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Asynchronous, finite dynamical systems 异步有限动力系统
IF 2.1 4区 计算机科学
Natural Computing Pub Date : 2023-05-25 DOI: 10.1007/s11047-023-09944-3
H. Mortveit
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引用次数: 0
Protein structure prediction with energy minimization and deep learning approaches. 利用能量最小化和深度学习方法进行蛋白质结构预测。
IF 2.1 4区 计算机科学
Natural Computing Pub Date : 2023-05-08 DOI: 10.1007/s11047-023-09943-4
Juan Luis Filgueiras, Daniel Varela, José Santos
{"title":"Protein structure prediction with energy minimization and deep learning approaches.","authors":"Juan Luis Filgueiras,&nbsp;Daniel Varela,&nbsp;José Santos","doi":"10.1007/s11047-023-09943-4","DOIUrl":"10.1007/s11047-023-09943-4","url":null,"abstract":"<p><p>In this paper we discuss the advantages and problems of two alternatives for ab initio protein structure prediction. On one hand, recent approaches based on deep learning, which have significantly improved prediction results for a wide variety of proteins, are discussed. On the other hand, methods based on protein conformational energy minimization and with different search strategies are analyzed. In this latter case, our methods based on a memetic combination between differential evolution and the fragment replacement technique are included, incorporating also the possibility of niching in the evolutionary search. Different proteins have been used to analyze the pros and cons in both approaches, proposing possibilities of integration of both alternatives.</p>","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":" ","pages":"1-12"},"PeriodicalIF":2.1,"publicationDate":"2023-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10165305/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9708719","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
Fractal dimension of assemblies in the abstract tile assembly model 抽象瓷砖装配模型中组件的分形维数
4区 计算机科学
Natural Computing Pub Date : 2023-04-26 DOI: 10.1007/s11047-023-09942-5
Daniel Hader, Matthew J. Patitz, Scott M. Summers
{"title":"Fractal dimension of assemblies in the abstract tile assembly model","authors":"Daniel Hader, Matthew J. Patitz, Scott M. Summers","doi":"10.1007/s11047-023-09942-5","DOIUrl":"https://doi.org/10.1007/s11047-023-09942-5","url":null,"abstract":"","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":"45 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136380695","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: 0
Cellular automata and Kan extensions 元胞自动机和Kan扩展
4区 计算机科学
Natural Computing Pub Date : 2023-01-27 DOI: 10.1007/s11047-022-09931-0
Alexandre Fernandez, Luidnel Maignan, Antoine Spicher
{"title":"Cellular automata and Kan extensions","authors":"Alexandre Fernandez, Luidnel Maignan, Antoine Spicher","doi":"10.1007/s11047-022-09931-0","DOIUrl":"https://doi.org/10.1007/s11047-022-09931-0","url":null,"abstract":"In this paper, we formalize precisely the sense in which the application of a cellular automaton to partial configurations is a natural extension of its local transition function through the categorical notion of Kan extension. In fact, the two possible ways to do such an extension and the ingredients involved in their definition are related through Kan extensions in many ways. These relations provide additional links between computer science and category theory, and also give a new point of view on the famous Curtis–Hedlund theorem of cellular automata from the extended topological point of view provided by category theory. These links also allow to relatively easily generalize concepts pioneered by cellular automata to arbitrary kinds of possibly evolving spaces. No prior knowledge of category theory is assumed for the most part.","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135743543","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: 5
Population diversity and inheritance in genetic programming for symbolic regression 符号回归遗传规划中的种群多样性与遗传
IF 2.1 4区 计算机科学
Natural Computing Pub Date : 2023-01-17 DOI: 10.1007/s11047-022-09934-x
Bogdan Burlacu, Kaifeng Yang, M. Affenzeller
{"title":"Population diversity and inheritance in genetic programming for symbolic regression","authors":"Bogdan Burlacu, Kaifeng Yang, M. Affenzeller","doi":"10.1007/s11047-022-09934-x","DOIUrl":"https://doi.org/10.1007/s11047-022-09934-x","url":null,"abstract":"","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":"1 1","pages":""},"PeriodicalIF":2.1,"publicationDate":"2023-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41587869","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: 1
