• Refine Query
  • Source
  • Publication year
  • to
  • Language
  • 32
  • 12
  • 3
  • 3
  • 2
  • 2
  • 1
  • 1
  • 1
  • Tagged with
  • 67
  • 20
  • 18
  • 17
  • 13
  • 13
  • 9
  • 9
  • 9
  • 9
  • 8
  • 8
  • 6
  • 6
  • 6
  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
21

Parsimony and Quantum Mechanics: An Analysis of the Copenhagen and Bohmian Interpretations

Voorhis, Jhenna 20 April 2012 (has links)
Parsimony, sometime referred to as simplicity, is an effective criterion of theory choice in the case of Quantum Mechanics. The Copenhagen and Bohmian interpretations are rival theories, with the Bohmian interpretation being more parsimonious. More parsimonious theories have a higher probability of being true than less parsimonious rivals. The Bohmian interpretation should thus be preferred on these grounds.
22

Developing Parsimonious and Efficient Algorithms for Water Resources Optimization Problems

Asadzadeh Esfahani, Masoud 13 November 2012 (has links)
In the current water resources scientific literature, a wide variety of engineering design problems are solved in a simulation-optimization framework. These problems can have single or multiple objective functions and their decision variables can have discrete or continuous values. The majority of current literature in the field of water resources systems optimization report using heuristic global optimization algorithms, including evolutionary algorithms, with great success. These algorithms have multiple parameters that control their behavior both in terms of computational efficiency and the ability to find near globally optimal solutions. Values of these parameters are generally obtained by trial and error and are case study dependent. On the other hand, water resources simulation-optimization problems often have computationally intensive simulation models that can require seconds to hours for a single simulation. Furthermore, analysts may have limited computational budget to solve these problems, as such, the analyst may not be able to spend some of the computational budget to fine-tune the algorithm settings and parameter values. So, in general, algorithm parsimony in the number of parameters is an important factor in the applicability and performance of optimization algorithms for solving computationally intensive problems. A major contribution of this thesis is the development of a highly efficient, single objective, parsimonious optimization algorithm for solving problems with discrete decision variables. The algorithm is called Hybrid Discrete Dynamically Dimensioned Search, HD-DDS, and is designed based on Dynamically Dimensioned Search (DDS) that was developed by Tolson and Shoemaker (2007) for solving single objective hydrologic model calibration problems with continuous decision variables. The motivation for developing HD-DDS comes from the parsimony and high performance of original version of DDS. Similar to DDS, HD-DDS has a single parameter with a robust default value. HD-DDS is successfully applied to several benchmark water distribution system design problems where decision variables are pipe sizes among the available pipe size options. Results show that HD-DDS exhibits superior performance in specific comparisons to state-of-the-art optimization algorithms. The parsimony and efficiency of the original and discrete versions of DDS and their successful application to single objective water resources optimization problems with discrete and continuous decision variables motivated the development of a multi-objective optimization algorithm based on DDS. This algorithm is called Pareto Archived Dynamically Dimensioned Search (PA-DDS). The algorithm parsimony is a major factor in the design of PA-DDS. PA-DDS has a single parameter from its search engine DDS. In each iteration, PA-DDS selects one archived non-dominated solution and perturbs it to search for new solutions. The solution perturbation scheme of PA-DDS is similar to the original and discrete versions of DDS depending on whether the decision variable is discrete or continuous. So, PA-DDS can handle both types of decision variables. PA-DDS is applied to several benchmark mathematical problems, water distribution system design problems, and water resources model calibration problems with great success. It is shown that hypervolume contribution, HVC1, as defined in Knowles et al. (2003) is the superior selection metric for PA-DDS when solving multi-objective optimization problems with Pareto fronts that have a general (unknown) shape. However, one of the main contributions of this thesis is the development of a selection metric specifically designed for solving multi-objective optimization problems with a known or expected convex Pareto front such as water resources model calibration problems. The selection metric is called convex hull contribution (CHC) and makes the optimization algorithm sample solely from a subset of archived solutions that form the convex approximation of the Pareto front. Although CHC is generally applicable to any stochastic search optimization algorithm, it is applied to PA-DDS for solving six water resources calibration case studies with two or three objective functions. These case studies are solved by PA-DDS with CHC and HVC1 selections using 1,000 solution evaluations and by PA-DDS with CHC selection and two popular multi-objective optimization algorithms, AMALGAM and ε-NSGAII, using 10,000 solution evaluations. Results are compared based on the best case and worst case performances (out of multiple optimization trials) from each algorithm to measure the expected performance range for each algorithm. Comparing the best case performance of these algorithms shows that, PA-DDS with CHC selection using 1,000 solution evaluations perform very well in five out of six case studies. Comparing the worst case performance of the algorithms shows that with 1,000 solution evaluations, PA-DDS with CHC selection perform well in four out of six case studies. Furthermore, PA-DDS with CHC selection using 10,000 solution evaluations perform comparable to AMALGAM and ε-NSGAII. Therefore, it is concluded that PA-DDS with CHC selection is a powerful optimization algorithm for finding high quality solutions of multi-objective water resources model calibration problems with convex Pareto front especially when the computational budget is limited.
23

