Skewed Factor Models Using Selection Mechanisms

Traditional factor models explicitly or implicitly assume that the factors follow a multivariate normal distribution; that is, only moments up to order two are involved. However, it may happen in real data problems that the first two moments cannot explain the factors. Based on this motivation, here we devise three new skewed factor models, the skew-normal, the skew-t, and the generalized skew-normal factor models depending on a selection mechanism on the factors. The ECME algorithms are adopted to estimate related parameters for statistical inference. Monte Carlo simulations validate our new models and we demonstrate the need for skewed factor models using the classic open/closed book exam scores dataset

Evolution of networks

We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of such a kind came into existence recently. This opens a wide field for the study of their topology, evolution, and complex processes occurring in them. Such networks possess a rich set of scaling properties. A number of them are scale-free and show striking resilience against random breakdowns. In spite of large sizes of these networks, the distances between most their vertices are short -- a feature known as the ``small-world'' effect. We discuss how growing networks self-organize into scale-free structures and the role of the mechanism of preferential linking. We consider the topological and structural properties of evolving networks, and percolation in these networks. We present a number of models demonstrating the main features of evolving networks and discuss current approaches for their simulation and analytical study. Applications of the general results to particular networks in Nature are discussed. We demonstrate the generic connections of the network growth processes with the general problems of non-equilibrium physics, econophysics, evolutionary biology, etc.Comment: 67 pages, updated, revised, and extended version of review, submitted to Adv. Phy

An investigation of multilevel refinement in routing and location problems

Multilevel refinement is a collaborative hierarchical solution technique. The multilevel technique aims to enhance the solution process of optimisation problems by improving the asymptotic convergence in the quality of solutions produced by its underlying local search heuristics and/or improving the convergence rate of these heuristics. To these aims, the central methodologies of the multilevel technique are filtering solutions from the search space (via coarsening), reducing the amount of problem detail considered at each level of the solution process and providing a mechanism to the underlying local search heuristics for efficiently making large moves around the search space. The neighbourhoods accessible by these moves are typically inaccessible if the local search heuristics are applied to the un-coarsened problems. The methodologies combine to meet the multilevel technique's aims, because, as the multilevel technique iteratively coarsens, extends and refines a given problem, it reduces the possibility of the local search heuristic becoming trapped in local optima of poor quality. The research presented in this thesis investigates the application of multilevel refinement to classes of location and routing problems and develops numerous multilevel algorithms. Some of these algorithms are collaborative techniques for metaheuristics and others are collaborative techniques for local search heuristics. Additionally, new methods of coarsening for location and routing problems and enhancements for the multilevel technique are developed. It is demonstrated that the multilevel technique is suited to a wide array of problems. By extending the investigations of the multilevel technique across routing and location problems, the research was able to present generalisations regarding the multilevel technique's suitability, for these and similar types of problems. Finally, results on a number of well known benchmarking suites for location and routing problem are presented, comparing equivalent single-level and multilevel algorithms. These results demonstrate that the multilevel technique provides significant gains over its single-level counterparts. In all cases, the multilevel algorithm was able to improve the asymptotic convergence in the quality of solutions produced by the standard (single-level) local search heuristics or metaheuristics. The multilevel technique did not improve the convergence rate of the single-level's local search heuristics in all cases. However, for large-scale problems the multilevel variants scaled in a manner superior to the single-level techniques. The research also demonstrated that for sufficiently large problems, the multilevel technique was able to improve the asymptotic convergence in the quality of solutions at a sufficiently fast rate, such that the multilevel algorithms were able to produce superior results compared to the single-level versions, without refining the solution down to the most detailed level

Role of physical and mental training in brain network configuration

Continuous remodeling of proteins of excitatory neurons is fine-tuning the scaling and strength of excitatory synapses up or down via regulation of intra-cellular metabolic and regulatory networks of the genome-transcriptome-proteome interface. Alzheimer's disease is a model of energy cost-driven small-world network disorder as the network global efficiency is impaired by the deposition of an informed agent, the amyloid-β, selectively targeting high-degree nodes. In schizophrenia, the interconnectivity and density of rich-club networks are significantly reduced. Training-induced homeostatic synaptogenesis-enhancement produces a reconfiguration of brain networks into greater small-worldness. Creation of synaptic connections in a macro-network, and, at the intra-cellular scale, micro-networks regulate the physiological mechanisms for the preferential attachment of synapses. The strongest molecular relationship of exercise and functional connectivity was identified for brain-derived neurotrophic factor (BDNF). The allele variant, rs7294919, also shows a powerful relationship with the hippocampal volume. How the brain achieves this unique quest of reconfiguration remains a puzzle. What are the underlying mechanisms of synaptogenesis promoting communications brain ↔ muscle and brain ↔ brain in such trainings? What is the respective role of independent mental, physical or combined-mental-physical trainings? Physical practice seems to be playing an instrumental role in the cognitive enhancement (brain ↔ muscle com.). However, mental training, meditation or virtual reality (films, games) require only minimal motor activity and cardio-respiratory stimulation. Therefore, other potential paths (brain ↔ brain com.) molding brain networks are nonetheless essential. Patients with motor neuron disease/injury (e.g. amyotrophic lateral sclerosis, traumatism) also achieve successful cognitive enhancement albeit they may only elicit mental practic

