Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem

The last decade of phylogenetics has seen the development of many methods that leverage constraints plus dynamic programming. The goal of this algorithmic technique is to produce a phylogeny that is optimal with respect to some objective function and that lies within a constrained version of tree space. The popular species tree estimation method ASTRAL, for example, returns a tree that (1) maximizes the quartet score computed with respect to the input gene trees and that (2) draws its branches (bipartitions) from the input constraint set. This technique has yet to be used for classic parsimony problems where the input are binary characters, sometimes with missing values. Here, we introduce the clade-constrained character parsimony problem and present an algorithm that solves this problem in polynomial time for the Dollo criterion score. Dollo parsimony, which requires traits/mutations to be gained at most once but allows them to be lost any number of times, is widely used for tumor phylogenetics as well as species phylogenetics, for example analyses of low-homoplasy retroelement insertions across the vertebrate tree of life. Thus, we implement our algorithm in a software package, called Dollo-CDP, and evaluate its utility in the context of species phylogenetics using both simulated and real data sets. Our results show that Dollo-CDP can improve upon heuristic search from a single starting tree, often recovering a better scoring tree. Moreover, Dollo-CDP scales to data sets with much larger numbers of taxa than branch-and-bound while still having an optimality guarantee, albeit a more restricted one. Lastly, we show that our algorithm for Dollo parsimony can easily be adapted to Camin-Sokal parsimony but not Fitch parsimony

Parallel and Distributed Computing

The 14 chapters presented in this book cover a wide variety of representative works ranging from hardware design to application development. Particularly, the topics that are addressed are programmable and reconfigurable devices and systems, dependability of GPUs (General Purpose Units), network topologies, cache coherence protocols, resource allocation, scheduling algorithms, peertopeer networks, largescale network simulation, and parallel routines and algorithms. In this way, the articles included in this book constitute an excellent reference for engineers and researchers who have particular interests in each of these topics in parallel and distributed computing

Supertree-like methods for genome-scale species tree estimation

A critical step in many biological studies is the estimation of evolutionary trees (phylogenies) from genomic data. Of particular interest is the species tree, which illustrates how a set of species evolved from a common ancestor. While species trees were previously estimated from a few regions of the genome (genes), it is now widely recognized that biological processes can cause the evolutionary histories of individual genes to differ from each other and from the species tree. This heterogeneity across the genome is phylogenetic signal that can be leveraged to estimate species evolution with greater accuracy. Hence, species tree estimation is expected to be greatly aided by current large-scale sequencing efforts, including the 5000 Insect Genomes Project, the 10000 Plant Genomes Project, the (~60000) Vertebrate Genomes Project, and the Earth BioGenome Project, which aims to assemble genomes (or at least genome-scale data) for 1.5 million eukaryotic species in the next ten years. To analyze these forthcoming datasets, species tree estimation methods must scale to thousands of species and tens of thousands of genes; however, many of the current leading methods, which are heuristics for NP-hard optimization problems, can be prohibitively expensive on datasets of this size. In this dissertation, we argue that new methods are needed to enable scalable and statistically rigorous species tree estimation pipelines; we then seek to address this challenge through the introduction of three supertree-like methods: NJMerge, TreeMerge, and FastMulRFS. For these methods, we present theoretical results (worst-case running time analyses and proofs of statistical consistency) as well as empirical results on simulated datasets (and a fungal dataset for FastMulRFS). Overall, these methods enable statistically consistent species tree estimation pipelines that achieve comparable accuracy to the dominant optimization-based approaches while dramatically reducing running time