A Phylogenetic Appraisal of Pachycormus bollensis: Implications for Pachycormiform Evolution

Lindkvist, Maria January 2012 (has links)
The Pachycormiformes were a successful group of stem-teleosts. Although they persisted for more than 100 million years in the Mesozoic seas and occupied a significant space of the ecosystem, little is known about this most diverse group. One of the earliest pachycormiformes is the lower Jurassic Pachycormus bollensis. A reconstruction of the phylogeny with the early P. bollensis together with more derived and earlier studied species has yielded important information about the relationships within the group. Both a parsimony analysis and a Bayesian analysis were performed. Three exceptionally complete specimens of P. bollensis from the Holzmaden-locality were used for the study. The resulting trees strongly supported pachycormiform monophyly. Three major ecomorphological clades were returned from the analyses: the filter-feeders, hyper carnivores and a more generalist predator radiation that included P. bollensis. Despite, node support within the pachycormiformes are generally weak. The tooth-structure and the phylogenetic position of P. bollensis might indicate an intermediate grade between the filter-feeders and the hyper carnivores. / Pachycormiformer var en mycket framgångsrik ordning utav stam-teleoster. Trots att de överlevde i mer än 100 miljoner år i de Mesosoiska haven och erövrat ett flertal olika platser i ekosystemet, är denna mågfacetterade grupp som helhet tämligen okänd. Pachycormus bollensis från yngre jura är en av de tidigste arterna i denna grupp. En fylogenetiskt rekonstruktion av den tidiga P. bollensis tillsammans med yngre, mer utvecklade arter kan ge viktig information om släktskapen inom gruppen. En parsimonisk analys och en Bayesian analys utfördes. Tre exceptionellt bevarade exemplar av Pachycormus bollensis från Holzmaden användes i studien. Resultatet visar på ett stark monofyletiskt sammanband inom pachycormiformerna. Båda analyserna visade robusta resultat för tre övergripande grupper; filtrerare, karnivorer och en mer generell predator linje som inkluderar P.  bollensis. Dock hade de interna släktskapen inom varje större grupp svagt stöd. Tand-stukturen tillsammans med den fylogenetiska placeringen av P. bollensis kan tyda på en intermediär grupp mellan filterarna och karnivorerna.
24

Developing Parsimonious and Efficient Algorithms for Water Resources Optimization Problems

