Abstract: Recently, a new model of computation that is inspired by genetic operations over strings such as mutation and crossover has been proposed. Networks of Genetic Processors (NGPs) are highly related to previously proposed models such as Networks of Evolutionary Processors (NEPs) and Networks of Splicing Processors (NSPs). NGPs are computationally complete and several complexity measures have been proposed to evaluate their computing power with restricted resources (mainly, the time and the number of processors in the network). In this work we evaluate NGPs in an experimental approach. We have selected a NP-complete decision problem, the Hamiltonian Cycle Problem, and we have solved different instances with the proposed model of computation. Our aim is to prove that the selected problem (and all NP problems) can be solved in polynomial time with NGPs. In this case, our experiments show that the problem can be solved in linear time with a fixed number of processors for a given size of the problem.

Keywords: Networks of biologically-inspired processors, Combinatorial Problems, Complexity.

Link:

Solving Combinatorial Problems with Networks of Genetic Processors

Marcelino Campos, José M. Sempere

http://www.foibg.com/ijitk/ijitk-vol07/ijitk07-01-p07.pdf

Abstract: The Networks of Evolutionary Processors (NEPs) are computing mechanisms directly inspired from the behavior of cell populations more specifically the point mutations in DNA strands. These mechanisms are been used for solving NP-complete problems by means of a parallel computation postulation. This paper describes an implementation of the basic model of NEP using Web technologies and includes the possibility of designing some of the most common variants of it by means the use of the web page design which eases the configuration of a given problem. It is a system intended to be used in a multicore processor in order to benefit from the multi thread use.

Keywords: Evolutionary processors, Implementation, natural computing, NEP.

ACM Classification Keywords: D.1.m Miscellaneous – Natural Computing

Link:

A WEB IMPLEMETATION OF A GENERALIZED NEP

David Batard, Sandra María Gómez and Abraham Gutiérrez

http://www.foibg.com/ijitk/ijitk-vol07/ijitk07-01-p06.pdf

Abstract: In this paper, the main characteristics that are expected from this kind of software and the major tools that can be found at the present time are explained, as well as a proposal of a possible program that solves and fixes all the current lacks, for instance, the nonexistance of a multiplatform software, concluded after an exhaustive study of this proof of concept. The computer-aided design (CAD) tools are essential to achieve right and realiable results in Synthetic Biology researches. Furthermore, a comparison between two CAD’s programs is made simulating a synthetic biological circuit, showing the results to study how new software improvements can be developed to get better conclusions in this kind of experiments, provided by new tools. The design of a tool that could be developed in the future is proposed, based on non conventional programming paradigms (DNA computing for instance), that allow researchers to solve multiple kind of real problems.

Keywords: Synthetic Biology, CAD tools, computational, free software, in silico, simulation

ACM Classification Keywords: J.6 COMPUTER-AIDED ENGINEERING, J.3 LIFE AND MEDICAL SCIENCES, I.6 SIMULATION AND MODELING

Link:

SIMULATION OF BIOLOGICAL MODELS USING CAD TOOLS: NEEDS AND FUTURE

Víctor de la Hoz, César Pumar, Nicolás Quintero, Paula Cordero

http://www.foibg.com/ijitk/ijitk-vol07/ijitk07-01-p05.pdf

Abstract: Recently, developments on DNA-based molecular system have been conducted, including information sensing, locomoting function, decision making, and so on. Stochastic decision making is an important mean to deal with the adaptability under the fluctuating environment and it has to be processed based on DNA computing in molecular level. Many applications are found in DNA brain, DNA computer, molecular robotics, etc. In this research, DNA Strand Displacement is chosen as a main framework to develop a nucleic acid based decision making. The idea of implementation is inspired by the principle of Clonal Selection Algorithm of the Immune System. The mechanism allows the system to self-organize an emergent behavior where DNA strands locally interact with each other according to Watson-Crick? complementary process. We define some DNA-based operations based on DNA Strand Displacement reaction to represent the stochastic decision process with multiple choices of actions. Through this algorithm, DNA agents select the best action for a given problem. The software-based simulation results imply the successful implementation of the proposed DNA-based decision making scheme.