Models to classify the difficulty of genetic algorithms to solve continuous optimization problems 模型分类困难的遗传算法求解连续优化问题
IF 2.1 4区 计算机科学
Natural Computing Pub Date : 2023-01-12 DOI: 10.1007/s11047-022-09936-9
Noel E. Rodríguez-Maya, J. Flores, S. Vérel, Mario Graff
{"title":"Models to classify the difficulty of genetic algorithms to solve continuous optimization problems","authors":"Noel E. Rodríguez-Maya, J. Flores, S. Vérel, Mario Graff","doi":"10.1007/s11047-022-09936-9","DOIUrl":"https://doi.org/10.1007/s11047-022-09936-9","url":null,"abstract":"","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2023-01-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48039030","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: 2
Gravitationally invariant subspaces in quantum computing 量子计算中的引力不变子空间
IF 2.1 4区 计算机科学
Natural Computing Pub Date : 2023-01-10 DOI: 10.1007/s11047-022-09938-7
T. Crowder, M. Lanzagorta
{"title":"Gravitationally invariant subspaces in quantum computing","authors":"T. Crowder, M. Lanzagorta","doi":"10.1007/s11047-022-09938-7","DOIUrl":"https://doi.org/10.1007/s11047-022-09938-7","url":null,"abstract":"","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2023-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49187289","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: 0
On von Neumann regularity of cellular automata 元胞自动机的von Neumann正则性
4区 计算机科学
Natural Computing Pub Date : 2023-01-10 DOI: 10.1007/s11047-022-09935-w
Ville Salo
{"title":"On von Neumann regularity of cellular automata","authors":"Ville Salo","doi":"10.1007/s11047-022-09935-w","DOIUrl":"https://doi.org/10.1007/s11047-022-09935-w","url":null,"abstract":"Abstract We show that a cellular automaton on a one-dimensional two-sided mixing subshift of finite type is a von Neumann regular element in the semigroup of cellular automata if and only if it is split epic onto its image in the category of sofic shifts and block maps. It follows from previous joint work of the author and Törmä that von Neumann regularity is a decidable condition, and we decide it for all elementary CA, obtaining the optimal radii for weak generalized inverses. Two sufficient conditions for non-regularity are having a proper sofic image or having a point in the image with no preimage of the same period. We show that the non-regular ECA 9 and 28 cannot be proven non-regular using these methods. We also show that a random cellular automaton is non-regular with high probability.","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":"179 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136326794","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: 0
Information theoretical properties of a spiking neuron trained with Hebbian and STDP learning rules 用Hebbian和STDP学习规则训练的尖峰神经元的信息理论性质
IF 2.1 4区 计算机科学
Natural Computing Pub Date : 2023-01-06 DOI: 10.1007/s11047-022-09939-6
Dominique F. Chu
{"title":"Information theoretical properties of a spiking neuron trained with Hebbian and STDP learning rules","authors":"Dominique F. Chu","doi":"10.1007/s11047-022-09939-6","DOIUrl":"https://doi.org/10.1007/s11047-022-09939-6","url":null,"abstract":"","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":" ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2023-01-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43285452","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: 1
On the power of membrane dissolution in polarizationless P systems with active membranes 具有活性膜的无极化P体系的膜溶解能力
IF 2.1 4区 计算机科学
Natural Computing Pub Date : 2022-12-16 DOI: 10.1007/s11047-022-09926-x
Zsolt Gazdag, Károly Hajagos
{"title":"On the power of membrane dissolution in polarizationless P systems with active membranes","authors":"Zsolt Gazdag, Károly Hajagos","doi":"10.1007/s11047-022-09926-x","DOIUrl":"https://doi.org/10.1007/s11047-022-09926-x","url":null,"abstract":"","PeriodicalId":49783,"journal":{"name":"Natural Computing","volume":"22 1","pages":"95 - 104"},"PeriodicalIF":2.1,"publicationDate":"2022-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46018515","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: 1
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