Asadzadeh Esfahani, Masoud 13 November 2012 (has links)
In the current water resources scientific literature, a wide variety of engineering design problems are solved in a simulation-optimization framework. These problems can have single or multiple objective functions and their decision variables can have discrete or continuous values. The majority of current literature in the field of water resources systems optimization report using heuristic global optimization algorithms, including evolutionary algorithms, with great success. These algorithms have multiple parameters that control their behavior both in terms of computational efficiency and the ability to find near globally optimal solutions. Values of these parameters are generally obtained by trial and error and are case study dependent. On the other hand, water resources simulation-optimization problems often have computationally intensive simulation models that can require seconds to hours for a single simulation. Furthermore, analysts may have limited computational budget to solve these problems, as such, the analyst may not be able to spend some of the computational budget to fine-tune the algorithm settings and parameter values. So, in general, algorithm parsimony in the number of parameters is an important factor in the applicability and performance of optimization algorithms for solving computationally intensive problems. A major contribution of this thesis is the development of a highly efficient, single objective, parsimonious optimization algorithm for solving problems with discrete decision variables. The algorithm is called Hybrid Discrete Dynamically Dimensioned Search, HD-DDS, and is designed based on Dynamically Dimensioned Search (DDS) that was developed by Tolson and Shoemaker (2007) for solving single objective hydrologic model calibration problems with continuous decision variables. The motivation for developing HD-DDS comes from the parsimony and high performance of original version of DDS. Similar to DDS, HD-DDS has a single parameter with a robust default value. HD-DDS is successfully applied to several benchmark water distribution system design problems where decision variables are pipe sizes among the available pipe size options. Results show that HD-DDS exhibits superior performance in specific comparisons to state-of-the-art optimization algorithms. The parsimony and efficiency of the original and discrete versions of DDS and their successful application to single objective water resources optimization problems with discrete and continuous decision variables motivated the development of a multi-objective optimization algorithm based on DDS. This algorithm is called Pareto Archived Dynamically Dimensioned Search (PA-DDS). The algorithm parsimony is a major factor in the design of PA-DDS. PA-DDS has a single parameter from its search engine DDS. In each iteration, PA-DDS selects one archived non-dominated solution and perturbs it to search for new solutions. The solution perturbation scheme of PA-DDS is similar to the original and discrete versions of DDS depending on whether the decision variable is discrete or continuous. So, PA-DDS can handle both types of decision variables. PA-DDS is applied to several benchmark mathematical problems, water distribution system design problems, and water resources model calibration problems with great success. It is shown that hypervolume contribution, HVC1, as defined in Knowles et al. (2003) is the superior selection metric for PA-DDS when solving multi-objective optimization problems with Pareto fronts that have a general (unknown) shape. However, one of the main contributions of this thesis is the development of a selection metric specifically designed for solving multi-objective optimization problems with a known or expected convex Pareto front such as water resources model calibration problems. The selection metric is called convex hull contribution (CHC) and makes the optimization algorithm sample solely from a subset of archived solutions that form the convex approximation of the Pareto front. Although CHC is generally applicable to any stochastic search optimization algorithm, it is applied to PA-DDS for solving six water resources calibration case studies with two or three objective functions. These case studies are solved by PA-DDS with CHC and HVC1 selections using 1,000 solution evaluations and by PA-DDS with CHC selection and two popular multi-objective optimization algorithms, AMALGAM and ε-NSGAII, using 10,000 solution evaluations. Results are compared based on the best case and worst case performances (out of multiple optimization trials) from each algorithm to measure the expected performance range for each algorithm. Comparing the best case performance of these algorithms shows that, PA-DDS with CHC selection using 1,000 solution evaluations perform very well in five out of six case studies. Comparing the worst case performance of the algorithms shows that with 1,000 solution evaluations, PA-DDS with CHC selection perform well in four out of six case studies. Furthermore, PA-DDS with CHC selection using 10,000 solution evaluations perform comparable to AMALGAM and ε-NSGAII. Therefore, it is concluded that PA-DDS with CHC selection is a powerful optimization algorithm for finding high quality solutions of multi-objective water resources model calibration problems with convex Pareto front especially when the computational budget is limited.
25

Biogeografia e sistemática dos peixes aulopiformes / Biogeography and systematics of aulopiformes fishes

