Natural Computing最新文献_第10页

Cellular automata and substitutions in topological spaces defined via edit distances 通过编辑距离定义的拓扑空间中的元胞自动机和替换

IF 2.1 4区计算机科学

Natural Computing Pub Date : 2022-03-30 DOI: 10.1007/s11047-023-09954-1

Firas Ben Ramdhane, Pierre Guillon

引用次数: 1

MRT-lattice Boltzmann hybrid model for the double diffusive mixed convection with thermodiffusion effect 具有热扩散效应的双扩散混合对流的MRT格子Boltzmann混合模型

IF 2.1 4区计算机科学

Natural Computing Pub Date : 2022-03-29 DOI: 10.1007/s11047-022-09884-4

Bouthayna Mhamdi, S. Bettaibi, O. Jellouli, M. Chafra

引用次数: 4

Preface 前言

IF 2.1 4区计算机科学

Natural Computing Pub Date : 2022-03-14 DOI: 10.1007/s11047-022-09883-5

C. Martín-Vide, Migue A. Vega-Rodríguez

引用次数: 0

Computational graph pangenomics: a tutorial on data structures and their applications. 计算图泛函学：数据结构及其应用教程。

IF 1.7 4区计算机科学

Natural Computing Pub Date : 2022-03-01 Epub Date: 2022-03-04 DOI: 10.1007/s11047-022-09882-6

Jasmijn A Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén

{"title":"Computational graph pangenomics: a tutorial on data structures and their applications.","authors":"Jasmijn A Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén","doi":"10.1007/s11047-022-09882-6","DOIUrl":"10.1007/s11047-022-09882-6","url":null,"abstract":"Computational pangenomics is an emerging research field that is changing the way computer scientists are facing challenges in biological sequence analysis. In past decades, contributions from combinatorics, stringology, graph theory and data structures were essential in the development of a plethora of software tools for the analysis of the human genome. These tools allowed computational biologists to approach ambitious projects at population scale, such as the 1000 Genomes Project. A major contribution of the 1000 Genomes Project is the characterization of a broad spectrum of genetic variations in the human genome, including the discovery of novel variations in the South Asian, African and European populations-thus enhancing the catalogue of variability within the reference genome. Currently, the need to take into account the high variability in population genomes as well as the specificity of an individual genome in a personalized approach to medicine is rapidly pushing the abandonment of the traditional paradigm of using a single reference genome. A graph-based representation of multiple genomes, or a graph pangenome, is replacing the linear reference genome. This means completely rethinking well-established procedures to analyze, store, and access information from genome representations. Properly addressing these challenges is crucial to face the computational tasks of ambitious healthcare projects aiming to characterize human diversity by sequencing 1M individuals (Stark et al. 2019). This tutorial aims to introduce readers to the most recent advances in the theory of data structures for the representation of graph pangenomes. We discuss efficient representations of haplotypes and the variability of genotypes in graph pangenomes, and highlight applications in solving computational problems in human and microbial (viral) pangenomes.","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":"21 1","pages":"81-108"},"PeriodicalIF":1.7,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10038355/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9199489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

On the computational power of swarm automata using agents with position information 基于位置信息的群体自动机的计算能力研究

IF 2.1 4区计算机科学

Natural Computing Pub Date : 2022-02-18 DOI: 10.1007/s11047-022-09881-7

Kaoru Fujioka

引用次数: 0

ALCH: An imperative language for chemical reaction network-controlled tile assembly ALCH：一种用于化学反应网络控制瓦片组装的命令式语言

IF 2.1 4区计算机科学

Natural Computing Pub Date : 2022-01-21 DOI: 10.4230/LIPIcs.DNA.2020.6

T. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, Matthew R. Riley

{"title":"ALCH: An imperative language for chemical reaction network-controlled tile assembly","authors":"T. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, Matthew R. Riley","doi":"10.4230/LIPIcs.DNA.2020.6","DOIUrl":"https://doi.org/10.4230/LIPIcs.DNA.2020.6","url":null,"abstract":"Schiefer and Winfree recently introduced the chemical reaction network-controlled tile assembly model (CRN-TAM), a variant of the abstract tile assembly model (aTAM). In the CRN-TAM, tile reactions are mediated via non-local chemical signals controlled by a chemical reaction network. This paper introduces ALCH, an imperative programming language for specifying CRN-TAM programs that can be compiled and simulated. ALCH includes standard language features such as Boolean variables, conditionals, loops, and CRN-TAM-specific constructs such as adding and removing tiles. ALCH also includes the branch and parallel structures which harness the nondeterministic and parallel nature of the CRN-TAM. ALCH also supports functional tileset specification. Using ALCH, we show that the discrete Sierpinski triangle and the discrete Sierpinski carpet can be strictly self-assembled in the CRN-TAM, which shows the CRN-TAM can self-assemble infinite shapes at scale 1 that the aTAM cannot. ALCH allows us to present these constructions at a high level, abstracting species and reactions into C-like code that is simpler to understand. We employ two new CRN-TAM techniques in our constructions. First, we use ALCH’s nondeterministic branching feature to probe previously placed tiles of the assembly and detect the presence and absence of tiles. Second, we use scaffolding tiles to precisely control tile placement by occluding any undesired binding sites. This paper is an extension of our previous work, updated to include a Sierpinski carpet construction and the parallel command.","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":"1 1","pages":"1-21"},"PeriodicalIF":2.1,"publicationDate":"2022-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43714029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

