42 research outputs found

    Evolution from the ground up with Amee – From basic concepts to explorative modeling

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    Evolutionary theory has been the foundation of biological research for about a century now, yet over the past few decades, new discoveries and theoretical advances have rapidly transformed our understanding of the evolutionary process. Foremost among them are evolutionary developmental biology, epigenetic inheritance, and various forms of evolu- tionarily relevant phenotypic plasticity, as well as cultural evolution, which ultimately led to the conceptualization of an extended evolutionary synthesis. Starting from abstract principles rooted in complexity theory, this thesis aims to provide a unified conceptual understanding of any kind of evolution, biological or otherwise. This is used in the second part to develop Amee, an agent-based model that unifies development, niche construction, and phenotypic plasticity with natural selection based on a simulated ecology. Amee is implemented in Utopia, which allows performant, integrated implementation and simulation of arbitrary agent-based models. A phenomenological overview over Amee’s capabilities is provided, ranging from the evolution of ecospecies down to the evolution of metabolic networks and up to beyond-species-level biological organization, all of which emerges autonomously from the basic dynamics. The interaction of development, plasticity, and niche construction has been investigated, and it has been shown that while expected natural phenomena can, in principle, arise, the accessible simulation time and system size are too small to produce natural evo-devo phenomena and –structures. Amee thus can be used to simulate the evolution of a wide variety of processes

    2022-2023 Course Catalog

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    An annual catalog of courses and course descriptions offered at the University of Montana.https://scholarworks.umt.edu/coursecatalogs_asc/1117/thumbnail.jp

    LIPIcs, Volume 248, ISAAC 2022, Complete Volume

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    LIPIcs, Volume 248, ISAAC 2022, Complete Volum

    In Memoriam, Solomon Marcus

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    This book commemorates Solomon Marcus’s fifth death anniversary with a selection of articles in mathematics, theoretical computer science, and physics written by authors who work in Marcus’s research fields, some of whom have been influenced by his results and/or have collaborated with him

    Basics and Applications in Quantum Optics

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    Quantum optics has received a lot of attention in recent decades due to the handiness and versatility of optical systems, which have been exploited both to study the foundations of quantum mechanics and for various applications. In this Special Issue, we collect some articles and a review focusing on some research activities that show the potential of quantum optics in the advancement of quantum technologies

    Weighted Tree Automata -- May it be a little more?

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    This is a book on weighted tree automata. We present the basic definitions and some of the important results in a coherent form with full proofs. The concept of weighted tree automata is part of Automata Theory and it touches the area of Universal Algebra. It originated from two sources: weighted string automata and finite-state tree automata

    Reversible Computation: Extending Horizons of Computing

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    This open access State-of-the-Art Survey presents the main recent scientific outcomes in the area of reversible computation, focusing on those that have emerged during COST Action IC1405 "Reversible Computation - Extending Horizons of Computing", a European research network that operated from May 2015 to April 2019. Reversible computation is a new paradigm that extends the traditional forwards-only mode of computation with the ability to execute in reverse, so that computation can run backwards as easily and naturally as forwards. It aims to deliver novel computing devices and software, and to enhance existing systems by equipping them with reversibility. There are many potential applications of reversible computation, including languages and software tools for reliable and recovery-oriented distributed systems and revolutionary reversible logic gates and circuits, but they can only be realized and have lasting effect if conceptual and firm theoretical foundations are established first

    On the k-Abelian Equivalence Relation of Finite Words

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    This thesis is devoted to the so-called k-abelian equivalence relation of sequences of symbols, that is, words. This equivalence relation is a generalization of the abelian equivalence of words. Two words are abelian equivalent if one is a permutation of the other. For any positive integer k, two words are called k-abelian equivalent if each word of length at most k occurs equally many times as a factor in the two words. The k-abelian equivalence defines an equivalence relation, even a congruence, of finite words. A hierarchy of equivalence classes in between the equality relation and the abelian equivalence of words is thus obtained. Most of the literature on the k-abelian equivalence deals with infinite words. In this thesis we consider several aspects of the equivalence relations, the main objective being to build a fairly comprehensive picture on the structure of the k-abelian equivalence classes themselves. The main part of the thesis deals with the structural aspects of k-abelian equivalence classes. We also consider aspects of k-abelian equivalence in infinite words. We survey known characterizations of the k-abelian equivalence of finite words from the literature and also introduce novel characterizations. For the analysis of structural properties of the equivalence relation, the main tool is the characterization by the rewriting rule called the k-switching. Using this rule it is straightforward to show that the language comprised of the lexicographically least elements of the k-abelian equivalence classes is regular. Further word-combinatorial analysis of the lexicographically least elements leads us to describe the deterministic finite automata recognizing this language. Using tools from formal language theory combined with our analysis, we give an optimal expression for the asymptotic growth rate of the number of k-abelian equivalence classes of length n over an m-letter alphabet. Explicit formulae are computed for small values of k and m, and these sequences appear in Sloane’s Online Encyclopedia of Integer Sequences. Due to the fact that the k-abelian equivalence relation is a congruence of the free monoid, we study equations over the k-abelian equivalence classes. The main result in this setting is that any system of equations of k-abelian equivalence classes is equivalent to one of its finite subsystems, i.e., the monoid defined by the k-abelian equivalence relation possesses the compactness property. Concerning infinite words, we mainly consider the (k-)abelian complexity function. We complete a classification of the asymptotic abelian complexities of pure morphic binary words. In other words, given a morphism which has an infinite binary fixed point, the limit superior asymptotic abelian complexity of the fixed point can be computed (in principle). We also give a new proof of the fact that the k-abelian complexity of a Sturmian word is n + 1 for length n 2k. In fact, we consider several aspects of the k-abelian equivalence relation in Sturmian words using a dynamical interpretation of these words. We reprove the fact that any Sturmian word contains arbitrarily large k-abelian repetitions. The methods used allow to analyze the situation in more detail, and this leads us to define the so-called k-abelian critical exponent which measures the ratio of the exponent and the length of the root of a k-abelian repetition. This notion is connected to a deep number theoretic object called the Lagrange spectrum

    Pseudo-contractions as Gentle Repairs

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    Updating a knowledge base to remove an unwanted consequence is a challenging task. Some of the original sentences must be either deleted or weakened in such a way that the sentence to be removed is no longer entailed by the resulting set. On the other hand, it is desirable that the existing knowledge be preserved as much as possible, minimising the loss of information. Several approaches to this problem can be found in the literature. In particular, when the knowledge is represented by an ontology, two different families of frameworks have been developed in the literature in the past decades with numerous ideas in common but with little interaction between the communities: applications of AGM-like Belief Change and justification-based Ontology Repair. In this paper, we investigate the relationship between pseudo-contraction operations and gentle repairs. Both aim to avoid the complete deletion of sentences when replacing them with weaker versions is enough to prevent the entailment of the unwanted formula. We show the correspondence between concepts on both sides and investigate under which conditions they are equivalent. Furthermore, we propose a unified notation for the two approaches, which might contribute to the integration of the two areas

    36th International Symposium on Theoretical Aspects of Computer Science: STACS 2019, March 13-16, 2019, Berlin, Germany

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