Relevant bibliographies by topics / Combinatorial nature

Academic literature on the topic 'Combinatorial nature'

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Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "Combinatorial nature"

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Armstrong, D. M. "The Nature of Possibility." Canadian Journal of Philosophy 16, no. 4 (December 1986): 575–94. http://dx.doi.org/10.1080/00455091.1986.10717137.

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I want to defend a Combinatorialtheory of possibility. Such a view traces the very idea of possibility to the idea of the combinations – all the combinations which respect a certain simple form – of given, actual, elements. Combination is to be understood widely enough to cover the notions of expansion and contraction. (My central metaphysical hypothesis is that all there is is the world of space and time. It is this world which is to supply the actual elements for the totality of combinations. So what is proposed is a Naturalistic form of a combinatorial theory.)The combinatorial idea is not new, of course. Wittgenstein gave a classical exposition of it in the Tractatus. Perhaps its charter is 3.4: ‘A proposition determines a place in logical space. The existence of this logical place is guaranteed by the mere existence of the constituents’ (my italics). There is a small additional combinatorial literature. I myself was converted to a combinatorial view by Brian Skyrms’ brief but fascinating article ‘Tractarian Nominalism.’
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Reynolds, K. A. "Combinatorial biosynthesis: Lesson learned from nature." Proceedings of the National Academy of Sciences 95, no. 22 (October 27, 1998): 12744–46. http://dx.doi.org/10.1073/pnas.95.22.12744.

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Timofieva, N. K. "The Fractal Nature of Combinatorial Sets and Finding Formulas for Combinatorial Numbers." Cybernetics and Systems Analysis 56, no. 1 (January 2020): 110–17. http://dx.doi.org/10.1007/s10559-020-00226-9.

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Kültz, Dietmar. "The Combinatorial Nature of Osmosensing in Fishes." Physiology 27, no. 4 (August 2012): 259–75. http://dx.doi.org/10.1152/physiol.00014.2012.

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Organisms exposed to altered salinity must be able to perceive osmolality change because metabolism has evolved to function optimally at specific intracellular ionic strength and composition. Such osmosensing comprises a complex physiological process involving many elements at organismal and cellular levels of organization. Input from numerous osmosensors is integrated to encode magnitude, direction, and ionic basis of osmolality change. This combinatorial nature of osmosensing is discussed with emphasis on fishes.
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ALTREUTER, D., and D. CLARK. "Combinatorial biocatalysis: taking the lead from Nature." Current Opinion in Biotechnology 10, no. 2 (April 1, 1999): 130–36. http://dx.doi.org/10.1016/s0958-1669(99)80022-6.

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Tymofijeva, Nadiya К. "Sign Combinatorial Spaces, Finite Sequences and Logarithmic Spirals." Control Systems and Computers, no. 1 (297) (2022): 32–43. http://dx.doi.org/10.15407/csc.2022.01.032.

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Introduction. Sign combinatorial spaces that exist in two states: convolute (tranquility) and deployed (dynamics), are considered. Spaces, in particular biological, physical, informational and some others, for which the axioms of sign combinatorial spaces, are valid, have a combinatorial nature. When they are deployed, combinatorial numbers (Fibonacci numbers) are formed, through which logarithmic spirals appear in living nature. These spirals are formed due to the finite sequences that take place during the deployment of the agreed spaces and which are presented geometrically using polar coordinates. Formulation of the problem. The logarithmic spiral is geometrically represented through a “golden rectangle” in which one side is 1,618 times longer (“golden” number or golden section). The presence of the golden ratio in nature is manifested through Fibonacci numbers, which are formed from an arithmetic triangle from elements of finite sequences formed by the deployment of sign combinatorial spaces. But this spiral is transmitted through the “golden rectangle” indirectly. The problem is to trace its formation in nature through constructed sequences, the elements of which are represented by polar coordinates. The approach proposed. Using the finite sequences that are formed during the unfolding of sign combinatorial spaces and the representation of their elements in polar coordinates, we can trace the dynamics of the formation of logarithmic spirals in nature. Conclusion. Representation of biological space as a sign combinatorial space can explain various phenomena in nature. When unfolding these spaces from the convolute spaces finite sequences are formed, the sums of the members of which determine the number of combinatorial configurations in a subset of isomorphic combinatorial configurations and form an arithmetic triangle (Pascal’s triangle). Fibonacci numbers and, accordingly, a golden number are formed from an arithmetic triangle. The logarithmic spiral fits into a golden rectangle. The dynamics of the formation of the logarithmic spiral is traced due to the finite sequences formed as a result of the deployment of the sign combinatorial spaces, the elements of which are presented in polar coordinates.
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Colorni, A., M. Dorigo, F. Maffioli, V. Maniezzo, G. Righini, and M. Trubian. "Heuristics from Nature for Hard Combinatorial Optimization Problems." International Transactions in Operational Research 3, no. 1 (January 1996): 1–21. http://dx.doi.org/10.1111/j.1475-3995.1996.tb00032.x.

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Rahman, Md Ashikur, Rajalingam Sokkalingam, Mahmod Othman, Kallol Biswas, Lazim Abdullah, and Evizal Abdul Kadir. "Nature-Inspired Metaheuristic Techniques for Combinatorial Optimization Problems: Overview and Recent Advances." Mathematics 9, no. 20 (October 19, 2021): 2633. http://dx.doi.org/10.3390/math9202633.