AccuSyn: Using Simulated Annealing to Declutter Genome Visualizations

We apply Simulated Annealing, a well-known metaheuristic for obtaining near-optimal solutions to optimization problems, to discover conserved synteny relations (similar features) in genomes. The analysis of synteny gives biologists insights into the evolutionary history of species and the functional relationships between genes. However, as even simple organisms have huge numbers of genomic features, syntenic plots initially present an enormous clutter of connections, making the structure difficult to understand. We address this problem by using Simulated Annealing to minimize link crossings. Our interactive web-based synteny browser, AccuSyn, visualizes syntenic relations with circular plots of chromosomes and draws links between similar blocks of genes. It also brings together a huge amount of genomic data by integrating an adjacent view and additional tracks, to visualize the details of the blocks and accompanying genomic data, respectively. Our work shows multiple ways to manually declutter a synteny plot and then thoroughly explains how we integrated Simulated Annealing, along with human interventions as a human-in-the-loop approach, to achieve an accurate representation of conserved synteny relations for any genome. The goal of AccuSyn was to make a fairly complete tool combining ideas from four major areas: genetics, information visualization, heuristic search, and human-in-the-loop. Our results contribute to a better understanding of synteny plots and show the potential that decluttering algorithms have for syntenic analysis, adding more clues for evolutionary development. At this writing, AccuSyn is already actively used in the research being done at the University of Saskatchewan and has already produced a visualization of the recently-sequenced Wheat genome

Optimizing parameters in fuzzy k-means for clustering microarray data.

Rapid advances of microarray technologies are making it possible to analyze and manipulate large amounts of gene expression data. Clustering algorithms, such as hierarchical clustering, self-organizing maps, k-means clustering and fuzzy k-means clustering, have become important tools for expression analysis of microarray data. However, the need of prior knowledge of the number of clusters, k, and the fuzziness parameter, b, limits the usage of fuzzy clustering. Few approaches have been proposed for assigning best possible values for such parameters. In this thesis, we use simulated annealing and fuzzy k-means clustering to determine the optimal parameters, namely the number of clusters, k, and the fuzziness parameter, b. To assess the performance of our method, we have used synthetic and real gene experiment data sets. To improve our approach, two methods, searching with Tabu List and Shrinking the scope of randomization, are applied. Our results show that a nearly-optimal pair of k and b can be obtained without exploring the entire search space.Dept. of Computer Science. Paper copy at Leddy Library: Theses & Major Papers - Basement, West Bldg. / Call Number: Thesis2005 .Y37. Source: Masters Abstracts International, Volume: 44-03, page: 1419. Thesis (M.Sc.)--University of Windsor (Canada), 2005

Estimation of Noisy Cost Functions by Conventional and Adjusted Simulated Annealing Techniques

