The Footprint Sorting Problem

Phylogenetic footprints are short pieces of noncoding DNA sequence in the vicinity of a gene that are conserved between evolutionary distant species. A seemingly simple problem is to sort footprints in their order along the genomes. It is complicated by the fact that not all footprints are collinear:  they may cross each other. The problem thus becomes the identification of the crossing footprints, the sorting of the remaining collinear cliques, and finally the insertion of the noncollinear ones at “reasonable” positions. We show that solving the footprint sorting problem requires the solution of the “Minimum Weight Vertex Feedback Set Problem”, which is known to be NP-complete and APX-hard. Nevertheless good approximations can be obtained for data sets of interest. The remaining steps of the sorting process are straightforward:  computation of the transitive closure of an acyclic graph, linear extension of the resulting partial order, and finally sorting w.r.t. the linear extension. Alternatively, the footprint sorting problem can be rephrased as a combinatorial optimization problem for which approximate solutions can be obtained by means of general purpose heuristics. Footprint sortings obtained with different methods can be compared using a version of multiple sequence alignment that allows the identification of unambiguously ordered sublists. As an application we show that the rat has a slighly increased insertion/deletion rate in comparison to the mouse genome

Clustering by compression

We present a new method for clustering based on compression. The method doesn't use subject-specific features or background knowledge, and works as follows: First, we determine a universal similarity distance, the normalized compression distance or NCD, computed from the lengths of compressed data files (singly and in pairwise concatenation). Second, we apply a hierarchical clustering method. The NCD is universal in that it is not restricted to a specific application area, and works across application area boundaries. A theoretical precursor, the normalized information distance, co-developed by one of the authors, is provably optimal but uses the non-computable notion of Kolmogorov complexity. We propose precise notions of similarity metric, normal compressor, and show that the NCD based on a normal compressor is a similarity metric that approximates universality. To extract a hierarchy of clusters from the distance matrix, we determine a dendrogram (binary tree) by a new quartet method and a fast heuristic to implement it. The method is implemented and available as public software, and is robust under choice of different compressors. To substantiate our claims of universality and robustness, we report evidence of successful application in areas as diverse as genomics, virology, languages, literature, music, handwritten digits, astronomy, and combinations of objects from completely different domains, using statistical, dictionary, and block sorting compressors. In genomics we presented new evidence for major questions in Mammalian evolution, based on whole-mitochondrial genomic analysis: the Eutherian orders and the Marsupionta hypothesis against the Theria hypothesis.Comment: LaTeX, 27 pages, 20 figure

Development of Imaging Fourier-Transform Spectroscopy for the Characterization of Turbulent Jet Flames

Recent advances in computational models to simulate turbulent, reactive flow fields have outpaced the ability to collect highly constraining data--throughout the entire flow field--for validating and improving such models. In particular, the ability to quantify in three dimensions both the mean scalar fields (i.e. temperature & species concentrations) and their respective fluctuation statistics via hyperspectral imaging would be a game-changing advancement in combustion diagnostics, with high impact in both validation and improvement efforts for computational combustion models. This research effort establishes imaging Fourier-transform spectrometry (IFTS) as a valuable tool (which complements laser diagnostics) for the study of turbulent combustion. Specifically, this effort (1) demonstrates that IFTS can be used to quantitatively measure spatially resolved spectra from a canonical turbulent flame; (2) establishes the utility of quantile spectra in first-ever quantitative comparisons between measured and modeled turbulent radiation interaction (TRI); (3) develops a simple onion-peeling-like spectral inversion methodology suitable for estimating radial scalar distributions in axisymmetric, optically-thick flames; (4) builds understanding of quantile spectra and demonstrates proof of concept for their use in estimating scalar fluctuation statistics

The development and application of metaheuristics for problems in graph theory: A computational study

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.It is known that graph theoretic models have extensive application to real-life discrete optimization problems. Many of these models are NP-hard and, as a result, exact methods may be impractical for large scale problem instances. Consequently, there is a great interest in developing e±cient approximate methods that yield near-optimal solutions in acceptable computational times. A class of such methods, known as metaheuristics, have been proposed with success. This thesis considers some recently proposed NP-hard combinatorial optimization problems formulated on graphs. In particular, the min- imum labelling spanning tree problem, the minimum labelling Steiner tree problem, and the minimum quartet tree cost problem, are inves- tigated. Several metaheuristics are proposed for each problem, from classical approximation algorithms to novel approaches. A compre- hensive computational investigation in which the proposed methods are compared with other algorithms recommended in the literature is reported. The results show that the proposed metaheuristics outper- form the algorithms recommended in the literature, obtaining optimal or near-optimal solutions in short computational running times. In addition, a thorough analysis of the implementation of these methods provide insights for the implementation of metaheuristic strategies for other graph theoretic problems

Problemas de asignación de recursos humanos a través del problema de asignación multidimensional