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Combinatorial optimization problems are often considered NP-hard problems in the field of decision science and the industrial revolution. As a successful transformation to tackle complex dimensional problems, metaheuristic algorithms have been implemented in a wide area of combinatorial optimization problems. Metaheuristic algorithms have been evolved and modified with respect to the problem nature since it was recommended for the first time. As there is a growing interest in incorporating necessary methods to develop metaheuristics, there is a need to rediscover the recent advancement of metaheuristics in combinatorial optimization. From the authors’ point of view, there is still a lack of comprehensive surveys on current research directions. Therefore, a substantial part of this paper is devoted to analyzing and discussing the modern age metaheuristic algorithms that gained popular use in mostly cited combinatorial optimization problems such as vehicle routing problems, traveling salesman problems, and supply chain network design problems. A survey of seven different metaheuristic algorithms (which are proposed after 2000) for combinatorial optimization problems is carried out in this study, apart from conventional metaheuristics like simulated annealing, particle swarm optimization, and tabu search. These metaheuristics have been filtered through some key factors like easy parameter handling, the scope of hybridization as well as performance efficiency. In this study, a concise description of the framework of the selected algorithm is included. Finally, a technical analysis of the recent trends of implementation is discussed, along with the impacts of algorithm modification on performance, constraint handling strategy, the handling of multi-objective situations using hybridization, and future research opportunities.
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Semenkina, Olga Ev, Eugene A. Popov, and Olga Er Semenkina. "Self-configuring Nature Inspired Algorithms for Combinatorial Optimization Problems." Journal of Siberian Federal University. Mathematics & Physics 10, no. 4 (December 2017): 463–73. http://dx.doi.org/10.17516/1997-1397-2017-10-4-463-473.

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Coja-Oghlan, Amin, Tobias Kapetanopoulos, and Noela Müller. "The replica symmetric phase of random constraint satisfaction problems." Combinatorics, Probability and Computing 29, no. 3 (December 3, 2019): 346–422. http://dx.doi.org/10.1017/s0963548319000440.

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AbstarctRandom constraint satisfaction problems play an important role in computer science and combinatorics. For example, they provide challenging benchmark examples for algorithms, and they have been harnessed in probabilistic constructions of combinatorial structures with peculiar features. In an important contribution (Krzakala et al. 2007, Proc. Nat. Acad. Sci.), physicists made several predictions on the precise location and nature of phase transitions in random constraint satisfaction problems. Specifically, they predicted that their satisfiability thresholds are quite generally preceded by several other thresholds that have a substantial impact both combinatorially and computationally. These include the condensation phase transition, where long-range correlations between variables emerge, and the reconstruction threshold. In this paper we prove these physics predictions for a broad class of random constraint satisfaction problems. Additionally, we obtain contiguity results that have implications for Bayesian inference tasks, a subject that has received a great deal of interest recently (e.g. Banks et al. 2016, Proc. 29th COLT).
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Dissertations / Theses on the topic "Combinatorial nature"

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Lakshminarayanan, Srinivasan. "Nature Inspired Discrete Integer Cuckoo Search Algorithm for Optimal Planned Generator Maintenance Scheduling." University of Toledo / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1438101954.

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Aschenbrenner, Jennifer [Verfasser], and Michael [Gutachter] Bott. "Combinatorial Biosynthesis of Natural and Non-natural Plant-derived Phenols in Microorganisms / Jennifer Aschenbrenner ; Gutachter: Michael Bott." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2019. http://d-nb.info/1197302077/34.

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Aubry, Céline. "Towards combinatorial biosynthesis of pyrrolamide antibiotics in Streptomyces." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS245.

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Depuis plus de 80 ans, le métabolisme spécialisé nous fournit de nombreuses molécules utilisées en médecine, en particulier comme anti-infectieux. Aujourd’hui, avec l’augmentation mondiale de la résistance aux antimicrobiens, de nouveaux antibiotiques sont indispensables. Une des réponses à cette pénurie grave pourrait provenir de la biologie synthétique. Dans le domaine du métabolisme spécialisé, la biologie synthétique est utilisée en particulier pour la biosynthèse de métabolites non naturels. Parmi les métabolites spécialisés, les peptides non ribosomiques constituent une cible attrayante, car ils nous ont déjà fourni des molécules à haute valeur clinique (ex. les antibiotiques vancomycine et daptomycine). De plus, la plupart sont synthétisés par des enzymes multimodulaires appelées synthétases de peptides non ribosomiques (NRPS), et sont diversifiés davantage par des enzymes de décoration. Ainsi, ces voies de biosynthèse se prêtent particulièrement à la biosynthèse combinatoire, consistant à combiner des gènes de biosynthèse provenant de divers groupes de gènes ou, dans le cas des NRPS, à combiner des modules ou domaines pour créer de nouvelles enzymes. Cependant, si plusieurs études ont établi la faisabilité de telles approches, de nombreux obstacles subsistent avant que les approches combinatoires de biosynthèse soient totalement efficaces pour la synthèse de nouveaux métabolites. Les travaux présentés ici s’inscrivent dans le cadre d’un projet visant à comprendre les facteurs limitant les approches de biosynthèse combinatoire basées sur les NRPS, en utilisant une approche de biologie synthétique. Nous avons choisi de travailler avec les NRPS responsables de la biosynthèse des pyrrolamides. En effet, ces NRPS sont constitués uniquement de modules et de domaines autonomes, et donc particulièrement adaptés aux manipulations génétiques et biochimiques. La caractérisation du groupe de gènes de biosynthèse du pyrrolamide anthelvencine constitue la première partie de cette thèse et nous a fourni de nouveaux gènes pour notre étude. La deuxième partie a consisté à construire de vecteurs intégratifs modulaires, outils essentiels pour la construction et l’assemblage de cassettes génétiques. La dernière partie présente la reconstruction du groupe de gènes du pyrrolamide congocidine, basée sur la construction et l’assemblage de cassettes de gènes synthétiques. Dans l’ensemble, ces travaux ouvrent la voie à de futures expériences de biosynthèse combinatoire, expériences qui devraient contribuer à une meilleure compréhension du fonctionnement précis des NRPS
For more than 80 years, specialized metabolism has provided us with many molecules used in medicine, especially as anti-infectives. Yet today, with the rise of antimicrobial resistance worldwide, new antibiotics are crucially needed. One of the answers to this serious shortage could arise from synthetic biology. In the field of specialized metabolism, synthetic biology is used in particular to biosynthesize unnatural metabolites. Among specialized metabolites, non-ribosomal peptides constitute an attractive target as they have already provided us with clinically valuable molecules (e.g. the vancomycin and daptomycin antibiotics). In addition, most are synthesized by multimodular enzymes called non-ribosomal peptide synthetases (NRPS) and further diversified by tailoring enzymes. Thus, such biosynthetic pathways are particularly amenable to combinatorial biosynthesis, which consists in combining biosynthetic genes coming from various gene clusters or, in the case of NRPSs, combining modules or domains to create a new enzyme. Yet, if several studies have established the feasibility of such approaches, many obstacles remain before combinatorial biosynthesis approaches are fully effective for the synthesis of new metabolites. The work presented here is part of a project aiming at understanding the limiting factors impeding NRPS-based combinatorial biosynthesis approaches, using a synthetic biology approach. We chose to work with the NRPSs involved in the biosynthesis of pyrrolamides. Indeed, these NRPS are solely constituted of stand-alone modules and domains, and thus, particularly amenable to genetic and biochemical manipulations. The characterization of the biosynthetic gene cluster of the pyrrolamide anthelvencin constitutes the first part of this thesis, and provided us with new genes for our study. The second part involved the construction of modular integrative vectors, essential tools for the construction and assembly of gene cassettes. The final part presents the successful refactoring of the congocidine pyrrolamide gene cluster, based on the construction and assembly of synthetic gene cassettes. Altogether, this work paves the way for future combinatorial biosynthesis experiments that should help deciphering the detailed functioning of NRPSs
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ANDRADE, Laís Sousa de. "A combinatorial study of soundness and normalization in n-graphs." Universidade Federal de Pernambuco, 2015. https://repositorio.ufpe.br/handle/123456789/18618.