A GIS-aided cellular automata system for monitoring and estimating graph-based spread of epidemics. 用于监测和估计基于图形的流行病传播的gis辅助元胞自动机系统。

IF 2.1 4区计算机科学

Natural Computing Pub Date : 2022-01-01 Epub Date: 2022-06-22 DOI: 10.1007/s11047-022-09891-5

Charilaos Kyriakou, Ioakeim G Georgoudas, Nick P Papanikolaou, Georgios Ch Sirakoulis

{"title":"A GIS-aided cellular automata system for monitoring and estimating graph-based spread of epidemics.","authors":"Charilaos Kyriakou, Ioakeim G Georgoudas, Nick P Papanikolaou, Georgios Ch Sirakoulis","doi":"10.1007/s11047-022-09891-5","DOIUrl":"https://doi.org/10.1007/s11047-022-09891-5","url":null,"abstract":"In this study, we introduce an application of a Cellular Automata (CA)-based system for monitoring and estimating the spread of epidemics in real world, considering the example of a Greek city. The proposed system combines cellular structure and graph representation to approach the connections among the area's parts more realistically. The original design of the model is attributed to a classical SIR (Susceptible-Infected-Recovered) mathematical model. Aiming to upgrade the application's effectiveness, we have enriched the model with parameters that advances its functionality to become self-adjusting and more efficient of approaching real situations. Thus, disease-related parameters have been introduced, while human interventions such as vaccination have been represented in algorithmic manner. The model incorporates actual geographical data (GIS, geographic information system) to upgrade its response. A methodology that allows the representation of any area with given population distribution and geographical data in a graph associated with the corresponding CA model for epidemic simulation has been developed. To validate the efficient operation of the proposed model and methodology of data display, the city of Eleftheroupoli, in Eastern Macedonia-Thrace, Greece, was selected as a testing platform (Eleftheroupoli, Kavala). Tests have been performed at both macroscopic and microscopic levels, and the results confirmed the successful operation of the system and verified the correctness of the proposed methodology.","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":"21 3","pages":"463-480"},"PeriodicalIF":2.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9214692/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40401950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Estimates of the collective immunity to COVID-19 derived from a stochastic cellular automaton based framework. 基于随机元胞自动机框架的COVID-19集体免疫力估计。

IF 2.1 4区计算机科学

Natural Computing Pub Date : 2022-01-01 Epub Date: 2022-06-18 DOI: 10.1007/s11047-022-09893-3

Isaías Lima, Pedro Paulo Balbi

{"title":"Estimates of the collective immunity to COVID-19 derived from a stochastic cellular automaton based framework.","authors":"Isaías Lima, Pedro Paulo Balbi","doi":"10.1007/s11047-022-09893-3","DOIUrl":"https://doi.org/10.1007/s11047-022-09893-3","url":null,"abstract":"In the context of the propagation of infectious diseases, when a sufficient degree of immunisation is achieved within a population, the spread of the disease is ended or significantly decreased, leading to collective immunity, meaning the indirect protection given by immune individuals to susceptible individuals. Here we describe the estimates of the collective immunity to COVID-19 from a stochastic cellular automaton based model designed to emulate the spread of SARS-CoV-2 in a population of static individuals interacting only via a Moore neighbourhood of radius one, with a view to analyze the impact of initially immune individuals on the dynamics of COVID-19. This impact was measured by comparing a progression of initial immunity ratio-the percentage of immunised individuals before patient zero starts infecting its neighbourhood-from 0 to 95% of the initial population, with the number of susceptible individuals not contaminated, the peak value of active cases, the total number of deaths and the emulated pandemic duration in days. The influence of this range of immunities over the model was tested with different parameterisations regarding the uncertainties involved in the model such as the durations of the cellular automaton states, the contamination contributions of each state and the state transition probabilities. A collective immunity threshold of <math><mrow><mn>55</mn> <mo>%</mo> <mo>±</mo> <mn>2.5</mn> <mo>%</mo></mrow> </math> on average was obtained from this procedure, under four distinct parameterisations, which is in tune with the estimates of the currently available medical literature, even increasing the uncertainty of the input parameters.","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":"21 3","pages":"449-461"},"PeriodicalIF":2.1,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9206103/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40401951","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

On the right combination of altruism and randomness in the motion of homogeneous distributed autonomous agents 均匀分布自治主体运动中利他主义与随机性的正确结合

IF 2.1 4区计算机科学

Natural Computing Pub Date : 2021-11-27 DOI: 10.1007/s11047-021-09876-w

M. Hassoun, Evgeny Kagan

引用次数: 1

Heuristic search of (semi-)bent functions based on cellular automata 基于元胞自动机的半弯曲函数的启发式搜索

IF 2.1 4区计算机科学

Natural Computing Pub Date : 2021-11-25 DOI: 10.1007/s11047-022-09885-3

L. Mariot, Martina Saletta, A. Leporati, L. Manzoni

引用次数: 5