Keywords: DNA Strand Displacement, DNA Computing, Stochastic Decision Making, Immune System, Clonal Selection Algorithm.

Link:

DNA Strand Displacement for Stochastic Decision Making based on Immune’s Clonal Selection Algorithm

Rizki Mardian, Kosuke Sekiyama, Toshio Fukuda

http://www.foibg.com/ijitk/ijitk-vol07/ijitk07-01-p04.pdf

Abstract: In this paper is aim to design a new software tool that allows to create synthetic biology complex systems and genetic circuit designs, as well as to carry out the development of these models using a wide set of biological and biochemical rules. Thus, it will keep a very close relationship respect to the real characteristics of the biological systems and their environment, obtaining then a high reproducibility in the progress and simulation systems in relation to the progress of the real experiment. It will describe a comparison between two software tools which allow us to design, build and simulate synthetic biology networks and biochemical processes. The progress, improvement and combination of the distinct possibilities that offer both software as well as the analysis of a joint usage of them will result the creation of the new software.

Keywords: synthetic biology, natural computation, COPASI, SynBioSS?, biological systems, synthetic biology,in silico, in vivo, in vitro, BioBricks?, SBML, XML, repressilator.

ACM Classification Keywords: D.2 SOFTWARE ENGINEERING, H.2 DATABASE MANAGEMENT J.3 LIFE AND MEDICAL SCIENCES, I.6 SIMULATION AND MODELING, J.2 PHYSICAL SCIENCES AND ENGINEERING.

Link:

BIOLOGICAL PROCESSES STUDIES THROUGH SOFTWARE TOOLS: DEVELOPMENT AND OPTIMIZATION IN THE SIMULATION OF SYNTHETIC BIOLOGICAL CONSTRUCTIONS

Perceval Vellosillo, Roberto Tomé, Verónica Llorens-Rico?, Juan B. Castellanos

http://www.foibg.com/ijitk/ijitk-vol07/ijitk07-01-p03.pdf

Abstract: At present, all methods in Evolutionary Computation are bioinspired by the fundamental principles of neo-Darwinism, as well as by a vertical gene transfer. Virus transduction is one of the key mechanisms of horizontal gene propagation in microorganisms (e.g. bacteria). In the present paper, we model and simulate a transduction operator, exploring the possible role and usefulness of transduction in a genetic algorithm. The genetic algorithm including transduction has been named PETRI (abbreviation of Promoting Evolution Through Reiterated Infection). Our results showed how PETRI approaches higher fitness values as transduction probability comes close to 100%. The conclusion is that transduction improves the performance of a genetic algorithm, assuming a population divided among several sub-populations or ‘bacterial colonies’.

Keywords: Bacterial genetic algorithm, horizontal gene transfer, conjugation operator, transduction operator.

ACM Classification Keywords: I.6 SIMULATION AND MODELING

Link:

MODELING, SIMULATION AND APPLICATION OF BACTERIAL TRANSDUCTION IN GENETIC ALGORITHMS

Carlos Perales-Gravan?, Javier de Vicente Buendia, Juan Castellanos,R. Lahoz-Beltra?

http://www.foibg.com/ijitk/ijitk-vol07/ijitk07-01-p02.pdf

Abstract: Nowadays the new "network sciences" work together with the systems biology trying to provide computational tools for analyzing large information derived from bioinformatics and 'omics' science, such as enzymes, complex, and gene networks. The Aragon Institute of Health Sciences ICS has developed an attenuated vaccine that offers better protection against tuberculosis than BCG. In order to improve the study of this large number of genes, it is necessary to use network analysis and visualization programs. In this paper, we present the development of a new integrated IDE software tool to represent the Genetic Network of the bacillus tuberculosis. This tool provides visual, intuitive and relevant information, helping in the research and the study of the new vaccine.