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CNPQ
N-Graphs is a multiple conclusion natural deduction with proofs as directed graphs, motivated by the idea of proofs as geometric objects and aimed towards the study of the geometry of Natural Deduction systems. Following that line of research, this work revisits the system under a purely combinatorial perspective, determining geometrical conditions on the graphs of proofs to explain its soundness criterion and proof growth during normalization. Applying recent developments in the fields of proof graphs, proof-nets and N-Graphs itself, we propose a linear time algorithm for proof verification of the full system, a result that can be related to proof-nets solutions from Murawski (2000) and Guerrini (2011), and a normalization procedure based on the notion of sub-N-Graphs, introduced by Carvalho, in 2014. We first present a new soundness criterion for meta-edges, along with the extension of Carvalho’s sequentization proof for the full system. For this criterion we define an algorithm for proof verification that uses a DFS-like search to find invalid cycles in a proof-graph. Since the soundness criterion in proof graphs is analogous to the proof-nets procedure, the algorithm can also be extended to check proofs in the multiplicative linear logic without units (MLL−) with linear time complexity. The new normalization proposed here combines a modified version of Alves’ (2009) original beta and permutative reductions with an adaptation of Carbone’s duplication operation on sub-N-Graphs. The procedure is simpler than the original one and works as an extension of both the normalization defined by Prawitz and the combinatorial study developed by Carbone, i.e. normal proofs enjoy the separation and subformula properties and have a structure that can represent how patterns lying in normal proofs can be recovered from the graph of the original proof with cuts.
N-Grafos é uma dedução natural de múltiplas conclusões onde provas são representadas como grafos direcionados, motivado pela idéia de provas como objetos geométricos e com o objetivo de estudar a geometria de sistemas de Dedução Natural. Seguindo esta linha de pesquisa, este trabalho revisita o sistema sob uma perpectiva puramente combinatorial, determinando condições geométricas nos grafos de prova para explicar seu critério de corretude e crescimento da prova durante a normalização. Aplicando desenvolvimentos recentes nos campos de grafos de prova, proof-nets e dos próprios N-Grafos, propomos um algoritmo linear para verificação de provas para o sistema completo, um resultado que pode ser comparado com soluções para roof-nets desenvolvidas por Murawski (2000) e Guerrini (2011), e um procedimento de normalização baseado na noção de sub-N-Grafos, introduzidas por Carvalho, em 2014. Apresentamos primeiramente um novo critério de corretude para meta-arestas, juntamente com a extensão para todo o sistema da prova da sequentização desenvolvida por Carvalho. Para este critério definimos um algoritmo para verificação de provas que utiliza uma busca parecida com a DFS (Busca em Profundidade) para encontrar ciclos inválidos em um grafo de prova. Como o critério de corretude para grafos de provas é análogo ao procedimento para proof-nets, o algoritmo pode também ser estendido para validar provas em Lógica Linear multiplicativa sem units (MLL−) com complexidade de tempo linear. A nova normalização proposta aqui combina uma versão modificada das reduções beta e permutativas originais de Alves com uma adaptação da operação de duplicação proposta por Carbone para ser aplicada a sub-N-Grafos. O procedimento é mais simples do que o original e funciona como uma extensão da normalização definida por Prawitz e do estudo combinatorial desenvolvido por Carbone, i.e. provas em forma normal desfrutam das propriedades da separação e subformula e possuem uma estrutura que pode representar como padrões existentes em provas na forma normal poderiam ser recuperados a partir do grafo da prova original com cortes.
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Demetriades, Marina. "Dynamic combinatorial mass spectrometry for 2-oxoglutarate oxygenase inhibition." Thesis, University of Oxford, 2013. http://ora.ox.ac.uk/objects/uuid:8c3a3a33-bc1a-407e-8b86-70c5eca58f38.