Hilda Maria Andrade da Silva 08 April 2011 (has links)
Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro / Os Aulopiformes são peixes marinhos com amplitude temporal do Eocretáceo ao Recente. Os táxons fósseis são encontrados em depósitos sedimentares das Américas do Sul e do Norte, Europa, Ásia e África. Os representantes viventes podem ser encontrados desde águas rasas costeiras, estuários, até profundidades abissais, excedendo 3.000 m. Os limites do grupo, suas intra e inter-relações são objeto de muitos estudos. O objetivo central desta tese é aplicar métodos de Biogeografia Histórica como Panbiogeografia e a Análise de Parcimônia de Endemismos aos peixes Aulopiformes. Adicionalmente, foi realizada a análise filogenética dos Aulopiformes. Como resultado foram obtidos: 21 traços generalizados de Synodontoidei, 28 de Chlorophthalmoidei, 3 de Giganturoidei e 7 de Enchodontoidei. O clado Synodontoidei apresenta um padrão de distribuição primordialmente em águas tropicais e subtropicais, associado à borda de placas tectônicas e ao tipo de substrato. O clado Chlorophthalmoidei apresenta padrões de distribuição associados a cadeias de montanhas submarinas e corais de profundidade. O clado Giganturoidei possui uma distribuição vicariante com a família Giganturidae ocupando águas mais quentes e Bathysauridae as regiões mais frias. O clado Enchodontoidei foi associado a recifes de coral e zonas de ressurgência pretéritos. Adicionalmente, foi analisada uma matriz de dados com 84 táxons e 105 caracteres morfológicos não ordenados e sem pesagem a priori. Como resultado foram obtidas sete árvores igualmente parcimoniosas com 1214 passos, índice de consistência de 0,1129 e índice de retenção de 0,4970. A ordem Aulopiformes não constituiu um grupo monofilético, com as famílias Chlorophthalmidae, Notosudidae, Synodontidae, Paraulopidae, Pseudotrichonotidae e Ipnopidae mais proximamente relacionados ao Myctophidea que aos Alepisauroidei. Assim a partir da combinação dos resultados alcançados conclui-se que a Biogeografia Histórica funcionou como uma ferramenta na identificação dos problemas taxonômicos dos Aulopiformes e a sua análise filogenética permitiu identificar controvérsias sistemáticas, indicando que são necessários maiores estudos sobre a anatomia dos aulopiformes, a fim de esclarecer suas inter-relações. / The Aulopiformes are marine fishes ranging from Early Cretaceous to Recent. Fossil taxa are found in sediments from South and North America, Europe, Asia and Africa. The living forms can be found from shallow coastal estuaries, to the abyssal depths, exceeding 3,000 m. Interrelationships among this group are subject of many studies. The aim of these studies is to apply historical biogeography methods as Panbiogeography and Parsimony Analysis of Endemicity to Aulopiformes fishes. Additionally, were performed a phylogenetic analysis of this taxon. As a result were obtained: 21 generalized tracks from Synodontoidei; 28, Chlorophthalmoidei; 3, Giganturoidei and 7 to Enchodontoidei. Synodontoidei shows a pattern of distribution primarily in tropical and subtropical regions, associated with the edge of tectonic plates and the substrate. Chlorophthalmoidei distributions are linked to chains of seamounts and deep water corals. Giganturoidei is a vicariant, group with Giganturidae occupying warmer waters and Bathysauridae colder regions. Enchodontoidei was associated with coral reefs and upwelling areas on past. Additionally, we analyzed a data matrix with 84 taxa and 105 morphological characters unordered and without a priori weighting. Results obtained with seven equally parsimonious trees with 1214 steps, consistency index of 0.1129 and retention index of 0.4970. The order Aulopiformes did not constitute a monophyletic group, with the families Chlorophthalmidae, Notosudidae, Synodontidae, Paraulopidae, Pseudotrichonotidae and Ipnopidae more closely related to Myctophidea than Alepisauroidei. From the composite of results it is concluded that the Historical Biogeography functioned as a tool to identifying taxonomic problems and its phylogenetic analysis recognized systematics disagreements, showing that more studies are required on Aulopiformess anatomy in order to clarify their interrelationships.
26

Biogeografia e sistemática dos peixes aulopiformes / Biogeography and systematics of aulopiformes fishes

