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  • A multi-level AI-based scheduler to increase adaptiveness in time-constrained mobile communication environments
    Nat. Comput. (IF 1.495) Pub Date : 2020-10-18
    Jesus Fernandez-Conde, Pedro Cuenca-Jimenez, Rafael Toledo-Moreo

    Scheduling is one of the classic problems in real-time adaptive systems. Due to the complex nature of these applications, the implementation of some sort of run-time intelligence is required, in order to build intelligent systems capable of operating adequately in dynamic environments. The incorporation of artificial intelligence planning techniques in a real-time scenario allows a timely reaction

    更新日期:2020-10-19
  • An evaluation of k-means as a local search operator in hybrid memetic group search optimization for data clustering
    Nat. Comput. (IF 1.495) Pub Date : 2020-10-06
    Luciano D. S. Pacifico, Teresa B. Ludermir

    Cluster analysis is one important field in pattern recognition and machine learning, consisting in an attempt to distribute a set of data patterns into groups, considering only the inner properties of those data. One of the most popular techniques for data clustering is the K-Means algorithm, due to its simplicity and easy implementation. But K-Means is strongly dependent on the initial point of the

    更新日期:2020-10-07
  • Correction to: A class of discrete dynamical systems with properties of both cellular automata and L-systems
    Nat. Comput. (IF 1.495) Pub Date : 2020-09-19
    Roderick Edwards, Aude Maignan

    In the pdf version of the original publication, in the proof of Theorem 8 (second column of p. 632), the T matrices appeared incorrectly. The correct values are given here.

    更新日期:2020-09-20
  • The representational entity in physical computing
    Nat. Comput. (IF 1.495) Pub Date : 2020-09-18
    Susan Stepney, Viv Kendon

    We have developed abstraction/representation (AR) theory to answer the question “When does a physical system compute?” AR theory requires the existence of a representational entity (RE), but the vanilla theory does not explicitly include the RE in its definition of physical computing. Here we extend the theory by showing how the RE forms a linked complementary model to the physical computing model

    更新日期:2020-09-20
  • Comparison of synchronous and asynchronous parallelization of extreme surrogate-assisted multi-objective evolutionary algorithm
    Nat. Comput. (IF 1.495) Pub Date : 2020-09-18
    Tomohiro Harada, Misaki Kaidan, Ruck Thawonmas

    This paper investigates the integration of a surrogate-assisted multi-objective evolutionary algorithm (MOEA) and a parallel computation scheme to reduce the computing time until obtaining the optimal solutions in evolutionary algorithms (EAs). A surrogate-assisted MOEA solves multi-objective optimization problems while estimating the evaluation of solutions with a surrogate function. A surrogate function

    更新日期:2020-09-20
  • Protein structure prediction in an atomic model with differential evolution integrated with the crowding niching method
    Nat. Comput. (IF 1.495) Pub Date : 2020-09-10
    Daniel Varela, José Santos

    A hybrid version between differential evolution and the fragment replacement technique was defined for protein structure prediction. The coarse-grained atomic model of the Rosetta system was used for protein representation. The high-dimensional and multimodal nature of protein energy landscapes requires an efficient search for obtaining the native structures with minimum energy. However, the energy

    更新日期:2020-09-10
  • Depicting probabilistic context awareness knowledge in deliberative architectures
    Nat. Comput. (IF 1.495) Pub Date : 2020-08-05
    Jonatan Ginés, Francisco J. Rodríguez-Lera, Francisco Martín, Ángel Manuel Guerrero, Vicente Matellán

    Facing long-term autonomy with a cognitive architecture raises several difficulties for processing symbolic and sub-symbolic information under different levels of uncertainty, and deals with complex decision-making scenarios. For reducing environment uncertainty and simplify the decision-making process, this paper establishes a method for translating robot knowledge to a conceptual graph to later extract

    更新日期:2020-08-06
  • Benchmarking the performance of genetic algorithms on constrained dynamic problems
    Nat. Comput. (IF 1.495) Pub Date : 2020-07-22
    P. A. Grudniewski, A. J. Sobey