Keywords: Systems Biology, Network Sciences, Genetic Network, IDE software Tool

ACM Classification Keywords: D.1.m Miscellaneous – Natural Computing

Link:

GENETIC NETWORK REPRESENTATION USING A SUITABLE IDE SOFTWARE TOOL TO THE BACILLUS MYCOBACTERIUM TUBERCULOSIS

Pablo del Moral, Sandra María Gómez, Jorge Navarro, Fernando Arroyo

http://www.foibg.com/ijitk/ijitk-vol07/ijitk07-01-p01.pdf

Аннотация. В статье проанализированы связи метода базисных матриц для решения задачи линейного программирования (анализа линейных систем) и матричной игры в смешанных стратегиях. На основе анализа основных рекуррентных соотношений, которые связывают элементы метода базисных матриц в двух смежных базисных матрицах, были установлены соотношения для анализа (и нахождения решения) матричной игры в смешанных стратегиях. Получены условия несущественности чистых стратегий игроков и единственности решений. Разработан алгоритм анализа свойств матричной игры и нахождения решения на основе метода базисных матриц.

Ключевые слова: принятие решений, теория игр, линейная система, матричная игра, смешанная стратегия, базисная матрица.

ACM Classification Keywords : H.4.2 Information Systems Applications : Types of Systems : Decision Support.

Link:

МЕТОД БАЗИСНЫХ МАТРИЦ И МАТРИЧНАЯ ИГРА В СМЕШАННЫХ СТРАТЕГИЯХ

Кудин В.И.

http://www.foibg.com/ijita/vol20/ijita20-04-p10.pdf

Аннотация: Исследованы чистые первопорядковые композиционно-номинативные логики частичных однозначных предикатов. Введено расширение логики специальными предикатами, которые определя- ют наличие значений для переменных. На этой основе для таких логик построены исчисления секвен- циального типа. Для этих исчислений доказаны теоремы корректности и полноты.

Ключевые слова: логика, предикат, логическое следствие, вывод, секвенциальное исчисление.

ACM классификация ключевых слов: F.3.1 Specifying and Verifying and Reasoning about Programs; F.4.1 Mathematical Logic – Proof theory

Link:

СЕМАНТИЧЕСКИЕ СВОЙСТВА И СЕКВЕНЦИАЛЬНЫЕ ИСЧИСЛЕНИЯ ЧИСТЫХ КОМПОЗИЦИОННО-НОМИНАТИВНЫХ ЛОГИК ПЕРВОГО ПОРЯДКА

Николай Никитченко, Степан Шкильняк

http://www.foibg.com/ijita/vol20/ijita20-04-p09.pdf

Аннотация: Исследованы программно-ориентированные логические формализмы – транзиционные композиционно-номинативные модальные логики частичных эквитонных предикатов. Описаны семан- тические модели и языки чистых первопорядковых транзиционных модальных логик. Для таких логик построены исчисления секвенциального типа, доказаны корректность и полнота этих исчислений.

Ключевые слова: модальная логика, предикат, логический вывод, секвенциальное исчисление.

ACM классификация ключевых слов: F.3.1 Specifying and Verifying and Reasoning about Programs; F.4.1 Mathematical Logic – Proof theory

Link:

МОДАЛЬНЫЕ ЛОГИКИ ЧАСТИЧНЫХ ПРЕДИКАТОВ И СЕКВЕНЦИАЛЬНЫЕ СИСТЕМЫ ЛОГИЧЕСКОГО ВЫВОДА В ЭТИХ ЛОГИК

Оксана Шкильняк

http://www.foibg.com/ijita/vol20/ijita20-04-p08.pdf

Abstract: We present analytical expressions for the perturbations of pseudoinverse and projection matrices pozvolyayuschienahodit solutions of optimal synthesis of linear systems with fuzzy parameters of the task. В работе приводятся аналитические выражения для возмущений псевдообратных и проекционных матриц позволяющиенаходить решений задач оптимального синтеза линейных систем с нечётко задаными параметрами.

Keywords: возмущения псевдообратных и проекционных матриц оптимальный синтез линейных систем.

