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Associating parallel automata network dynamics and strictly one-way cellular automata 关联并行自动机网络动力学与严格单向元胞自动机
IF 2.1 4区 计算机科学 Q2 Computer Science
Natural Computing
Pub Date : 2023-06-09 DOI: 10.1007/s11047-023-09948-z
Pacôme Perrotin
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引用次数: 0
Asynchronous, finite dynamical systems 异步有限动力系统
IF 2.1 4区 计算机科学 Q2 Computer Science
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 Q2 Computer Science
Natural Computing
Pub Date : 2023-05-08 DOI: 10.1007/s11047-023-09943-4
Juan Luis Filgueiras, Daniel Varela, José Santos

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.

在本文中，我们讨论了两种从头计算蛋白质结构预测方法的优点和问题。一方面，讨论了最近基于深度学习的方法，这些方法显著改善了对各种蛋白质的预测结果。另一方面，分析了基于蛋白质构象能量最小化和不同搜索策略的方法。在后一种情况下，我们基于差异进化和片段替换技术之间的模因组合的方法也被包括在内，在进化搜索中也加入了小生境的可能性。已经使用不同的蛋白质来分析这两种方法的优缺点，提出了整合这两种替代方案的可能性。
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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 Q2 Computer Science
Natural Computing
Pub Date : 2023-04-26 DOI: 10.1007/s11047-023-09942-5
Daniel Hader, Matthew J. Patitz, Scott M. Summers
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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 Q2 Computer Science
Natural Computing
Pub Date : 2023-01-27 DOI: 10.1007/s11047-022-09931-0
Alexandre Fernandez, Luidnel Maignan, Antoine Spicher
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.
本文通过Kan扩展的范畴概念，精确地形式化了元胞自动机对局部构型的应用是其局部过渡函数的自然扩展的意义。实际上，进行这种扩展的两种可能的方法及其定义中涉及的成分在许多方面都通过Kan扩展相关联。这些关系为计算机科学和范畴论之间提供了额外的联系，也从范畴论提供的扩展拓扑的角度对著名的元胞自动机的Curtis-Hedlund定理提供了一个新的观点。这些联系也允许相对容易地将由元胞自动机开创的概念推广到任意种类的可能进化的空间。在大多数情况下，没有先验知识的范畴论假设。
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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 Q2 Computer Science
Natural Computing
Pub Date : 2023-01-17 DOI: 10.1007/s11047-022-09934-x
Bogdan Burlacu, Kaifeng Yang, M. Affenzeller
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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 Q2 Computer Science
Natural Computing
Pub Date : 2023-01-12 DOI: 10.1007/s11047-022-09936-9
Noel E. Rodríguez-Maya, J. Flores, S. Vérel, Mario Graff
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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 Q2 Computer Science
Natural Computing
Pub Date : 2023-01-10 DOI: 10.1007/s11047-022-09938-7
T. Crowder, M. Lanzagorta
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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 Q2 Computer Science
Natural Computing
Pub Date : 2023-01-10 DOI: 10.1007/s11047-022-09935-w
Ville Salo
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.
摘要本文证明了一维有限型双向混合子位移上的元胞自动机是元胞自动机半群中的von Neumann正则元素，当且仅当它在微位移和块映射的范畴内被分割成它的像。从作者和Törmä前人的共同工作中得出von Neumann正则性是一个可判定的条件，并对所有初等CA都判定了它，得到了弱广义逆的最优半径。非正则性的两个充分条件是有一个正确的图像或图像中有一个点没有同时期的预像。我们表明，使用这些方法不能证明非规则ECA 9和28是非规则的。我们还证明了随机元胞自动机具有高概率的非规则性。
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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 Q2 Computer Science
Natural Computing
Pub Date : 2023-01-06 DOI: 10.1007/s11047-022-09939-6
Dominique F. Chu
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引用次数: 1
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