L'algorithme de recuit simulé est largement utilisé dans la communauté d'optimisation pour résoudre divers types de problèmes, discrets et continus. L'objectif de cette thèse est d'analyser le recuit simulé dans des environnements déterministes et stochastiques pour des problèmes discrets. Les objectifs précis sont de classer des problèmes clés, d'offrir des suggestions et des recommandations à suivre en utilisant l'algorithme de recuit simulé et de recuit simulé sous bruit. Plus spécifiquement, des problèmes apparaissent en optimisation en présence de bruit, et sur la manière de le contrôler. Nous proposons la méthode de recuit simulé bruité (NSA: Noisy Simulated Annealing), basée sur la modification de l'algorithme de Metropolis-Hastings présentée par Ceperlay and Dewing, qui surpasse les techniques de recuit simulé analogues, délivrant des solutions numériques similaires, à coût réduit. Nous considérons les principales approches qui traitent le bruit dans le cadre du recuit simulé afin d'en extraire leurs attributs distinctifs et de produire une comparaison plus pertinente. Nous évaluons ensuite les performances numériques de l'approche sur des instances du problème du voyageur de commerce. Les résultats obtenus montrent un clair avantage pour le recuit simulé bruité, en présence de bruit.The Simulated Annealing (SA) algorithm is extensively used in the optimization community for solving various kinds of problems, discrete and continuous. This thesis aims to analyze SA in both deterministic and stochastic environments for discrete problems. Precise objectives are to classify key problems, offer suggestions and recommendations to be undertaken by using SA and Simulated Annealing Under Noise (SAUN). More specifically, problems appear in optimization due to the existence of noise when evaluating the objective function, and how to control this noise. We propose a method, called Noisy Simulated Annealing (NSA), based on the Metropolis-Hasting algorithm modification presented by Ceperlay and Dewing, that outperforms analogous SA techniques, delivering similar numerical solutions, at a reduced cost. We consider the main approaches in the SA setting that handle noise in order to extract their distinctive attributes and make the comparison more relevant. We next assess the numerical performance of the approach on traveling salesman problem instances. The outcomes of our tests show a clear advantage for NSA when solving different problems to get high-quality solutions in presence of noise

Trivial Excitation Energy Transfer to Carotenoids Is an Unlikely Mechanism for Non-photochemical Quenching in LHCII

Higher plants defend themselves from bursts of intense light via the mechanism of Non-Photochemical Quenching (NPQ). It involves the Photosystem II (PSII) antenna protein (LHCII) adopting a conformation that favors excitation quenching. In recent years several structural models have suggested that quenching proceeds via energy transfer to the optically forbidden and short-lived S(1) states of a carotenoid. It was proposed that this pathway was controlled by subtle changes in the relative orientation of a small number of pigments. However, quantum chemical calculations of S(1) properties are not trivial and therefore its energy, oscillator strength and lifetime are treated as rather loose parameters. Moreover, the models were based either on a single LHCII crystal structure or Molecular Dynamics (MD) trajectories about a single minimum. Here we try and address these limitations by parameterizing the vibronic structure and relaxation dynamics of lutein in terms of observable quantities, namely its linear absorption (LA), transient absorption (TA) and two-photon excitation (TPE) spectra. We also analyze a number of minima taken from an exhaustive meta-dynamical search of the LHCII free energy surface. We show that trivial, Coulomb-mediated energy transfer to S(1) is an unlikely quenching mechanism, with pigment movements insufficiently pronounced to switch the system between quenched and unquenched states. Modulation of S(1) energy level as a quenching switch is similarly unlikely. Moreover, the quenching predicted by previous models is possibly an artifact of quantum chemical over-estimation of S(1) oscillator strength and the real mechanism likely involves short-range interaction and/or non-trivial inter-molecular states

Extensions of sampling-based approaches to path planning in complex cost spaces: applications to robotics and structural biology

Planifier le chemin d’un robot dans un environnement complexe est un problème crucial en robotique. Les méthodes de planification probabilistes peuvent résoudre des problèmes complexes aussi bien en robotique, qu’en animation graphique, ou en biologie structurale. En général, ces méthodes produisent un chemin évitant les collisions, sans considérer sa qualité. Récemment, de nouvelles approches ont été créées pour générer des chemins de bonne qualité : en robotique, cela peut être le chemin le plus court ou qui maximise la sécurité ; en biologie, il s’agit du mouvement minimisant la variation énergétique moléculaire. Dans cette thèse, nous proposons plusieurs extensions de ces méthodes, pour améliorer leurs performances et leur permettre de résoudre des problèmes toujours plus difficiles. Les applications que nous présentons viennent de la robotique (inspection industrielle et manipulation aérienne) et de la biologie structurale (mouvement moléculaire et conformations stables). ABSTRACT : Planning a path for a robot in a complex environment is a crucial issue in robotics. So-called probabilistic algorithms for path planning are very successful at solving difficult problems and are applied in various domains, such as aerospace, computer animation, and structural biology. However, these methods have traditionally focused on finding paths avoiding collisions, without considering the quality of these paths. In recent years, new approaches have been developed to generate high-quality paths: in robotics, this can mean finding paths maximizing safety or control; in biology, this means finding motions minimizing the energy variation of a molecule. In this thesis, we propose several extensions of these methods to improve their performance and allow them to solve ever more difficult problems. The applications we present stem from robotics (industrial inspection and aerial manipulation) and structural biology (simulation of molecular motions and exploration of energy landscapes)