    The growing interest in dynamic optimisation has accelerated the development of genetic algorithms with specific mechanisms for these problems. To ensure that these developed mechanisms are capable of solving a wide range of practical problems it is important to have a diverse set of benchmarking functions to ensure the selection of the most appropriate Genetic Algorithm. However, the currently available

    更新日期:2020-07-22
  • A memetic algorithm for restoring feasibility in scheduling with limited makespan
    Nat. Comput. (IF 1.495) Pub Date : 2020-07-06
    Raúl Mencía, Carlos Mencía, Ramiro Varela

    When solving a scheduling problem, users are often interested in finding a schedule optimizing a given objective function. However, in some settings there can be hard constraints that make the problem unfeasible. In this paper we focus on the task of repairing infeasibility in job shop scheduling problems with a hard constraint on the makespan. In this context, earlier work addressed the problem of

    更新日期:2020-07-07
  • Hairpin completions and reductions: semilinearity properties
    Nat. Comput. (IF 1.495) Pub Date : 2020-06-27
    Henning Bordihn, Victor Mitrana, Andrei Păun, Mihaela Păun

    This paper is part of the investigation of some operations on words and languages with motivations coming from DNA biochemistry, namely three variants of hairpin completion and three variants of hairpin reduction. Since not all the hairpin completions or reductions of semilinear languages remain semilinear, we study sufficient conditions for semilinear languages to preserve their semilinearity property

    更新日期:2020-06-28
  • Combining hyper-heuristics to evolve ensembles of priority rules for on-line scheduling
    Nat. Comput. (IF 1.495) Pub Date : 2020-06-08
    Francisco J. Gil-Gala, María R. Sierra, Carlos Mencía, Ramiro Varela

    Combining metaheuristics is a common technique that may produce high quality solutions to complex problems. In this paper, we propose a combination of Genetic Programming (GP) and Genetic Algorithm (GA) to obtain ensembles of priority rules to solve a scheduling problem, denoted \((1,Cap(t)||\sum T_i)\), on-line. In this problem, a set of jobs must be scheduled on a single machine whose capacity varies

    更新日期:2020-06-08
  • Powering DNA strand-displacement reactions with a continuous flow reactor
    Nat. Comput. (IF 1.495) Pub Date : 2020-06-03
    Xinyu Cui, Dominic Scalise, Rebecca Schulman

    Living systems require a sustained supply of energy and nutrients to survive. These nutrients are ingested, transformed into low-energy waste products, and excreted. In contrast, synthetic DNA strand-displacement reactions typically run within closed systems provided with a finite initial supply of reactants. Once the reactants are consumed, all net reactions halt and the system ceases to function

    更新日期:2020-06-03
  • Ensemble learning based on fitness Euclidean-distance ratio differential evolution for classification
    Nat. Comput. (IF 1.495) Pub Date : 2020-05-27
    Jing Liang, Yunpeng Wei, Boyang Qu, Caitong Yue, Hui Song

    Ensemble learning is a system that combines a set of base learners to improve the performance in machine learning, where accuracy and diversity of base learners are two important factors. However, these two factors are usually contradictory. To address this problem, in this paper, we propose a novel ensemble learning algorithm based on fitness Euclidean-distance ratio differential evolution, to train

    更新日期:2020-05-27
  • An enhanced monarch butterfly optimization with self-adaptive crossover operator for unconstrained and constrained optimization problems
    Nat. Comput. (IF 1.495) Pub Date : 2020-05-21
    Mingyang Chen

    Inspired by the phenomenon of migration of monarch butterflies, Wang et al. developed a novel promising swarm intelligence algorithm, called monarch butterfly optimization (MBO), for addressing unconstrained low-dimensional optimization problems. In this paper, we firstly extend the application area of the basic MBO to solve the constrained optimization problems. At the same time, the crossover operator

    更新日期:2020-05-21
  • Attractor landscapes in Boolean networks with firing memory: a theoretical study applied to genetic networks
    Nat. Comput. (IF 1.495) Pub Date : 2020-05-09
    Eric Goles; Fabiola Lobos; Gonzalo A. Ruz; Sylvain Sené

    In this paper we study the dynamical behavior of Boolean networks with firing memory, namely Boolean networks whose vertices are updated synchronously depending on their proper Boolean local transition functions so that each vertex remains at its firing state a finite number of steps. We prove in particular that these networks have the same computational power than the classical ones, i.e. any Boolean