Representation and Exploitation of Event Sequences

Programa Oficial de Doutoramento en Computación . 5009V01[Abstract] The Ten Commandments, the thirty best smartphones in the market and the five most wanted people by the FBI. Our life is ruled by sequences: thought sequences, number sequences, event sequences. . . a history book is nothing more than a compilation of events and our favorite film is just a sequence of scenes. All of them have something in common, it is possible to acquire relevant information from them. Frequently, by accumulating some data from the elements of each sequence we may access hidden information (e.g. the passengers transported by a bus on a journey is the sum of the passengers who got on in the sequence of stops made); other times, reordering the elements by any of their characteristics facilitates the access to the elements of interest (e.g. the publication of books in 2019 can be ordered chronologically, by author, by literary genre or even by a combination of characteristics); but it will always be sought to store them in the smallest space possible. Thus, this thesis proposes technological solutions for the storage and subsequent processing of events, focusing specifically on three fundamental aspects that can be found in any application that needs to manage them: compressed and dynamic storage, aggregation or accumulation of elements of the sequence and element sequence reordering by their different characteristics or dimensions. The first contribution of this work is a compact structure for the dynamic compression of event sequences. This structure allows any sequence to be compressed in a single pass, that is, it is capable of compressing in real time as elements arrive. This contribution is a milestone in the world of compression since, to date, this is the first proposal for a variable-to-variable dynamic compressor for general purpose. Regarding aggregation, a data warehouse-like proposal is presented capable of storing information on any characteristic of the events in a sequence in an aggregated, compact and accessible way. Following the philosophy of current data warehouses, we avoid repeating cumulative operations and speed up aggregate queries by preprocessing the information and keeping it in this separate structure. Finally, this thesis addresses the problem of indexing event sequences considering their different characteristics and possible reorderings. A new approach for simultaneously keeping the elements of a sequence ordered by different characteristics is presented through compact structures. Thus, it is possible to consult the information and perform operations on the elements of the sequence using any possible rearrangement in a simple and efficient way.[Resumen] Los diez mandamientos, los treinta mejores móviles del mercado y las cinco personas más buscadas por el FBI. Nuestra vida está gobernada por secuencias: secuencias de pensamientos, secuencias de números, secuencias de eventos. . . un libro de historia no es más que una sucesión de eventos y nuestra película favorita no es sino una secuencia de escenas. Todas ellas tienen algo en común, de todas podemos extraer información relevante. A veces, al acumular algún dato de los elementos de cada secuencia accedemos a información oculta (p. ej. los viajeros transportados por un autobús en un trayecto es la suma de los pasajeros que se subieron en la secuencia de paradas realizadas); otras veces, la reordenación de los elementos por alguna de sus características facilita el acceso a los elementos de interés (p. ej. la publicación de obras literarias en 2019 puede ordenarse cronológicamente, por autor, por género literario o incluso por una combinación de características); pero siempre se buscará almacenarlas en el espacio más reducido posible sin renunciar a su contenido. Por ello, esta tesis propone soluciones tecnológicas para el almacenamiento y posterior procesamiento de secuencias, centrándose concretamente en tres aspectos fundamentales que se pueden encontrar en cualquier aplicación que precise gestionarlas: el almacenamiento comprimido y dinámico, la agregación o acumulación de algún dato sobre los elementos de la secuencia y la reordenación de los elementos de la secuencia por sus diferentes características o dimensiones. La primera contribución de este trabajo es una estructura compacta para la compresión dinámica de secuencias. Esta estructura permite comprimir cualquier secuencia en una sola pasada, es decir, es capaz de comprimir en tiempo real a medida que llegan los elementos de la secuencia. Esta aportación es un hito en el mundo de la compresión ya que, hasta la fecha, es la primera propuesta de un compresor dinámico “variable to variable” de carácter general. En cuanto a la agregación, se presenta una propuesta de almacén de datos capaz de guardar la información acumulada sobre alguna característica de los eventos de la secuencia de modo compacto y fácilmente accesible. Siguiendo la filosofía de los actuales almacenes de datos, el objetivo es evitar repetir operaciones de acumulación y agilizar las consultas agregadas mediante el preprocesado de la información manteniéndola en esta estructura. Por último, esta tesis aborda el problema de la indexación de secuencias de eventos considerando sus diferentes características y posibles reordenaciones. Se presenta una nueva forma de mantener simultáneamente ordenados los elementos de una secuencia por diferentes características a través de estructuras compactas. Así se permite consultar la información y realizar operaciones sobre los elementos de la secuencia usando cualquier posible ordenación de una manera sencilla y eficiente

Proceedings of the 2009 Joint Workshop of Fraunhofer IOSB and Institute for Anthropomatics, Vision and Fusion Laboratory

The joint workshop of the Fraunhofer Institute of Optronics, System Technologies and Image Exploitation IOSB, Karlsruhe, and the Vision and Fusion Laboratory (Institute for Anthropomatics, Karlsruhe Institute of Technology (KIT)), is organized annually since 2005 with the aim to report on the latest research and development findings of the doctoral students of both institutions. This book provides a collection of 16 technical reports on the research results presented on the 2009 workshop

Lifestyle modifications for nonalcohol-related fatty liver disease: a network meta-analysis

