among them the ones based on distance transform of the shape and skeleton pruning based on branch analysis. In this chapter, we focus on how the skeletonization of an image can be studied in the Cellular Automata framework and, as a case study, we consider in detail the Guo and Hall skeletonizing algorithm.Ponencia Synthetizing Qualitative (Logical) Patterns for Pedestrian Simulation from Data(Springer, 2016) Aranda Corral, Gonzalo A.; Borrego Díaz, Joaquín; Galán Páez, Juan; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Ministerio de Economía y Competitividad (MINECO). EspañaThis work introduces a (qualitative) data-driven framework to extract patterns of pedestrian behaviour and synthesize Agent-Based Models. The idea consists in obtaining a rule-based model of pedestrian behaviour by means of automated methods from data mining. In order to extract qualitative rules from data, a mathematical theory called Formal Concept Analysis (FCA) is used. FCA also provides tools for implicational reasoning, which facilitates the design of qualitative simulations from both, observations and other models of pedestrian mobility. The robustness of the method on a general agent-based setting of movable agents within a grid is shown.Capítulo de Libro On Experimental Efficiency for Retraction Operator to Stem Basis(Springer, 2018) Aranda Corral, Gonzalo A.; Borrego Díaz, Joaquín; Galán Páez, Juan; Trujillo Caballero, Alejandro; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia ArtificialIn this paper, we introduce an implementation of an inference rule called “Independence Rule” which lets us reduce the size of knowledge basis based on the retraction problem. This implementation is made in a functional language, Scala, and specialized on attribute implications. We evaluate its efficiency related to the Stem Base generation.Capítulo de Libro Topología simplicial en ACL2(Universidad de la Rioja, 2010) Lambán Pardo, Laureano; Martín Mateos, Francisco Jesús; Ruiz Reina, José Luis; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Lambán Pardo, Laureano; Romero, Ana; Rubio, Julio; Ministerio de Educación y Ciencia (MEC). EspañaPonencia Towards Emotion Recognition: A Persistent Entropy Application(Springer, 2019) González Díaz, Rocío; Paluzo Hidalgo, Eduardo; Quesada Moreno, José Francisco; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. Departamento de Matemática Aplicada I (ETSII)Emotion recognition and classification is a very active area of research. In this paper, we present a first approach to emotion classification using persistent entropy and support vector machines. A topology-based model is applied to obtain a single real number from each raw signal. These data are used as input of a support vector machine to classify signals into 8 different emotions (calm, happy, sad, angry, fearful, disgust and surprised).Capítulo de Libro A Simulation Workflow for Membrane Computing: From MeCoSim to PMCGPU Through P-Lingua(Springer, 2018) Valencia Cabrera, Luis; Martínez del Amor, Miguel Ángel; Pérez Hurtado de Mendoza, Ignacio; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación NaturalP system simulators are of high importance in Membrane Computing, since they provide tools to assist on model validation and verification. Keeping a balance between generality and flexibility, on the one side, and efficiency, on the other hand, is always challenging, but it is worth the effort. Besides, in order to prove the feasibility of P system models as practical tools for solving problems and aid in decision making, it is essential to provide functional mechanisms to have all the elements required at disposal of the potential users smoothly integrated in a robust workflow. The aim of this paper is to describe the main components and connections within the approach followed in this pipeline.Capítulo de Libro A Kernel-Based Membrane Clustering Algorithm(Springer, 2018) Yang, Jinyu; Chen, Ru; Zhang, GuoZhou; Peng, Hong; Wang, Jun; Riscos Núñez, Agustín; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación NaturalThe existing membrane clustering algorithms may fail to handle the data sets with non-spherical cluster boundaries. To overcome the shortcoming, this paper introduces kernel methods into membrane clustering algorithms and proposes a kernel-based membrane clustering algorithm, KMCA. By using non-linear kernel function, samples in original data space are mapped to data points in a high-dimension feature space, and the data points are clustered by membrane clustering algorithms. Therefore, a data clustering problem is formalized as a kernel clustering problem. In KMCA algorithm, a tissue-like P system is designed to determine the optimal cluster centers for the kernel clustering problem. Due to the use of non-linear kernel function, the proposed KMCA algorithm can well deal with the data sets with non-spherical cluster boundaries. The proposed KMCA algorithm is evaluated on nine benchmark data sets and is compared with four existing clustering algorithms.Capítulo de Libro Design Patterns for Efficient Solutions to NP-Complete Problems in Membrane Computing(Springer, 2018) Romero Jiménez, Álvaro; Orellana Martín, David; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación NaturalMany variants of P systems have the ability to generate an exponential number of membranes in linear time. This feature has been exploited to elaborate (theoretical) efficient solutions to NP-complete, or even harder, problems. A thorough review of the existent solutions shows the utilization of common techniques and procedures. The abstraction of the latter into design patterns can serve to ease and accelerate the construction of efficient solutions to new hard problems.Capítulo de Libro Other Buds in Membrane Computing(Springer, 2018) Gutiérrez Naranjo, Miguel Ángel; Universidad de Sevilla. Departamento de Ciencias de la Computación e Inteligencia Artificial; Universidad de Sevilla. TIC193: Computación NaturalIt is well-known the huge Mario’s contribution to the development of Membrane Computing. Many researchers may relate his name to the theory of complexity classes in P systems, the research of frontiers of the tractability or the application of Membrane Computing to model real-life situations as the Quorum Sensing System in Vibrio fischeri or the Bearded Vulture ecosystem. Beyond these research areas, in the last years Mario has presented many new research lines which can be considered as buds in the robust Membrane Computing tree. Many of them were the origin of new research branches, but some others are still waiting to be developed. This paper revisits some of these buds.