ACM Classification Keywords: Computing Methodologies. Simulation and modeling. optimum synthesis

Link:

ПРИМЕНЕНИЕ МЕТОДОВ ПСЕВДООБРАЩЕНИЯ К ЗАДАЧАМ ОПТИМИЗАЦИИ СТРУКТУР

Григорий Кудин

http://www.foibg.com/ijita/vol20/ijita20-04-p07.pdf

Аннотация: Обсуждаются вычислительные аспекты аксиоматического подхода к решению проблемы сужения множества Парето на основе определённой числовой информации об отношении предпочтения лица, принимающего решение (ЛПР). Этот подход развивается автором, начиная с 1983 г. Его применение предполагает принятие определённых четырёх аксиом «разумного» поведения ЛПР в процессе принятия решений. Предполагается, что в дополнение к указанным аксиомам известны некоторые сведения об отношении предпочтения ЛПР («кванты» информации). На основе этих сведений можно сократить множество Парето и, тем самым, облегчить последующий выбор выбираемых (наилучших) решений. Прослеживается эволюция развития аксиоматического подхода и формулируется алгоритм учёта произвольного конечного набора «квантов» информации об отношении предпочтения ЛПР. Работа алгоритма проиллюстрирована примером.

Ключевые слова: множество Парето, многокритериальный выбор, сужение множества Парето

ACM Classification Keywords: F.4.3 – Decision problems

Link:

АКСИОМАТИЧЕСКИЙ ПОДХОД К СУЖЕНИЮ МНОЖЕСТВА ПАРЕТО: ВЫЧИСЛИТЕЛЬНЫЕ АСПЕКТЫ

Владимир Ногин

http://www.foibg.com/ijita/vol20/ijita20-04-p06.pdf

Аннотация: В практических задачах сравнения альтернатив с интервальными, из-за неопределенности, показателями качества нередко применяются точечные (одно-числовые) оценки, предположительно эквивалентные исходным интервальным. В работе показано, что использование в таких задачах точечных оценок, в частности оценок математического ожидания, без квантификации и дополнительного анализа величины шансов истинности проверяемой гипотезы о предпочтительности одной из альтернатив в их паре неадекватно проблеме сравнения интервальных оценок. Предложен метод вычисления шансов истинности проверяемой гипотезы и риска, связанного с возможной истинностью гипотезы, противоположной анализируемой. Для ряда примеров сравнения интервальных альтернатив проведено сопоставление результатов сравнения по предложенному методу и по средним оценкам. Продемонстрировано, что упомянутые шансы далеко не во всех случаях могут быть представлены как функции математических ожиданий распределений на сравниваемых интервалах. Показано, что корректный анализ задачи сравнения интервальных альтернатив требует расчета указанных шансов и сопоставления их величины с предпочтениями лиц, принимающих решения.

Keywords: comparing interval alternatives, method for estimation of chances of preferability compared alternatives, analysis of adequacy of average point estimates to comparing process

ACM Classification Keywords: H.1.2 Human information processing. G3 Distribution functions. I.2.3 Uncertainty, “fuzzy”, and probabilistic reasoning.

Link:

О ПРИМЕНИМОСТИ ОЦЕНКО МАТЕМАТИЧЕСКОГО ОЖИДАНИЯ ПРИ СРАВНЕНИИ ИНТЕРВАЛЬНЫХ АЛЬТЕРНАТИВ

Стернин М.Ю., Шепелев Г.И.

http://www.foibg.com/ijita/vol20/ijita20-04-p05.pdf

Аннотация: Рассматривается проблема построения монотонной логики Флойда-Хоара, которая является расширением классической логики Флойда-Хоара для случая частичных предикатов. Обобщается построенная монотонная логика на случай многосортных логик. Для этого вводятся номинативные данные с типами. Доказывается монотонность композиций представленной логики, а также непрерывность композиции Флойда-Хоара.

Ключевые слова: программные логики, композиционно-номинативный подход, монотонные композиции, типизированные данные.

ACM Classification Keywords: F.3.1 Specifying and Verifying and Reasoning about Programs – Logics of Programs

Link:

МНОГОСОРТНАЯ МОНОТОННАЯ ЛОГИКА ФЛОЙДА-ХОАРА

Андрей Криволап, Николай Никитченко

http://www.foibg.com/ijita/vol20/ijita20-04-p04.pdf

Аннотация: Рассматриваются два основных подхода к решению многокритериальных задач принятия решений и векторной оптимизации систем управления. Один из них состоит в формализации многокритериальных задач при заданных (фиксированных) ограничениях и ресурсных возможностях системы. Второй подход показывает, какие новые перспективы открываются перед разработчиками, если они имеют возможность в определенных пределах распоряжаться ресурсными запасами (ограничениями) многокритериальных систем.