    更新日期:2020-05-09
  • Search space reduction of asynchrony immune cellular automata
    Nat. Comput. (IF 1.495) Pub Date : 2020-04-27
    Luca Mariot; Luca Manzoni; Alberto Dennunzio

    We continue the study of asynchrony immunity in cellular automata (CA), which can be considered as a generalization of correlation immunity in the case of vectorial Boolean functions. The property could have applications as a countermeasure for side-channel attacks in CA-based cryptographic primitives, such as S-boxes and pseudorandom number generators. We first give some theoretical results on the

    更新日期:2020-04-27
  • Solving two-dimensional cutting stock problem via a DNA computing algorithm
    Nat. Comput. (IF 1.495) Pub Date : 2020-03-07
    M. Dodge, S. A. MirHassani, F. Hooshmand

    Two-dimensional cutting stock problem (TDCSP) is a well-known combinatorial optimization problem in which a given set of two-dimensional small pieces with different shapes should be cut from a given main board so that the demand of each small piece is satisfied and the total waste is minimized. Since TDCSP is an NP-complete problem, it is unsolvable in polynomial time on electronic computers. However

    更新日期:2020-04-23
  • On the minimal number of generators of endomorphism monoids of full shifts
    Nat. Comput. (IF 1.495) Pub Date : 2020-02-14
    Alonso Castillo-Ramirez

    For a group G and a finite set A, denote by \(\mathrm{End}(A^G)\) the monoid of all continuous shift commuting self-maps of \(A^G\) and by \(\mathrm{Aut}(A^G)\) its group of units. We study the minimal cardinality of a generating set, known as the rank, of \(\mathrm{End}(A^G)\) and \(\mathrm{Aut}(A^G)\). In the first part, when G is a finite group, we give upper and lower bounds for the rank of \(\mathrm{Aut}(A^G)\)

    更新日期:2020-04-23
  • The impact of alphabet size on pattern complexity of maxmin- $$\omega$$ω cellular automata
    Nat. Comput. (IF 1.495) Pub Date : 2020-04-14
    Ebrahim L. Patel

    We present an analysis of an additive cellular automaton (CA) under asynchronous dynamics. The asynchronous scheme is maxmin-\(\omega\), a deterministic system, introduced in our previous work with a binary alphabet. Extending this work, we study the impact of a larger alphabet, which also allows a meaningful inference of the behaviour of the resultant CA from the asymptotic behaviour of the maxmin-\(\omega\)

    更新日期:2020-04-14
  • Perception of cloth in assistive robotic manipulation tasks
    Nat. Comput. (IF 1.495) Pub Date : 2020-02-12
    Pablo Jiménez; Carme Torras

    Assistive robots need to be able to perform a large number of tasks that imply some type of cloth manipulation. These tasks include domestic chores such as laundry handling or bed-making, among others, as well as dressing assistance to disabled users. Due to the deformable nature of fabrics, this manipulation requires a strong perceptual feedback. Common perceptual skills that enable robots to complete

    更新日期:2020-02-12
  • Hybrid ant colony optimization algorithm applied to the multi-depot vehicle routing problem
    Nat. Comput. (IF 1.495) Pub Date : 2020-01-27
    Petr Stodola

    The article deals with the hybrid Ant Colony Optimization algorithm and its application to the Multi-Depot Vehicle Routing Problem (MDVRP). The algorithm combines both probabilistic and exact techniques. The former implements the bio-inspired approach based on the behaviour of ants in the nature when searching for food together with simulated annealing principles. The latter complements the former

    更新日期:2020-01-27
  • A tutorial on elementary cellular automata with fully asynchronous updating
    Nat. Comput. (IF 1.495) Pub Date : 2020-01-23
    Nazim Fatès

    We present a panorama of the convergence properties of the 256 Elementary Cellular Automata under fully asynchronous updating, that is, when only one cell is updated at each time step. We regroup here various results which have been presented in different articles and expose a full analysis of the behaviour of finite systems with periodic boundary conditions. Our classification relies on the scaling

    更新日期:2020-01-23
  • About block-parallel Boolean networks: a position paper
    Nat. Comput. (IF 1.495) Pub Date : 2020-01-03
    Jacques Demongeot; Sylvain Sené