149 páginas. Doctorado en Optimización.El problema de asignación de personal aparece en diversas industrias. La asignación eficiente de personal a trabajos, proyectos, herramientas, horarios, entre otros, tiene un impacto directo en términos monetarios para el negocio. El problema de asignación multidimensional (PAM) es la extensión natural del problema de asignación y puede ser utilizado en aplicaciones donde se requiere la asignación de personal. El caso más estudiado de PAM es el problema de asignación en tres dimensiones, sin embargo en años recientes han sido propuestas algunas heurísticas de búsqueda local y algoritmos meméticos para el caso general. En este trabajo de tesis se realiza un estudio profundo de PAM comenzando con un resumen del estado del arte de algoritmos, heurísticas y metaheurísticas para su resolución. Se describen algunos algoritmos y se propone uno nuevo que resuelve instancias de tamaño medio para PAM. Se propone la generalización de las conocidas heurísticas de variación de dimensión como una búsqueda local generalizada que proporciona un nuevo estado del arte de búsquedas locales para PAM. Adicionalmente, se propone un algoritmo memético con una estructura sencilla pero efectiva y que es competitivo con el mejor algoritmo memético conocido para PAM. Finalmente, se presenta un caso particular de problema de asignación de personal: el Problema de Asignación de Horarios (PAH). El PAH considera la asignación de personal a uno, dos o más conjuntos de objetos, por ejemplo puede ser requerida la asignación de profesores a cursos a periodos de tiempo a salones, para determinados grupos de estudiantes. Primero, se presenta el PAH así como una breve descripción de su estado del arte. Luego, se propone una nueva forma de modelar este problema a través de la resolución de PAM y se aplica sobre el PAH en la Universidad Autónoma Metropolitana, unidad Azcapotzalco (UAM-A). Se describen las consideraciones particulares del PAH en la UAM-A y proponemos una nueva solución para éste. Nuestra solución se basa en la resolución de múltiples PA3 a través de los algoritmos y heurísticas propuestos.Personnel assignment problems appear in several industries. The e cient assignment of personnel to jobs, projects, tools, time slots, etcetera, has a direct impact in terms monetary for the business. The Multidimensional Assignment Problem (MAP) is a natural extension of the well-known assignment problem and can be used on applications where the assignment of personnel is required. The most studied case of the MAP is the three dimensional assignment problem, though in recent years some local search heuristics and memetic algorithms have been proposed for the general case. Let X1; : : : ;Xs be a collection of s 3 disjoint sets, consider all combinations that belong to the Cartesian product X = X1 Xs such that each vector x 2 X, where x = (x1; : : : ; xs) with xi 2 Xi 8 1 i s, has associated a weight w(x). A feasible assignment is a collection A = (x1; : : : ; xn) of n vectors if xi k 6= xj k for each i 6= j and 1 k s. The weight of an assignment A is given by w(A) = Pn i=1 w(xi). A MAP in s dimensions is denoted as sAP. The objective of sAP is to nd an assignment of minimal weight. In this thesis we make an in depth study of MAP beginning with the state-ofthe- art algorithms, heuristics, and metaheuristics for solving it. We describe some algorithms and we propose a new one for solving optimally medium size instances of MAP. We propose the generalization of the called dimensionwise variation heuristics for MAP and a new generalized local search heuristic that provides new state-of-theart local searches for MAP. We also propose a new simple memetic algorithm that is competitive against the state-of-the-art memetic algorithm for MAP. In the last part of this thesis, we study a particular case of personnel assignment problem: the School Timetabling Problem (STP). The STP considers the assignment of personnel to other two or more sets, for example the assignment of professors to courses to time slots to rooms can be required. First, we provide a brief description of the state-of-the-art for STP. Then, we introduce a new approach for modeling this problem through the resolution of several MAP and we apply our solution on a real life case of study: STP at the Universidad Autonoma Metropolitana campus Azcapotzalco (UAM-A). We provide the particular aspects for STP at UAM-A and we provide a new solution for this problem. Our approach is based on solving several 3AP considering the introduced model and our proposed techniques.Consejo Mexiquense de Ciencia y Tecnología (Comecyt).Consejo Nacional de Ciencia y Tecnología (México

Heuristics and metaheuristics in the design of sound-absorbing porous materials

Inexact optimisation techniques such as heuristics and metaheuristics that quickly find near-optimal solutions are widely used to solve hard problems. While metaheuristics are well studied on specific problem domains such as travelling salesman, timetabling, vehicle routing etc., their extension to engineering domains is largely unexplored due to the requirement of domain expertise. In this thesis, we address a specific engineering domain: the design of sound-absorbing porous materials. Porous materials are foams, fibrous materials, woven and non-woven textiles, etc., that are widely used in automotive, aerospace and household applications to isolate and absorb noise to prevent equipment damage, protect hearing or ensure comfort. These materials constitute a significant amount of dead weight in aircraft and space applications, and choosing sub-optimal designs would lead to inefficiency and increased costs. By carefully choosing the material properties and shapes of these materials, favourable resonances can be created making it possible to improve absorption while also reducing weight. The optimisation problem structure is yet to be well-explored and not many comparison studies are available in this domain. This thesis aims to address the knowledge gap by analysing the performance of existing and novel heuristic and metaheuristic methods. Initially, the problem structure is explored by considering a one-dimensional layered sound package problem. Then, the challenging two-dimensional foam shape and topology optimisation is addressed. Topology optimisation involves optimally distributing a given volume of material in a design region such that a performance measure is maximised. Although extensive studies exist for the compliance minimisation problem domain, studies and comparisons on porous material problems are relatively rare. Firstly, a single objective absorption maximisation problem with a constraint on the weight is considered. Then a multi-objective problem of simultaneously maximising absorption and minimising weight is considered. The unique nature of the topology optimisation problem allows it to be solved using combinatorial or continuous, gradient or non-gradient methods. In this work, several optimisation methods are studied, including solid isotropic material with penalisation (SIMP), hill climbing, constructive heuristics, genetic algorithms, tabu search, co-variance matrix adaptation evolution strategy (CMA-ES), differential evolution, non-dominated sorting genetic algorithm (NSGA-II) and hybrid strategies. These approaches are tested on a benchmark of seven acoustics problem instances. The results are used to extract domain-specific insights. The findings highlight that the problem domain is rich with unique varieties of solutions, and by using domain-specific insights, one can design hybrid gradient and non-gradient methods that consistently outperform state-of-the-art ones

Data Structures & Algorithm Analysis in C++

This is the textbook for CSIS 215 at Liberty University.https://digitalcommons.liberty.edu/textbooks/1005/thumbnail.jp