Ключевые слова: схемы компромиссов, консенсус, ресурсы и ограничения, противоречивость критериев, принцип рациональной организации.

ACM Classification Keywords: H.1 Models and Principles – H.1.1 – Systems and Information Theory; H.4.2 – Types of Systems.

Link:

КОМПРОМИСС И КОНСЕНСУС В ТЕОРИИ ПРИНЯТИЯ РЕШЕНИЙ

Альберт Воронин

http://www.foibg.com/ijita/vol20/ijita20-04-p03.pdf

Abstract: In this paper the application of the least squares method (LSM) has been substantiated. Case of matrix of observations for the arguments and values of the renewable function of the linear relationship between the components of observation has been considered. The solution of matrix optimization problem for the evaluation of the least squares method explicitly has been submitted, pseudo inverse means have been used. The importance of the results on applied problems of prediction media and macroeconomic indicators was illustrated.

Keywords: Moore-Penrose? pseudo inverse, regression, least squares method, macroeconomic indicators, media indicators, prediction.

ACM Classification Keywords: G.3 Probability and statistics, G.1.6. Numerical analysis: Optimization, H.1.m. Models and Principles: miscellaneous.

Link:

VECTORS AND MATRIXES LEAST SQUARES METHOD: FOUNDATION AND APPLICATION EXAMPLES

Vladimir S. Donchenko, Inna M. Nazaraga, Olga V. Tarasova

http://www.foibg.com/ijita/vol20/ijita20-04-p02.pdf

Abstract: We consider rationing problem as a group decision making problem. Fuzzy and crisp generalizations of the classical rationing methods are proposed. The proposed generalizations are illustrated by numerical examples.

Keywords: rationing problem, fuzzy models and methods, decision making.

ACM Classification Keywords: I. Computing Methodologies – I.6. Simulation and modeling – I.6.5. Model Development –Modeling Methodologies.

Link:

GENERALIZATION OF DISTRIBUTING METHODS FOR FUZZY PROBLEMS

Voloshyn O., Laver V.

http://www.foibg.com/ijita/vol20/ijita20-04-p01.pdf

Аннотация: В статье рассмотрены оптоволоконные коммутационные устройства на основе трубчатых и монолитных пьезоэлектрических актуаторов.

Ключевые слова: Волоконная оптика  Коммутационные устройства  Пьезоэлектрические актуаторы.

Ключевые слова классификации ACM: H.4.3 Communications Applications.

Link:

ПЬЕЗООПТИЧЕСКИЕ СКАНИРУЮЩИЕ КОММУТАТОРЫ

Рябцов А.В.

http://www.foibg.com/ijita/vol20/ijita20-03-p11.pdf

Abstract: This paper examines security problems of biometric based authentication. An authentication method is suggested, which is based on fingerprints with steganographic data protection in all stages of functioning. Suggested procedures of fingerprint based enrollment and authentication are also functionally described.

Link:

AUTHENTICATION BASED ON FINGERPRINTS WITH STEGANOGRAPHIC DATA PROTECTION

Narek Malkhasyan

http://www.foibg.com/ijita/vol20/ijita20-03-p10.pdf

Abstract: The possibility of creating a knowledge-based management information systems (MIS) for support of solving personnel motivation tasks in principle is considered in this article, there is an emphasis and description of the main issues that need to be addressed when developing such systems.

Keywords: management information systems.

Link:

COMMON BUILDING ISSUES OF KNOWLEDGE-BASED MANAGEMENT INFORMATION SYSTEM FOR SUPPORTING PERSONNEL MOTIVATION

Elena Antonova, Nikita Lyalyakin

http://www.foibg.com/ijita/vol20/ijita20-03-p09.pdf

Abstract: This paper introduces an approach to storing graphs based on the Natural Language Addressing in multidimensional numbered information spaces. A sample graph is analyzed to find its proper L-representation. Taking in account the interrelations between nodes and edges, a “multi-layer” representation is possible and identifiers of nodes and edges can be avoided. The advantages and disadvantages of NL-addressing for the multi-layer representation of graphs are discussed.

Keywords: graphs; addressing; natural language addressing.

ACM Classification Keywords: D.4.3 File Systems Management, Access methods.