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In the last decade, dynamic combinatorial mass spectrometry (DCMS) with protein targets has emerged as a promising method for the identification of enzyme-inhibitors. 2-Oxoglutarate (2OG) oxygenases are involved in important biological processes related to many diseases; several human 2OG oxygenases are targeted for pharmaceutical intervention. This thesis describes inhibition studies on three 2OG oxygenases using DCMS and structure activity relation (SAR) studies. Disulphide based DCMS was used for the identification of N-oxalyl based lead inhibitors for the 2OG oxygenase AlkB from Escherichia coli. Crystallographic analyses of AlkB with a lead inhibitor assisted in the design of a second generation of inhibitors using N-oxalyl, pyridyl and quinolinyl scaffolds. Crystallographic and kinetic data of three potent and selective AlkB inhibitors validates the DCMS approach for the development of 2OG oxygenase inhibitors. The hypoxia inducible factor hydroxylase, prolyl hydroxylase domain 2 (PHD2), was then used as the model enzyme for the development of a novel DCMS approach employing the reversible reaction of boronic acids with diols to form boronate esters. The ‘boronate’ DCMS method was used to identify pyridyl- substituted lead compounds. Further modification of the pyridine scaffold, based on structural analyses, led to the development of highly potent and selective PHD2 inhibitors. To identify inhibitors for the fat mass and obesity associated protein (FTO), another 2OG oxygenase, an inhibition assay was developed. The inhibition assay was used in conjunction with a differential scanning fluorimetry (DSF) binding assay to identify isoquinolinyl and pyridyl inhibitor scaffolds, related to those used in the DCMS studies. FTO complexed structures of these compounds, and with a natural product anthraquinone, enabled the design and synthesis of new inhibitors that are both co-substrate and substrate competitors of FTO. One such compound proved to be a potent FTO inhibitor with improved selectivity over other 2OG oxygenases. Overall, the work validates the use of DCMS methods for the development of potent and selective inhibitors for 2OG oxygenases, and by implication of other enzyme families.
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Roberts, Alexandra Anne Biotechnology &amp Biomolecular Sciences Faculty of Science UNSW. "Unnatural production of natural products: Heterologous expression and combinatorial biosynthesis of cyanobacterial-derived compounds." Publisher:University of New South Wales. Biotechnology & Biomolecular Sciences, 2008. http://handle.unsw.edu.au/1959.4/41533.

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Cyanobacteria produce a myriad of structurally unique secondary metabolites with useful bioactive properties. Heterologous expression of a variety of microbial natural compounds has been used to harness their diversity and facilitate their combinatorial biosynthesis. However, these genetic techniques have not been developed for secondary metabolite-producing cyanobacteria. Therefore the genetically manipulable Escherichia coli and Synechocystis sp. PCC6803 were engineered in order to develop effective heterologous hosts and promoters for the expression of cyanobacterial-derived compounds. The phosphopanthetheinyl transferase (PPT), Sppt, from Synechocystis sp. PCC6803 was characterised to determine its ability to activate carrier proteins from secondary metabolite pathways. Despite in silico evidence which suggested Sppt was able to activate a wide range of carrier proteins, biochemical analysis revealed that it is dedicated for fatty acid synthesis. Consequently, E. coli and Synechocystis sp. PCC6803 were engineered to encode a broad-range PPT, from the filamentous cyanobacteria Nodularia spumigena NSOR10, for the activation of carrier proteins from nonribosomal peptide synthesis. Cyanobacterial natural product engineering was also explored with the characterisation of two relaxed specificity adenylation domains (A-domains) from the biosynthetic pathway of the toxin microcystin. The wide variety of microcystin compounds produced by cyanobacterial species suggests that multiple amino acids can be activated by the same A-domain. This was supported by preliminary ATP-[32P]PPi exchange assays and was subsequently harnessed in the production of a variety of dipeptides using two reconstituted modules in vitro. Transposition was investigated as a potential mechanism for the transfer of nonribosomal peptide synthetase gene clusters to heterologous hosts. This was performed via the characterisation of the putative transposase, Mat, physically linked with the microcystin synthetase gene cluster (mcyS). PCR screening, in silico analysis and nitrocellulose filter binding assays indicated that this transposase may have mediated mcyS gene cluster rearrangements but not entire gene cluster mobilisation between species. The potential role of transposases in the natural combinatorial biosynthesis of microcystin has evolutionary implications for the dynamic nature of cyanobacterial genomes and applications for use in the engineering of novel bioactive compounds. Therefore, the results from this study may provide a biotechnological platform for the transfer, expression and combinatorial biosynthesis of novel cyanobacterial-derived natural products.
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Lee, Wing Kuen. "Interpreting tables in text using probabilistic two-dimensional context-free grammars /." View abstract or full-text, 2005. http://library.ust.hk/cgi/db/thesis.pl?COMP%202005%20LEEW.

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Edson, de Albuquerque Filho José. "JNOM : uma ferramenta para encontrar motifs." Universidade Federal de Pernambuco, 2005. https://repositorio.ufpe.br/handle/123456789/2801.

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A regulação gênica está intimamente ligada com a transcrição de proteínas, e esse mecanismo é muito importante para o desenvolvimento dos seres vivos, pois é através dele que os organismos conseguem sintetizar proteínas. Um interessante problema da biologia moderna é o entendimento de mecanismos da regulação da transcrição. Muitos aspectos dessa regulação envolvem fatores de transcrição (proteínas ligantes ao DNA). Esses fatores regulam a expressão gênica pela conexão em posições específicas de regiões do genoma (conjunto de genes de uma espécie) que podem estar próximas ou não, como veremos em maiores detalhes oportunamente. Os fatores de transcrição conectam-se a subseqüências especificas de DNA, os promotores, que podem, com dificuldade, ser determinados por análises biológicas. Esse alto grau de dificuldade motiva os cientistas a procurarem meios computacionais mais rápidos e eficientes para solucionar o problema da busca pelos sítios de ligação dos promotores. O crescente aumento da disponibilidade de seqüências completas de genoma motiva tentativas de entender e modelar o mecanismo regulatório através de análises computacionais. A identificação de sítios de ligação envolve duas etapas principais: aprender modelos de sítios de ligação e buscar sítios em novas seqüências. Parte do trabalho foi desenvolver uma ferramenta para auxiliar os cientistas na busca por essas regiões especiais, os motifs, no genoma. Como desenvolvemos essa ferramenta usando Java, combinamos o fonema inglês da letra "J" com o sufixo "nom" da palavra "genom" para compor o nome da ferramenta e a chamamos de Jnom. A primeira tarefa é aprender modelos de sítios de ligação em potencial em um dado genoma. Usam-se exemplos de sítios de ligação verificados biologicamente e tenta-se encontrar sítios similares em outras regiões promotoras. Em seguida, é necessário descobrir uma seqüência de motifs em uma coleção de longas seqüências que são supostamente ligadas pelo mesmo fator. Neste caso, um motif encontrado indica um possível fator desconhecido que regula o conjunto de genes. A natureza combinatória dos fatores de transcrição é o mecanismo pelo qual as células dos seres superiores (eucariotes) atuam para controlar a expressão de conjuntos inteiros de genes. A intenção deste trabalho é investigar essa natureza combinante e tentar utilizar esse fato para melhorar o desempenho em relação a ferramentas existentes. O principal objetivo dessa pesquisa é construir uma ferramenta capaz de considerar a ação combinada dos fatores de transcrição através da seqüência de genes para encontrar novos motifs a partir de alguns já conhecidos
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Passos, Alexandre Tachard 1986. "Combinatorial algorithms and linear programming for inference in natural language processing = Algoritmos combinatórios e de programação linear para inferência em processamento de linguagem natural." [s.n.], 2013. http://repositorio.unicamp.br/jspui/handle/REPOSIP/275609.