Hilda Maria Andrade da Silva 08 April 2011 (has links)
Fundação de Amparo à Pesquisa do Estado do Rio de Janeiro / Os Aulopiformes são peixes marinhos com amplitude temporal do Eocretáceo ao Recente. Os táxons fósseis são encontrados em depósitos sedimentares das Américas do Sul e do Norte, Europa, Ásia e África. Os representantes viventes podem ser encontrados desde águas rasas costeiras, estuários, até profundidades abissais, excedendo 3.000 m. Os limites do grupo, suas intra e inter-relações são objeto de muitos estudos. O objetivo central desta tese é aplicar métodos de Biogeografia Histórica como Panbiogeografia e a Análise de Parcimônia de Endemismos aos peixes Aulopiformes. Adicionalmente, foi realizada a análise filogenética dos Aulopiformes. Como resultado foram obtidos: 21 traços generalizados de Synodontoidei, 28 de Chlorophthalmoidei, 3 de Giganturoidei e 7 de Enchodontoidei. O clado Synodontoidei apresenta um padrão de distribuição primordialmente em águas tropicais e subtropicais, associado à borda de placas tectônicas e ao tipo de substrato. O clado Chlorophthalmoidei apresenta padrões de distribuição associados a cadeias de montanhas submarinas e corais de profundidade. O clado Giganturoidei possui uma distribuição vicariante com a família Giganturidae ocupando águas mais quentes e Bathysauridae as regiões mais frias. O clado Enchodontoidei foi associado a recifes de coral e zonas de ressurgência pretéritos. Adicionalmente, foi analisada uma matriz de dados com 84 táxons e 105 caracteres morfológicos não ordenados e sem pesagem a priori. Como resultado foram obtidas sete árvores igualmente parcimoniosas com 1214 passos, índice de consistência de 0,1129 e índice de retenção de 0,4970. A ordem Aulopiformes não constituiu um grupo monofilético, com as famílias Chlorophthalmidae, Notosudidae, Synodontidae, Paraulopidae, Pseudotrichonotidae e Ipnopidae mais proximamente relacionados ao Myctophidea que aos Alepisauroidei. Assim a partir da combinação dos resultados alcançados conclui-se que a Biogeografia Histórica funcionou como uma ferramenta na identificação dos problemas taxonômicos dos Aulopiformes e a sua análise filogenética permitiu identificar controvérsias sistemáticas, indicando que são necessários maiores estudos sobre a anatomia dos aulopiformes, a fim de esclarecer suas inter-relações. / The Aulopiformes are marine fishes ranging from Early Cretaceous to Recent. Fossil taxa are found in sediments from South and North America, Europe, Asia and Africa. The living forms can be found from shallow coastal estuaries, to the abyssal depths, exceeding 3,000 m. Interrelationships among this group are subject of many studies. The aim of these studies is to apply historical biogeography methods as Panbiogeography and Parsimony Analysis of Endemicity to Aulopiformes fishes. Additionally, were performed a phylogenetic analysis of this taxon. As a result were obtained: 21 generalized tracks from Synodontoidei; 28, Chlorophthalmoidei; 3, Giganturoidei and 7 to Enchodontoidei. Synodontoidei shows a pattern of distribution primarily in tropical and subtropical regions, associated with the edge of tectonic plates and the substrate. Chlorophthalmoidei distributions are linked to chains of seamounts and deep water corals. Giganturoidei is a vicariant, group with Giganturidae occupying warmer waters and Bathysauridae colder regions. Enchodontoidei was associated with coral reefs and upwelling areas on past. Additionally, we analyzed a data matrix with 84 taxa and 105 morphological characters unordered and without a priori weighting. Results obtained with seven equally parsimonious trees with 1214 steps, consistency index of 0.1129 and retention index of 0.4970. The order Aulopiformes did not constitute a monophyletic group, with the families Chlorophthalmidae, Notosudidae, Synodontidae, Paraulopidae, Pseudotrichonotidae and Ipnopidae more closely related to Myctophidea than Alepisauroidei. From the composite of results it is concluded that the Historical Biogeography functioned as a tool to identifying taxonomic problems and its phylogenetic analysis recognized systematics disagreements, showing that more studies are required on Aulopiformess anatomy in order to clarify their interrelationships.
27