    In automata networks, it is well known that the way entities update their states over time has a major impact on their dynamics. In particular, depending on the chosen update schedule, the underlying dynamical systems may exhibit more or less asymptotic dynamical behaviours such as fixed points or limit cycles. Since such mathematical models have been used in the framework of biological networks modelling

    更新日期:2020-01-03
  • CRN ++: Molecular programming language
    Nat. Comput. (IF 1.495) Pub Date : 2020-01-03
    Marko Vasić; David Soloveichik; Sarfraz Khurshid

    Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic micro-controllers cannot be inserted. This necessitates effective representation of computation using molecular components. While previous work established the Turing-completeness

    更新日期:2020-01-03
  • Hierarchical growth is necessary and (sometimes) sufficient to self-assemble discrete self-similar fractals
    Nat. Comput. (IF 1.495) Pub Date : 2019-12-05
    Jacob Hendricks; Joseph Opseth; Matthew J. Patitz; Scott M. Summers

    In this paper, we prove that in the abstract Tile Assembly Model (aTAM), an accretion-based model which only allows for a single tile to attach to a growing assembly at each step, there are no tile assembly systems capable of self-assembling the discrete self-similar fractals known as the “H” and “U” fractals. We then show that in a related model which allows for hierarchical self-assembly, the 2-Handed

    更新日期:2019-12-05
  • Forming tile shapes with simple robots
    Nat. Comput. (IF 1.495) Pub Date : 2019-12-03
    Robert Gmyr; Kristian Hinnenthal; Irina Kostitsyna; Fabian Kuhn; Dorian Rudolph; Christian Scheideler; Thim Strothmann

    Motivated by the problem of manipulating nanoscale materials, we investigate the problem of reconfiguring a set of tiles into certain shapes by robots with limited computational capabilities. As a first step towards developing a general framework for these problems, we consider the problem of rearranging a connected set of hexagonal tiles by a single deterministic finite automaton. After investigating

    更新日期:2019-12-03
  • Transcript design problem of oritatami systems
    Nat. Comput. (IF 1.495) Pub Date : 2019-11-28
    Yo-Sub Han; Hwee Kim; Shinnosuke Seki

    RNA cotranscriptional folding refers to the phenomenon in which an RNA transcript folds upon itself while being synthesized out of a gene. Oritatami model is a computation model of this phenomenon, which lets its sequence (transcript) of beads (abstract molecules) fold cotranscriptionally by the interactions between beads according to its ruleset. We study the problem of designing a transcript that

    更新日期:2019-11-28
  • Multiplying with DNA.
    Nat. Comput. (IF 1.495) Pub Date : 2006-11-01
    Gang Wu,Nadrian C Seeman

    A functional machine is not only an assembly of parts, but also an assembly of processes. The processing of each part must obey laws that respect to the property of this part. For example, building any kind of computer entails selecting appropriate components and assembling their properties to function in computation. Here, we describe computation using a DNA strand as the basic unit and we have used

    更新日期:2019-11-01
  • Reversible causal graph dynamics: invertibility, block representation, vertex-preservation
    Nat. Comput. (IF 1.495) Pub Date : 2019-10-24
    P. Arrighi; S. Martiel; S. Perdrix

    Causal Graph Dynamics extend Cellular Automata to arbitrary time-varying graphs of bounded degree. The whole graph evolves in discrete time steps, and this global evolution is required to have a number of symmetries: shift-invariance (it acts everywhere the same) and causality (information has a bounded speed of propagation). We add a further physics-like symmetry, namely reversibility. In particular

    更新日期:2019-10-24
  • State-efficient realization of fault-tolerant FSSP algorithms
    Nat. Comput. (IF 1.495) Pub Date : 2019-10-17
    Hiroshi Umeo; Naoki Kamikawa; Masashi Maeda; Gen Fujita

    The firing squad synchronization problem (FSSP, for short) on cellular automata has been studied extensively for more than fifty years, and a rich variety of FSSP algorithms has been proposed. Here we study the classical FSSP on a model of fault-tolerant cellular automata that might have possibly some defective cells and present the first state-efficient implementations of fault-tolerant FSSP algorithms