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Orientador: Jacques Wainer
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Computação
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Resumo: Em processamento de linguagem natural, e em aprendizado de máquina em geral, é comum o uso de modelos gráficos probabilísticos (probabilistic graphical models). Embora estes modelos sejam muito convenientes, possibilitando a expressão de relações complexas entre várias variáveis que se deseja prever dado uma sentença ou um documento, algoritmos comuns de aprendizado e de previsão utilizando estes modelos são frequentemente ineficientes. Por isso têm-se explorado recentemente o uso de relaxações usando programação linear deste problema de inferência. Esta tese apresenta duas contribuições para a teoria e prática de relaxações de programação linear para inferência em modelos probabilísticos gráficos. Primeiro, apresentamos um novo algoritmo, baseado na técnica de geração de colunas (dual à técnica dos planos de corte) que acelera a execução do algoritmo de Viterbi, a técnica mais utilizada para inferência em modelos lineares. O algoritmo apresentado também se aplica em modelos que são árvores e em hipergrafos. Em segundo mostramos uma nova relaxação linear para o problema de inferência conjunta, quando se quer acoplar vários modelos, em cada qual inferência é eficiente, mas em cuja junção inferência é NP-completa. Esta tese propõe uma extensão à técnica de decomposição dual (dual decomposition) que permite além de juntar vários modelos a adição de fatores que tocam mais de um submodelo eficientemente
Abstract: In natural language processing, and in general machine learning, probabilistic graphical models (and more generally structured linear models) are commonly used. Although these models are convenient, allowing the expression of complex relationships between many random variables one wants to predict given a document or sentence, most learning and prediction algorithms for general models are inefficient. Hence there has recently been interest in using linear programming relaxations for the inference tasks necessary when learning or applying these models. This thesis presents two contributions to the theory and practice of linear programming relaxations for inference in structured linear models. First we present a new algorithm, based on column generation (a technique which is dual to the cutting planes method) to accelerate the Viterbi algorithm, the most popular exact inference technique for linear-chain graphical models. The method is also applicable to tree graphical models and hypergraph models. Then we present a new linear programming relaxation for the problem of joint inference, when one has many submodels and wants to predict using all of them at once. In general joint inference is NP-complete, but algorithms based on dual decomposition have proven to be efficiently applicable for the case when the joint model can be expressed as many separate models plus linear equality constraints. This thesis proposes an extension to dual decomposition which allows also the presence of factors which score parts that belong in different submodels, improving the expressivity of dual decomposition at no extra computational cost
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Ciência da Computação
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Crepaldi, Bruno Espinosa 1991. "Um algoritmo eficiente para o problema do posicionamento natural de antenas." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/275534.

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Orientadores: Cid Carvalho de Souza, Pedro Jussieu de Rezende
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Computação
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Resumo: Considerado uma variação do problema da galeria de arte, o problema do posicionamento de antenas trata do posicionamento do menor número de antenas requerido para determinar se uma pessoa está dentro ou fora da galeria. Uma antena propaga uma chave única dentro de um ângulo específico de transmissão, de modo que o conjunto de chaves recebidas em um dado ponto do plano seja suficiente para decidir se ele pertence ou não ao polígono que representa a galeria. Para verificar esta propriedade de localização, uma fórmula Booleana deve ser produzida junto com o posicionamento de antenas. Dizemos que as antenas estão em posição natural se elas estão localizadas nos vértices ou nas arestas do polígono e transmitindo sinal no ângulo formado pelos lados deste último no ponto onde a antena está posicionada. O problema do posicionamento natural de antenas é NP-difícil. Nesta dissertação, apresentamos um algoritmo exato para resolvê-lo. Para tanto, propomos um modelo inicial de programação linear inteira para o problema que, ao ser computado por um resolvedor comercial, se mostrou capaz de encontrar soluções ótimas de instâncias correspondentes a polígonos com algumas dezenas de vértices. Em seguida, através de estudos de propriedades geométricas, são introduzidas várias melhorias no modelo matemático e também na forma de computá-lo. Como consequência desta pesquisa, desenvolvemos um algoritmo iterativo baseado em programação linear inteira com o qual conseguimos solucionar o problema para instâncias consideravelmente maiores. A eficiência do nosso algoritmo é certificada por resultados experimentais que compreendem as soluções ótimas de 720 instâncias de até 1000 vértices, incluindo polígono com buracos, as quais foram calculadas em menos de seis minutos em um computador desktop padrão
Abstract: Considered a variation of the art gallery problem, the wireless localization problem deals with the placement of the smallest number of broadcasting antennas required to determine if someone is inside or outside the gallery. Each antenna propagates a unique key within a certain antenna-specific angle of broadcast, so that the set of keys received at any given point is sufficient to determine whether that point is inside or outside the polygon that represents the gallery. To ascertain this localization property, a Boolean formula must be produced along with the placement of the antennas. We say that the antennas are in natural position if they are located at the vertices or the edges of the polygon and transmitting their signals in the angle formed by the sides of the polygon at the point where the antenna is positioned. The natural wireless localization problem is NP-hard. In this dissertation, we present an exact algorithm to solve it. To this end, we propose an initial integer linear programming model for the problem that, after being computed by a commercial solver, proved to be capable of finding optimal solutions for instances corresponding to polygons with tens of vertices. Then, through studies of geometric properties, several improvements are introduced in the mathematical model and also in the way of computing it. As a result of this research, we develop an iterative algorithm based on integer linear programming with which we can solve the problem for considerably larger instances. The efficiency of our algorithm is certified by experimental results comprising the solutions of 720 instances, including polygon with holes with up to 1000 vertices, in less than six minutes on a standard desktop computer
Mestrado
Ciência da Computação
Mestre em Ciência da Computação
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Books on the topic "Combinatorial nature"

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Coello, Carlos A. Coello. Advances in multi-objective nature inspired computing. Berlin: Springer, 2010.