Advanced methods to solve the maximum parsimony problem / Méthodes avancées pour la résolution du problème de maximum parcimonie

Vazquez ortiz, Karla Esmeralda 14 June 2016 (has links)
La reconstruction phylogénétique est considérée comme un élément central de divers domaines comme l’écologie, la biologie et la physiologie moléculaire pour lesquels les relations généalogiques entre séquences d’espèces ou de gènes, représentées sous forme d’arbres, peuvent apporter des éclairages significatifs à la compréhension de phénomènes biologiques. Le problème de Maximum de Parcimonie est une approche importante pour résoudre la reconstruction phylogénétique en se basant sur un critère d’optimalité pour lequel l’arbre comprenant le moins de mutations est préféré. Dans cette thèse nous proposons différentes méthodes pour s’attaquer à la nature combinatoire de ce problème NP-complet. Premièrement, nous présentons un algorithme de Recuit Simulé compétitif qui nous a permis de trouver des solutions de meilleure qualité pour un ensemble de problèmes. Deuxièmement, nous proposons une nouvelle technique de Path-Relinking qui semble intéressante pour comparer des arbres mais pas pour trouver des solutions de meilleure qualité. Troisièmement, nous donnons le code d’une implantation sur GPU de la fonction objectif dont l’intérêt est de réduire le temps d’exécution de la recherche pour des instances dont la longueur des séquences est importante. Finalement, nous introduisons un prédicteur capable d’estimer le score optimum pour un vaste ensemble d’instances avec une très grande précision. / Phylogenetic reconstruction is considered a central underpinning of diverse fields like ecology, molecular biology and physiology where genealogical relationships of species or gene sequences represented as trees can provide the most meaningful insights into biology. Maximum Parsimony (MP) is an important approach to solve the phylogenetic reconstruction based on an optimality criterion under which the tree that minimizes the total number of genetic transformations is preferred. In this thesis we propose different methods to cope with the combinatorial nature of this NP-complete problem. First we present a competitive Simulated Annealing algorithm which helped us find trees of better parsimony score than the ones that were known for a set of instances. Second, we propose a Path-Relinking technique that appears to be suitable for tree comparison but not for finding trees of better quality. Third, we give a GPU implementation of the objective function of the problem that can reduce the runtime for instances that have an important number of residues per taxon. Finally, we introduce a predictor that is able to estimate the best parsimony score of a huge set of instances with a high accuracy.
28

New Perspectives on the Paradox of Participation : A Theoretical Evaluation of Rational Choice Theory as it Applies to Political Participation

Stendahl, Elin January 2020 (has links)
Theory is vital for our scientific understanding of the social world. Building, developing, and evaluating theory are therefore central practices within the social sciences. This study performs an evaluation of rational choice theory within the field of political participation. This is a theoretical framework that has had significant problems reconciling theoretical prediction with empirical findings, causing what is called the paradox of participation. For more than sixty years rational choice theorists have tried to develop new formulations of the theory to avoid this paradox. The purpose of this study is to forward this debate by providing a new perspective on rational choice theory that is purely theoretical. Using the evaluative criteria of falsifiability and leverage, the study finds that a theory using both collective and selective incentives, while also allowing the formulation of the theory to change depending on the form of political participation one wants to explain provides the most promising approach. However, the evaluation does reveal some issues in connection to selective incentives. A potential alternative solution to the paradox is therefore briefly discussed, yet a more thorough exploration of this venue is left to future research.
29