Link:

INTRODUCTION TO STORING GRAPHS BY NL-ADDRESSING

Krassimira B. Ivanova, Koen Vanhoof, Krassimir Markov, Vitalii Velychko

http://www.foibg.com/ijita/vol20/ijita20-03-p08.pdf

Abstract: It is shown that genetic algorithms can be used successfully in problems of definite integral calculation especially when an integrand has a primitive which can't be expressed analytically through elementary functions. A testing of the program, which uses the genetic algorithm developed by authors, showed that the best results are reached if the size of population makes 30-50 chromosomes, approximately 40-60% of its take a part in crossover, and the program stops if the population's leader didn't change during 5-10 generations. An answer of genetic algorithm is more exact than answer received by the classical numerical methods, even if a quantity of partition’s points into segment is small or if an integrand is quickly oscillating. So genetic algorithms can compete both on the accuracy of calculations and on operating time with well-known classical numerical methods such as midpoint approximation, top-left corner approximation, top-right corner approximation, trapezoidal rule, Simpson's rule.

Keywords: definite integral, integral sum, numerical integration, genetic algorithm, fitness-function.

ACM Classification Keywords: F.1.2 COMPUTATION BY ABSTRACT DEVICES: Models of computation – Probabilistic computation. G.1.6 NUMERICAL ANALYSIS: Optimization – Stochastic programming.

Link:

NUMERICAL INTEGRATION BY GENETIC ALGORITHMS

Vladimir Morozenko, Irina Pleshkova

http://www.foibg.com/ijita/vol20/ijita20-03-p07.pdf

Abstract: This work introduces a solution based on genetic algorithms to find the overlapping area between two point cloud captures obtained from a three-dimensional scanner. Considering three translation coordinates and three rotation angles, the genetic algorithm evaluates the matching points in the overlapping area between the two captures given that transformation. Genetic simulated annealing is used to improve the accuracy of the results obtained by the genetic algorithm.

Keywords: Range images, genetic algorithms, overlaping point cloud captures, genetic simulated annealing.

Link:

OVERLAPPING RANGE IMAGES USING GENETIC ALGORITHMS

Fernando Ortega, Javier San Juan, Francisco Serradilla, Dionisio Cortes

http://www.foibg.com/ijita/vol20/ijita20-03-p06.pdf

Abstract: During last 50 years, the markets have been object of study. Technical and fundamental indicators have been used to try to predict the behaviour of the market and then execute buying or selling orders. This paper use the capabilities and functionalities of the transition P-systems to create an intelligent model which is able to process the information returned by the indicators in a efficient way .Membrane techniques provide a new approach of markets behaviour estimation

Keywords: Trading strategies, Technical indicators, Intelligent Transition P-Systems?.

Link:

TECHNICAL P-SYSTEMS: OPERATING IN THE STOCK MARKETS WITH TRANSITION P-SYSTEMS

Alberto Arteta, Angel Luis Castellanos, Nuria Gómez Blas

http://www.foibg.com/ijita/vol20/ijita20-03-p05.pdf

Abstract: In this paper we propose the use of Networks of Bio-inspired Processors (NBP) to model some biological phenomena within a computational framework. In particular, we propose the use of an extension of NBP named Network Evolutionary Processors Transducers to simulate chemical transformations of substances. Within a biological process, chemical transformations of substances are basic operations in the change of the state of the cell. Previously, it has been proved that NBP are computationally complete, that is, they are able to solve NP complete problems in linear time, using massively parallel computations. In addition, we propose a multilayer architecture that will allow us to design models of biological processes related to cellular communication as well as their implications in the metabolic pathways. Subsequently, these models can be applied not only to biological-cellular instances but, possibly, also to configure instances of interactive processes in many other fields like population interactions, ecological trophic networks, industrial ecosystems, etc.

Keywords: Networks of biologically-inspired processors, Bioinspired Architectures, Computational Models, Natural Computing.

ACM Classification Keywords: F.1.1 Models of Computation - Unbounded-action devices.

Link:

Self-Organizing? Architectural design based on Morphogenetic Programming

Nuria Gómez Blas, Luis F. de Mingo, Miguel A. Muriel

http://www.foibg.com/ijita/vol20/ijita20-03-p04.pdf