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Rudin, Donald O. The Nature of the world: New horizons for mankind. Annapolis, Md: Core Books, 1998.

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Rothlauf, Franz. Design of modern heuristics: Principles and application. Heidelberg: Springer, 2011.

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P, Devlin John, ed. High throughput screening: The discovery of bioactive substances. New York: M. Dekker, 1997.

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Model theoretic methods in finite combinatorics: AMS-ASL special session, January 5-8, 2009 Washington, DC. Providence, R.I: American Mathematical Society, 2011.

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Chiong, Raymond, and Sandeep Dhakal. Natural intelligence for scheduling, planning and packing problems. Berlin: Springer, 2009.

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1948-, Bartlett Paul Allan, and Entzeroth Michael, eds. Exploiting chemical diversity for drug discovery. Cambridge: RSC Publishing, 2006.

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Reverse chemical genetics: Methods and protocols. New York, NY: Humana Press, 2009.

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Chemogenomics: Methods and applications. New York, NY: Humana Press, 2009.

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Cozzens, Margaret B. Biomath in the schools. Providence, R.I: American Mathematical Society, 2011.

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Book chapters on the topic "Combinatorial nature"

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Hutchinson, C. R. "Combinatorial Biosynthesis of Antibiotics." In Drug Discovery from Nature, 233–54. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-642-60250-4_13.

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Christie, Lee A. "Decentralized Combinatorial Optimization." In Parallel Problem Solving from Nature – PPSN XVI, 360–72. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-58112-1_25.

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Bertels, Simon, Sven Frormann, Gerhard Jas, and Kai U. Bindseil. "Synergistic Use of Combinatorial and Natural Product Chemistry." In Drug Discovery from Nature, 72–105. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-642-60250-4_5.

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Thomson, Sarah L., Sébastien Verel, Gabriela Ochoa, Nadarajen Veerapen, and Paul McMenemy. "On the Fractal Nature of Local Optima Networks." In Evolutionary Computation in Combinatorial Optimization, 18–33. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-77449-7_2.

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Blondelle, Sylvie E., and Richard A. Houghten. "Synthetic Combinatorial Libraries: A New Tool for Antimicrobial Agent Discovery." In Drug Discovery from Nature, 311–19. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-642-60250-4_17.

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Coello Coello, Carlos A., Clarisse Dhaenens, and Laetitia Jourdan. "Multi-Objective Combinatorial Optimization: Problematic and Context." In Advances in Multi-Objective Nature Inspired Computing, 1–21. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-11218-8_1.

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Berny, A. "Selection and Reinforcement Learning for Combinatorial Optimization." In Parallel Problem Solving from Nature PPSN VI, 601–10. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/3-540-45356-3_59.

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Ouaarab, Aziz, and Xin-She Yang. "Cuckoo Search: From Cuckoo Reproduction Strategy to Combinatorial Optimization." In Nature-Inspired Computation in Engineering, 91–110. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-30235-5_5.

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Thomson, Sarah L., Sébastien Verel, Gabriela Ochoa, Nadarajen Veerapen, and Paul McMenemy. "Erratum to: On the Fractal Nature of Local Optima Networks." In Evolutionary Computation in Combinatorial Optimization, E1. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-77449-7_13.

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Chira, Camelia, Camelia M. Pintea, and Dumitru Dumitrescu. "Cooperative Learning Sensitive Agent System for Combinatorial Optimization." In Nature Inspired Cooperative Strategies for Optimization (NICSO 2007), 347–55. Berlin, Heidelberg: Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-78987-1_31.

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Conference papers on the topic "Combinatorial nature"

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Tsumoto, Shusaku, and Shoji Hirano. "Geometrical and Combinatorial Nature of Pearson Residuals." In 2010 IEEE International Conference on Granular Computing (GrC-2010). IEEE, 2010. http://dx.doi.org/10.1109/grc.2010.96.

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Kromer, Pavel, Jan Platos, and Vaclav Snasel. "Practical results of artificial immune Systems for combinatorial optimization problems." In 2012 World Congress on Nature and Biologically Inspired Computing (NaBIC). IEEE, 2012. http://dx.doi.org/10.1109/nabic.2012.6402261.

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Vasin, D. Ju, and S. I. Rotkov. "Combinatorial-geometric Problems of Intelligent Information Technologies for Processing Graphic Documents with a Weakly Formalized Description of Objects of Various Physical Nature." In 32nd International Conference on Computer Graphics and Vision. Keldysh Institute of Applied Mathematics, 2022. http://dx.doi.org/10.20948/graphicon-2022-925-936.