Nonparametric Bayesian Clustering under Structural Restrictions

Hanxi Sun (11009154) 23 July 2021 (has links)
<div>Model-based clustering, with its flexibility and solid statistical foundations, is an important tool for unsupervised learning, and has numerous applications in a variety of fields. This dissertation focuses on nonparametric Bayesian approaches to model-based clustering under structural restrictions. These are additional constraints on the model that embody prior knowledge, either to regularize the model structure to encourage interpretability and parsimony or to encourage statistical sharing through underlying tree or network structure.</div><div><br></div><div>The first part in the dissertation focuses on the most commonly used model-based clustering models, mixture models. Current approaches typically model the parameters of the mixture components as independent variables, which can lead to overfitting that produces poorly separated clusters, and can also be sensitive to model misspecification. To address this problem, we propose a novel Bayesian mixture model with the structural restriction being that the clusters repel each other.The repulsion is induced by the generalized Matérn type-III repulsive point process. We derive an efficient Markov chain Monte Carlo (MCMC) algorithm for posterior inference, and demonstrate its utility on a number of synthetic and real-world problems. <br></div><div><br></div><div>The second part of the dissertation focuses on clustering populations with a hierarchical dependency structure that can be described by a tree. A classic example of such problems, which is also the focus of our work, is the phylogenetic tree with nodes often representing biological species. The structure of this problem refers to the hierarchical structure of the populations. Clustering of the populations in this problem is equivalent to identify branches in the tree where the populations at the parent and child node have significantly different distributions. We construct a nonparametric Bayesian model based on hierarchical Pitman-Yor and Poisson processes to exploit this, and develop an efficient particle MCMC algorithm to address this problem. We illustrate the efficacy of our proposed approach on both synthetic and real-world problems.</div>
30

Escape from Parsimony of Different Models of Genome Evolution Processes

Meghdari Miardan, Mona 09 March 2022 (has links)
In the course of evolution, genomes diverge from their ancestors either via global mutations and by rearrangement of their chromosomal segments, or through local mutations within their genes. In this thesis (Chapters: 2, 3 and 4) we analyze the evolution of genomes based on different rearrangement operations including: in Chapter 2 both restricted and unrestricted double-cut-and-join (DCJ) operations, in Chapter 3 both internal and general reversal and translocation (IRT and HP, respectively) operations, and in Chapter 4 translocation, weighted reversal (WR) and maximum length reversal (MLR) operations. Based on the rearrangement operation chosen we can model the evolution of genomes as a discrete or continuous-time Markov chain process on the space of signed genomes. For each model of evolution, we study the stochastic process by investigating the time up to which the difference between the number of operations along the evolutionary trajectory and the edit distance of the genome from its ancestor is negligible, as soon as these two values starts diverging drastically from one another we say the process escapes from parsimony. One of the major parameters in the known edit distance formulas between any two genomes (such as reversal, DCJ, IRT, HP and translocation) is the number of cycles in their breakpoint graph. For DCJ, IRT and HP models by adopting the method elaborated by Berestycki and Durret, we estimate the number of cycles in the breakpoint graph of the genome at time t and its ancestor by the number of tree components of the random graph constructed from the model of evolution at time t, which is an Erdös-Rényi. We also proved that for each of the DCJ, IRT and HP models of evolution, the process on a genome of size n is bound to its parsimonious estimate up to t ≈ n/2 steps. Since the random graph constructed from the models of evolution for the translocation, WR and MLR processes are not Erdös-Rényi, the proofs of their parsimony- bound require more advanced mathematical tools, however our simulation shows for the translocation, two types of WR, and MLR (except for reversals with very short maximum length) models, the escape from parsimony do not occur before n/2 steps, where n is the number of genes in the genome. A basic result in this field is due to Berestycki and Durrett, from 2006, who found that a random transposition (pairwise exchange of the elements in the corresponding permutation of the genome) evolves along its parsimonious path of evolution up to n/2 steps, where n is the number of the genes. Although, this transposition model is applicable solely for evolution of a unichromosomal ancestor which remains unichromosomal at each step t of the process; however for the DCJ, IRT, HP and translocation models the genomes are multichromosomal which increases the difficulty of the problem at hand. The models studied in Chapters 2 - 4 are all based on signed permutation representations of genomes, where each "gene" occurs exactly once, with either positive or negative polarity. The same genes occur in all the genomes being considered. There is no distinction between the same gene in two different genomes. In Chapter 5 we generalize our representation to genes that may have several copies of a gene, which differ only by a few point mutations. This leads to problems of identifying copies in two genomes that are primary orthologs, under the assumptions of differentials in point mutation rate. We provide algorithms, software and test examples.

Page generated in 0.49 seconds