    更新日期:2019-10-17
  • Turns of different angles and discrete-continuous pedestrian dynamics model
    Nat. Comput. (IF 1.495) Pub Date : 2019-10-11
    Ekaterina Kirik; Tat’yana Vitova; Andrey Malyshev

    In the paper we discuss a problem of correct simulation of movement of the people on the pathes with angles. The shortest path strategy does not work in this cases and gives unrealistic trajectories and increased evacuation time. The discrete-continuous pedestrian dynamics model have been discussed. Angles from \(90^\circ\) to \(180^\circ\) were considered: “L”-, “Z”- and “U”-shaped geometries. A way

    更新日期:2019-10-11
  • Optimal and suboptimal regional control of probabilistic cellular automata
    Nat. Comput. (IF 1.495) Pub Date : 2019-10-05
    Franco Bagnoli; Sara Dridi; Samira El Yacoubi; Raúl Rechtman

    Probabilistic cellular automata are extended stochastic systems, widely used for modelling phenomena in many disciplines. The possibility of controlling their behaviour is therefore an important topic. We shall present here an approach to the problem of controlling such systems by acting only on the boundary of a target region. In particular we are interested in optimal control, which is rather demanding

    更新日期:2019-10-05
  • Lattice-based versus lattice-free individual-based models: impact on coexistence in competitive communities
    Nat. Comput. (IF 1.495) Pub Date : 2019-10-04
    Aisling J. Daly; Ward Quaghebeur; Tim M. A. Depraetere; Jan M. Baetens; Bernard De Baets

    Individual-based modelling is an increasingly popular framework for modelling biological systems. Many of these models represent space as a lattice, thus imposing unrealistic limitations on the movement of the modelled individuals. We adapt an existing model of three competing species by using a lattice-free approach, thereby improving the realism of the spatial dynamics. We retrieve the same qualitative

    更新日期:2019-10-04
  • A cellular automata based approach to track salient objects in videos
    Nat. Comput. (IF 1.495) Pub Date : 2019-10-04
    Luca Crociani; Giuseppe Vizzari; Antonio Carrieri; Stefania Bandini

    In this paper we present an algorithm to track the motion of a salient object using Cellular Automata (CA). The overall work, taking inspiration from recent research on insect sensory motor system, investigates the application of non conventional computer vision approaches to evaluate their effectiveness in fulfilling this task. The proposed system employs the Sobel operator to individual frames, performing

    更新日期:2019-10-04
  • An overview of quantum cellular automata
    Nat. Comput. (IF 1.495) Pub Date : 2019-09-20
    P. Arrighi

    Quantum cellular automata are arrays of identical finite-dimensional quantum systems, evolving in discrete-time steps by iterating a unitary operator G. Moreover the global evolution G is required to be causal (it propagates information at a bounded speed) and translation-invariant (it acts everywhere the same). Quantum cellular automata provide a model/architecture for distributed quantum computation

    更新日期:2019-09-20
  • From electric circuits to chemical networks
    Nat. Comput. (IF 1.495) Pub Date : 2019-09-16
    Luca Cardelli; Mirco Tribastone; Max Tschaikowski

    Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same functionality is useful to biological organisms, where it is implemented by a completely different set of discrete components (typically proteins) and signal representations

    更新日期:2019-09-16
  • A self-adaptive multi-population differential evolution algorithm
    Nat. Comput. (IF 1.495) Pub Date : 2019-08-26
    Lin Zhu; Yongjie Ma; Yulong Bai

    Differential evolution (DE) is an efficient population-based search algorithm for solving numerical optimization problems. However, the performance of DE is very sensitive to the choice of mutation strategies and their associated control parameters. In this paper, we propose a self-adaptive multi-population differential evolution algorithm, called SAMDE. The population is randomly divided into three

    更新日期:2019-08-26
  • Approximate majority analyses using tri-molecular chemical reaction networks
    Nat. Comput. (IF 1.495) Pub Date : 2019-08-08
    Anne Condon; Monir Hajiaghayi; David Kirkpatrick; Ján Maňuch

    Approximate Majority is a well-studied problem in the context of chemical reaction networks (CRNs) and their close relatives, population protocols: Given a mixture of two types of species with an initial gap between their counts, a CRN computation must reach consensus on the majority species. Angluin, Aspnes, and Eisenstat proposed a simple population protocol for Approximate Majority and proved correctness