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The article deals with combinatorial-geometric modern approaches to the creation and use of automatic / automated information technologies for processing complexly structured raster graphic documents with a poorly formalized description of objects. At the heart of the used combinatorialgeometric approach, the analysis of video data is considered from a unified point of view of building a hierarchy of interrelated models of description, representation of data structures and decision making, as well as highly specialized processing algorithms. At the lower level of the hierarchy, raster information is processed from a digital input device (scanners, digital video cameras, various sensors), and the upper level of the hierarchy corresponds to the description of a graphic document in terms of the corresponding subject area. The features of technologies for processing the specified class of documents are determined. The basic problems of analyzing graphic documents with a weakly formalized description of the depicted objects are formulated as problems of computational geometry on polygons (contours), broken lines and points. Combinatorial-geometric problems of image input are considered. Estimates of the time complexity of the main combinatorial-geometric algorithms are given. The issues of development of the methodological, algorithmic and software base are considered in order to further increase the efficiency of the developed software and hardware systems and automatic technologies for processing the specified class of documents.
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Sun, Shengjie, and Hui Lu. "Self-Adaptive Parameter Control in Genetic Algorithms Based on Entropy and Rules of Nature for Combinatorial Optimization Problems." In 2019 IEEE Symposium Series on Computational Intelligence (SSCI). IEEE, 2019. http://dx.doi.org/10.1109/ssci44817.2019.9003054.

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Mishra, Mrityunjay Kumar, and S. K. Parida. "A Game Theoretic Approach for Demand-Side Management Considering Generation, Storage and the Combinatorial Nature of Load Scheduling." In 2018 International Conference and Utility Exhibition on Green Energy for Sustainable Development (ICUE). IEEE, 2018. http://dx.doi.org/10.23919/icue-gesd.2018.8635720.

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Wilmes, Lindsay, and Zahed Siddique. "Applicability of Design Spaces to Utilize Current Assembly Plant Resources to Produce New Product Family Members." In ASME 2004 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/detc2004-57528.

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Utilizing available assembly resources can greatly reduce the development time and cost for platforms and new product family members. This paper presents a method to utilize existing assembly plant resources, during the development of new product family members, by comparing existing assembly plant with feasible assembly processes. An assembly sequence design space that can be used to perform new family member process and existing plant utilization trade-off study is presented in the paper. The assembly sequence design space is combinatorial in nature. This research seeks to provide a systematic method to represent and reason with combinatorial design spaces in which these assembly process combinations lie. Models that capture effects of constraints on these spaces, explicitly represent feasible regions, and efficiently enumerate designs within this space are investigated. Application of the assembly sequence space to perform assembly plant utilization trade-off study is demonstrated using a coffeemaker family.
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Corbett, Brian P., and David W. Rosen. "Platform Commonization With Discrete Design Spaces: Introduction of the Flow Design Space." In ASME 2003 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2003. http://dx.doi.org/10.1115/detc2003/dtm-48678.

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Many companies have adopted the usage of common platforms to support the development of product families. The problem addressed in this paper deals with the development of a common platform for an existing set of products that may or may not already form a product family. The common platform embodies the core function, form, and technology base shared across the product family. In this work, we focus on configuration aspects of the platform commonization problem to determine which components are in the platform and the relationships among these components. Configuration design spaces are discrete and combinatorial in nature, but not necessarily purely combinatorial, as certain combinations represent infeasible designs. By carefully forming discrete design spaces and applying constraints to them, feasible design regions can be found and their sizes predicted. The purpose of this paper is to outline our approach to defining configuration design spaces for engineering design, with an emphasis on the mathematics of the spaces and their combinations into larger spaces that more completely capture design requirements. A new design space that models flows among components is introduced. Other design spaces that model physical connectivity, functionality, and assembly considerations are summarized. An example of a family of rechargeable flashlights illustrates the application of the discrete design space approach to develop a common platform.
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Motte, Damien, and Robert Bjärnemo. "Dealing With the Combinatorial Explosion of the Morphological Matrix in a “Manual Engineering Design” Context." In ASME 2013 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/detc2013-12040.

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The morphological matrix is an important element of the engineering design methodology and is present in many textbooks. This method originally aimed at generating an exhaustive set of solutions for a given problem, by decomposing it into subproblems, finding solutions to each subproblem, and combining them. One issue associated with the morphological matrix has been the necessity to deal with the combinatorial explosions of solutions, especially at the conceptual design phase, when the still fuzzy nature of the design problem precludes the use of automated search for an optimal solution by means of specific algorithms (the “manual engineering design” context), apart from a few exceptions. Several heuristics based on the reduction of the number of combinations are investigated, and their efficiency is assessed. It is showed that the often-recommended compatibility matrix heuristic is the least efficient and can result in overlooking potentially interesting combinations. In fact all heuristics, even combined, generally fail to decrease the number of combinations to a level that can be handled by the designers, unless the original number of combinations is low. However, if one abandons the principle of an exhaustive investigation of the combinations in order to find the “best” solution, it can be showed statistically that the probability of ending up with a “good” concept among a very large number of combinations can be attained. Moreover, it is showed that the number of combinations one is willing to investigate also can contribute to increase this probability. Moreover the experience gained from the first round of investigation can serve as a guide to choose and assess other combinations. Based on those results, some recommendations for using the morphological matrix with all the different heuristics are given. Moreover, this paper discusses and relativizes the importance of the combinatorial explosion issue of morphological matrix compared with some other advantages and shortcomings of the method.
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Li, Hui, and Shapour Azarm. "Product Line Design Selection Under Uncertainty and With Competitive Advantage." In ASME 2001 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. American Society of Mechanical Engineers, 2001. http://dx.doi.org/10.1115/detc2001/dac-21022.

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Abstract An approach for product line design is presented in which a line of products is selected for launching into the market. In the approach, the product line design is viewed as a selection process with two main stages: design alternative generation and design alternative evaluation. The focus of this paper is on the design alternative evaluation stage. Issues considered include a large variety of customer preferences, market competitions, multiple business goals, uncertainty, and commonality among the alternatives in a product line. Because of the combinatorial nature of the problem, genetic algorithms are used in the design evaluation stage. Product line design selection of a cordless screwdriver is used as a demonstration example. However, the emphasis in the example is on the approach and not in the details per se.
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Lees, David S., and Gregory S. Chirikjian. "An Efficient Trajectory Planning Method for Binary Manipulators." In ASME 1996 Design Engineering Technical Conferences and Computers in Engineering Conference. American Society of Mechanical Engineers, 1996. http://dx.doi.org/10.1115/96-detc/mech-1161.