    更新日期:2019-08-08
  • Variants of P systems with activation and blocking of rules
    Nat. Comput. (IF 1.495) Pub Date : 2019-08-01
    Artiom Alhazov; Rudolf Freund; Sergiu Ivanov

    We introduce new possibilities to control the application of rules based on the preceding applications, which can be defined in a general way for (hierarchical) P systems and the main known derivation modes. Computational completeness can be obtained even with non-cooperative rules and using both activation and blocking of rules, especially for the set modes of derivation, when allowing derivation

    更新日期:2019-08-01
  • Maximum sensitivity to update schedules of elementary cellular automata over periodic configurations
    Nat. Comput. (IF 1.495) Pub Date : 2019-07-10
    Kévin Perrot; Marco Montalva-Medel; Pedro P. B. de Oliveira; Eurico L. P. Ruivo

    This work is a thoughtful extension of the ideas sketched in Montalva et al. (AUTOMATA 2017 exploratory papers proceedings, 2017), aiming at classifying elementary cellular automata (ECA) according to their maximal one-step sensitivity to changes in the schedule of cells update. It provides a complete classification of the ECA rule space for all period sizes \(n > 9\) and, together with the classification

    更新日期:2019-07-10
  • Self-assembly of 3-D structures using 2-D folding tiles
    Nat. Comput. (IF 1.495) Pub Date : 2019-07-09
    Jérôme Durand-Lose; Jacob Hendricks; Matthew J. Patitz; Ian Perkins; Michael Sharp

    Self-assembly is a process which is ubiquitous in natural, especially biological systems. It occurs when groups of relatively simple components spontaneously combine to form more complex structures. While such systems have inspired a large amount of research into designing theoretical models of self-assembling systems, and even laboratory-based implementations of them, these artificial models and systems

    更新日期:2019-07-09
  • Concurrency in Boolean networks
    Nat. Comput. (IF 1.495) Pub Date : 2019-06-08
    Thomas Chatain; Stefan Haar; Juraj Kolčák; Loïc Paulevé; Aalok Thakkar

    Boolean networks (BNs) are widely used to model the qualitative dynamics of biological systems. Besides the logical rules determining the evolution of each component with respect to the state of its regulators, the scheduling of component updates can have a dramatic impact on the predicted behaviours. In this paper, we explore the use of Read (contextual) Petri Nets (RPNs) to study dynamics of BNs

    更新日期:2019-06-08
  • Bionic vision system and its application in license plate recognition
    Nat. Comput. (IF 1.495) Pub Date : 2019-06-06
    Zhenjie Yao; Weidong Yi

    Conventional computer vision systems detect object after super-resolution (SR) or image reconstruction of the whole image, which is not an economical manner. By imitating the visual system of human beings, we proposed the bionic vision system (BVS), which is mainly composed by three parts: object detection by visual attention model, object-oriented SR reconstruction and object recognition by convolutional

    更新日期:2019-06-06
  • Computational completeness of simple semi-conditional insertion–deletion systems of degree (2,1)
    Nat. Comput. (IF 1.495) Pub Date : 2019-05-30
    Henning Fernau; Lakshmanan Kuppusamy; Indhumathi Raman

    Insertion–deletion (or ins–del for short) systems are simple models of bio-inspired computing. They are well studied in formal language theory, especially regarding their computational completeness. This concerns the question if all recursively enumerable languages can be generated. This ultimately addresses the question if one can build general-purpose computers rooted in this formalism. The descriptional

    更新日期:2019-05-30
  • A class of discrete dynamical systems with properties of both cellular automata and L-systems
    Nat. Comput. (IF 1.495) Pub Date : 2019-05-17
    Roderick Edwards; Aude Maignan

    We introduce and explore a type of discrete dynamic system inheriting some properties of both cellular automata (CA) and L-systems. Originally suggested by Jean Della Dora, and thus called DEM-systems after him and the two current authors, these systems can have the structural flexibility of an L-system as well as algebraic properties of CA. They are defined as sequences on a one-dimensional loop with