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Abstract Binary manipulators have actuators with only two stable states. Therefore, they can reach only a finite number of locations. Compared to a manipulator built with continuous actuators, a binary manipulator provides reasonable performance, robustness, and is relatively inexpensive (up to an order of magnitude cheaper). The number of states attainable by a binary manipulator grows exponentially with the number of actuators. This makes brute force calculation of the inverse kinematics impossible for binary manipulators with many actuators. This paper presents a combinatorial method for planning trajectories for a binary manipulator while reducing the search space to a manageable size. Despite the discrete nature of binary actuation, it also creates motions that follow a specified trajectory accurately (in both position and orientation) without large deviations of the end-effector from the specified path.
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Reports on the topic "Combinatorial nature"

1

Altstein, Miriam, and Ronald J. Nachman. Rational Design of Insect Control Agent Prototypes Based on Pyrokinin/PBAN Neuropeptide Antagonists. United States Department of Agriculture, August 2013. http://dx.doi.org/10.32747/2013.7593398.bard.

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The general objective of this study was to develop rationally designed mimetic antagonists (and agonists) of the PK/PBAN Np class with enhanced bio-stability and bioavailability as prototypes for effective and environmentally friendly pest insect management agents. The PK/PBAN family is a multifunctional group of Nps that mediates key functions in insects (sex pheromone biosynthesis, cuticular melanization, myotropic activity, diapause and pupal development) and is, therefore, of high scientific and applied interest. The objectives of the current study were: (i) to identify an antagonist biophores (ii) to develop an arsenal of amphiphilic topically active PK/PBAN antagonists with an array of different time-release profiles based on the previously developed prototype analog; (iii) to develop rationally designed non-peptide SMLs based on the antagonist biophore determined in (i) and evaluate them in cloned receptor microplate binding assays and by pheromonotropic, melanotropic and pupariation in vivo assays. (iv) to clone PK/PBAN receptors (PK/PBAN-Rs) for further understanding of receptor-ligand interactions; (v) to develop microplate binding assays for screening the above SMLs. In the course of the granting period A series of amphiphilic PK/PBAN analogs based on a linear lead antagonist from the previous BARD grant was synthesized that incorporated a diverse array of hydrophobic groups (HR-Suc-A[dF]PRLa). Others were synthesized via the attachment of polyethylene glycol (PEG) polymers. A hydrophobic, biostablePK/PBAN/DH analog DH-2Abf-K prevented the onset of the protective state of diapause in H. zea pupae [EC50=7 pmol/larva] following injection into the preceding larval stage. It effectively induces the crop pest to commit a form of ‘ecological suicide’. Evaluation of a set of amphiphilic PK analogs with a diverse array of hydrophobic groups of the formula HR-Suc-FTPRLa led to the identification of analog T-63 (HR=Decyl) that increased the extent of diapause termination by a factor of 70% when applied topically to newly emerged pupae. Another biostablePK analog PK-Oic-1 featured anti-feedant and aphicidal properties that matched the potency of some commercial aphicides. Native PK showed no significant activity. The aphicidal effects were blocked by a new PEGylated PK antagonist analog PK-dF-PEG4, suggesting that the activity is mediated by a PK/PBAN receptor and therefore indicative of a novel and selective mode-of-action. Using a novel transPro mimetic motif (dihydroimidazole; ‘Jones’) developed in previous BARD-sponsored work, the first antagonist for the diapause hormone (DH), DH-Jo, was developed and shown to block over 50% of H. zea pupal diapause termination activity of native DH. This novel antagonist development strategy may be applicable to other invertebrate and vertebrate hormones that feature a transPro in the active core. The research identifies a critical component of the antagonist biophore for this PK/PBAN receptor subtype, i.e. a trans-oriented Pro. Additional work led to the molecular cloning and functional characterization of the DH receptor from H. zea, allowing for the discovery of three other DH antagonist analogs: Drosophila ETH, a β-AA analog, and a dF analog. The receptor experiments identified an agonist (DH-2Abf-dA) with a maximal response greater than native DH. ‘Deconvolution’ of a rationally-designed nonpeptide heterocyclic combinatorial library with a cyclic bis-guanidino (BG) scaffold led to discovery of several members that elicited activity in a pupariation acceleration assay, and one that also showed activity in an H. zea diapause termination assay, eliciting a maximal response of 90%. Molecular cloning and functional characterization of a CAP2b antidiuretic receptor from the kissing bug (R. prolixus) as well as the first CAP2b and PK receptors from a tick was also achieved. Notably, the PK/PBAN-like receptor from the cattle fever tick is unique among known PK/PBAN and CAP2b receptors in that it can interact with both ligand types, providing further evidence for an evolutionary relationship between these two NP families. In the course of the granting period we also managed to clone the PK/PBAN-R of H. peltigera, to express it and the S. littoralis-R Sf-9 cells and to evaluate their interaction with a variety of PK/PBAN ligands. In addition, three functional microplate assays in a HTS format have been developed: a cell-membrane competitive ligand binding assay; a Ca flux assay and a whole cell cAMP ELISA. The Ca flux assay has been used for receptor characterization due to its extremely high sensitivity. Computer homology studies were carried out to predict both receptor’s SAR and based on this analysis 8 mutants have been generated. The bioavailability of small linear antagonistic peptides has been evaluated and was found to be highly effective as sex pheromone biosynthesis inhibitors. The activity of 11 new amphiphilic analogs has also been evaluated. Unfortunately, due to a problem with the Heliothis moth colony we were unable to select those with pheromonotropic antagonistic activity and further check their bioavailability. Six peptides exhibited some melanotropic antagonistic activity but due to the low inhibitory effect the peptides were not further tested for bioavailability in S. littoralis larvae. Despite the fact that no new antagonistic peptides were discovered in the course of this granting period the results contribute to a better understanding of the interaction of the PK/PBAN family of Nps with their receptors, provided several HT assays for screening of libraries of various origin for presence of PK/PBAN-Ragonists and antagonists and provided important practical information for the further design of new, peptide-based insecticide prototypes aimed at the disruption of key neuroendocrine physiological functions in pest insects.
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