    更新日期:2019-05-17
  • Perturbations and phase transitions in swarm optimization algorithms
    Nat. Comput. (IF 1.495) Pub Date : 2019-05-11
    Tomáš Vantuch; Ivan Zelinka; Andrew Adamatzky; Norbert Marwan

    Natural systems often exhibit chaotic behavior in their space-time evolution. Systems transiting between chaos and order manifest a potential to compute, as shown with cellular automata and artificial neural networks. We demonstrate that swarm optimization algorithms also exhibit transitions from chaos, analogous to a motion of gas molecules, when particles explore solution space disorderly, to order

    更新日期:2019-05-11
  • Optimal staged self-assembly of linear assemblies
    Nat. Comput. (IF 1.495) Pub Date : 2019-05-06
    Cameron Chalk; Eric Martinez; Robert Schweller; Luis Vega; Andrew Winslow; Tim Wylie

    We analyze the complexity of building linear assemblies, sets of linear assemblies, and \({\mathcal{O}}(1)\)-scale general shapes in the staged tile assembly model. For systems with at most b bins and t tile types, we prove that the minimum number of stages to uniquely assemble a \(1 \times n\)line is \(\varTheta (\log _t{n} + \log _b{\frac{n}{t}} + 1)\). Generalizing to \({\mathcal{O}}(1) \times n\)

    更新日期:2019-05-06
  • The alchemy of computation: designing with the unknown
    Nat. Comput. (IF 1.495) Pub Date : 2019-04-24
    Julian Francis Miller

    Modern computers allow a methodical search of possibly billions of experiments and the exploitation of interactions that are not known in advance. This enables a bottom-up process of design by assembling or configuring systems and testing the degree to which they fulfill the desired goal. We give two detailed examples of this process. One is referred to as Cartesian genetic programming and the other

    更新日期:2019-04-24
  • Quantum information processing in the neighborhood of a black hole
    Nat. Comput. (IF 1.495) Pub Date : 2019-04-19
    Tanner Crowder; Marco Lanzagorta

    Using an imperfectly prepared state, we show that in relativistic settings, the evolution of a massive spin-1/2 particle violates many standard assumptions made in quantum information theory, including complete positivity. Unlike other recent endeavors in relativistic quantum information, we are able to quantify and maximize how much information can be transferred through such a quantum process by

    更新日期:2019-04-19
  • Molecular computing for Markov chains
    Nat. Comput. (IF 1.495) Pub Date : 2019-04-11
    Chuan Zhang; Ziyuan Shen; Wei Wei; Jing Zhao; Zaichen Zhang; Xiaohu You

    In this paper, it is presented a methodology for implementing arbitrarily constructed time-homogenous Markov chains with biochemical systems. Not only discrete but also continuous-time Markov chains are allowed to be computed. By employing chemical reaction networks as a programmable language, molecular concentrations serve to denote both input and output values. One reaction network is elaborately

    更新日期:2019-04-11
  • A proposal of quantum data representation to improve the discrimination power
    Nat. Comput. (IF 1.495) Pub Date : 2019-02-25
    Rosilda B. de Sousa; Emeson J. S. Pereira; Marina P. Cipolletti; Tiago A. E. Ferreira

    This work proposes a quantum representation for improvement of data discrimination power, transforming a non linearly separable problem into a linearly separable problem. This methodology proposed here can be naturally employed as data preprocessing for classification task. A classical real world system will be viewed as a composition of quantum systems, where any observable measurement process of

    更新日期:2019-02-25
  • Generation and robustness of Boolean networks to model Clostridium difficile infection
    Nat. Comput. (IF 1.495) Pub Date : 2019-02-14
    Dante Travisany; Eric Goles; Mauricio Latorre; María-Paz Cortés; Alejandro Maass

    One of the more common healthcare associated infection is Chronic diarrhea. This disease is caused by the bacterium Clostridium difficile which alters the normal composition of the human gut flora. The most successful therapy against this infection is the fecal microbial transplant (FMT). They displace C. difficile and contribute to gut microbiome resilience, stability and prevent further episodes

    更新日期:2019-02-14
  • On the influence of the interaction graph on a finite dynamical system
    Nat. Comput. (IF 1.495) Pub Date : 2019-02-13
    Maximilien Gadouleau

    A finite dynamical system (FDS) is a system of multivariate functions over a finite alphabet, that is typically used to model a network of interacting entities. The main feature of a finite dynamical system is its interaction graph, which indicates which local functions depend on which variables; the interaction graph is a qualitative representation of the interactions amongst entities on the network

    更新日期:2019-02-13
  • Computing with chemical reaction networks: a tutorial
    Nat. Comput. (IF 1.495) Pub Date : 2019-01-21
    Robert Brijder

    Chemical reaction networks (CRNs) model the behavior of chemical reactions in well-mixed solutions and they can be designed to perform computations. In this tutorial we give an overview of various computational models for CRNs. Moreover, we discuss a method to implement arbitrary (abstract) CRNs in a test tube using DNA. Finally, we discuss relationships between CRNs and other models of computation

    更新日期:2019-01-21
  • Spiking neural networks modelled as timed automata: with parameter learning
    Nat. Comput. (IF 1.495) Pub Date : 2019-01-17
    Elisabetta De Maria; Cinzia Di Giusto; Laetitia Laversa

    In this paper we address the issue of automatically learning parameters of spiking neural networks. Biological neurons are formalized as timed automata and synaptical connections are represented as shared channels among these automata. Such a formalism allows us to take into account several time-related aspects, such as the influence of past inputs in the computation of the potential value of each

    更新日期:2019-01-17
  • An enhanced genetic algorithm for constrained knapsack problems in dynamic environments
    Nat. Comput. (IF 1.495) Pub Date : 2019-01-16
    Shuqu Qian; Yanmin Liu; Yongqiang Ye; Guofeng Xu

    In this paper, an enhanced genetic algorithm (ERGA), based on memory updating and environment reaction schemes, has been proposed to solve constrained knapsack problems in dynamic environments (DKPs). Its key operators, e.g., the memory updating and the environment reaction schemes, have been further investigated to improve the ability of adapting to different dynamic environments. To maintain the

    更新日期:2019-01-16
  • Data clustering based on quantum synchronization
    Nat. Comput. (IF 1.495) Pub Date : 2018-11-14
    Aladin Crnkić; Vladimir Jaćimović

    There exists a specific class of methods for data clustering problem inspired by synchronization of coupled oscillators. This approach requires an extension of the classical Kuramoto model to higher dimensions. In this paper, we propose a novel method based on so-called non-Abelian Kuramoto models. These models provide a natural extension of the classical Kuramoto model to the case of abstract particles

    更新日期:2018-11-14
  • Self-assembly of 4-sided fractals in the Two-Handed Tile Assembly Model
    Nat. Comput. (IF 1.495) Pub Date : 2018-10-30
    Jacob Hendricks; Joseph Opseth

    We consider the self-assembly of fractals in one of the most well-studied models of tile based self-assembling systems known as the Two-Handed Tile Assembly Model (2HAM). In particular, we focus our attention on a class of fractals called discrete self-similar fractals (a class of fractals that includes the discrete Sierpiński carpet). We present a 2HAM system that finitely self-assembles the discrete

    更新日期:2018-10-30
  • Boolean dynamics revisited through feedback interconnections
    Nat. Comput. (IF 1.495) Pub Date : 2018-10-25
    Madalena Chaves; Daniel Figueiredo; Manuel A. Martins

    Boolean models of physical or biological systems describe the global dynamics of the system and their attractors typically represent asymptotic behaviors. In the case of large networks composed of several modules, it may be difficult to identify all the attractors. To explore Boolean dynamics from a novel viewpoint, we will analyse the dynamics emerging from the composition of two known Boolean modules

    更新日期:2018-10-25
  • Scaling up genetic circuit design for cellular computing: advances and prospects.
    Nat. Comput. (IF 1.495) Pub Date : 2018-10-05
    Yiyu Xiang,Neil Dalchau,Baojun Wang

    Synthetic biology aims to engineer and redesign biological systems for useful real-world applications in biomanufacturing, biosensing and biotherapy following a typical design-build-test cycle. Inspired from computer science and electronics, synthetic gene circuits have been designed to exhibit control over the flow of information in biological systems. Two types are Boolean logic inspired TRUE or

    更新日期:2018-10-05
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