BACKGROUND: The prevalence of nonalcohol-related fatty liver disease (NAFLD) varies between 19% and 33% in different populations. NAFLD decreases life expectancy and increases the risks of liver cirrhosis, hepatocellular carcinoma, and requirement for liver transplantation. There is uncertainty surrounding the relative benefits and harms of various lifestyle interventions for people with NAFLD. OBJECTIVES: To assess the comparative benefits and harms of different lifestyle interventions in the treatment of NAFLD through a network meta-analysis, and to generate rankings of the different lifestyle interventions according to their safety and efficacy. SEARCH METHODS: We searched CENTRAL, MEDLINE, Embase, Science Citation Index Expanded, Conference Proceedings Citation Index - Science, World Health Organization International Clinical Trials Registry Platform, and trials registers until February 2021 to identify randomised clinical trials in people with NAFLD. SELECTION CRITERIA: We included only randomised clinical trials (irrespective of language, blinding, or status) in people with NAFLD, whatever the method of diagnosis, age, and diabetic status of participants, or presence of non-alcoholic steatohepatitis (NASH). We excluded randomised clinical trials in which participants had previously undergone liver transplantation. DATA COLLECTION AND ANALYSIS: We planned to perform a network meta-analysis with OpenBUGS using Bayesian methods and to calculate the differences in treatments using hazard ratios (HRs), odds ratios (ORs), and rate ratios (RaRs) with 95% credible intervals (CrIs) based on an available-participant analysis, according to National Institute of Health and Care Excellence Decision Support Unit guidance. However, the data were too sparse for the clinical outcomes. We therefore performed only direct comparisons (head-to-head comparisons) with OpenBUGS using Bayesian methods. MAIN RESULTS: We included a total of 59 randomised clinical trials (3631 participants) in the review. All but two trials were at high risk of bias. A total of 33 different interventions, ranging from advice to supervised exercise and special diets, or a combination of these and no additional intervention were compared in these trials. The reference treatment was no active intervention. Twenty-eight trials (1942 participants) were included in one or more comparisons. The follow-up ranged from 1 month to 24 months. The remaining trials did not report any of the outcomes of interest for this review. The follow-up period in the trials that reported clinical outcomes was 2 months to 24 months. During this short follow-up period, clinical events related to NAFLD such as mortality, liver cirrhosis, liver decompensation, liver transplantation, hepatocellular carcinoma, and liver-related mortality were sparse. This is probably because of the very short follow-up periods. It takes a follow-up of 8 years to 28 years to detect differences in mortality between people with NAFLD and the general population. It is therefore unlikely that differences by clinical outcomes will be noted in trials with less than 5 years to 10 years of follow-up. In one trial, one participant developed an adverse event. There were no adverse events in any of the remaining participants in this trial, or in any of the remaining trials, which seemed to be directly related to the intervention. AUTHORS' CONCLUSIONS: The evidence indicates considerable uncertainty about the effects of the lifestyle interventions compared with no additional intervention (to general public health advice) on any of the clinical outcomes after a short follow-up period of 2 months to 24 months in people with nonalcohol-related fatty liver disease. Accordingly, high-quality randomised clinical trials with adequate follow-up are needed. We propose registry-based randomised clinical trials or cohort multiple randomised clinical trials (a study design in which multiple interventions are trialed within large longitudinal cohorts of participants to gain efficiencies and align trials more closely to standard clinical practice), comparing aerobic exercise and dietary advice versus standard of care (exercise and dietary advice received as part of national health promotion). The reason for the choice of aerobic exercise and dietary advice is the impact of these interventions on indirect outcomes which may translate to clinical benefit. The outcomes in such trials should be mortality, health-related quality of life, decompensated liver cirrhosis, liver transplantation, and resource use measures including costs of intervention and decreased healthcare use after a minimum follow-up of eight years, to find meaningful differences in the clinically important outcomes

The impact of open spaces in the social life : the case of Jeddah, Saudi Arabia

This study discusses social life in public open spaces within an urban context of Jeddah city, by examining the quality and design of these spaces. Jeddah is a multicultural city, with a high proportion of immigrant people, so also provides a research context for critiquing transnational practices and social interaction. The study strategy was developed from two key methodological principles. The first develops investigation of open space as an integration of form, fabric and cultural practice, allowing the study to link social patterns with the physical design of the public realm. The second foregrounds storytelling methods to elicit complexity of social interaction, enabling investigation of intangible influences, such as social norms, gender norms, religion and ethnicity. A qualitative case study approach was used to investigate users’ cultural practices and experiences of public spaces. The methods used in this study were a review of documents and maps, car surveys, observations and on-site interviews. It was fundamental to develop an open space typology to meet the diversity of use in a case study selection specific to a Gulf region context. The present study has the potential to make an important contribution to academic research on the value and roles of open space in social life and interaction. The focus on Saudi Arabian open spaces is rare, and contributes to address the Western and North European bias in academic literature. The practical implications of the study are also important, as it highlights the necessity to develop open spaces design, planning, and management in order to better meet residents’ social needs. However, despite the numerous weaknesses of the open space provision in Jeddah, the study confirms the potential of creation of strong social relations between the residents of Jeddah when they are provided public spaces that attract them and meet their needs and expectations.Este estudio discute la vida social en espacios públicos abiertos dentro de un contexto urbano de la ciudad de Jiddah, examinando la calidad y el diseño de estos espacios. Jiddah es una ciudad multicultural, con una alta proporción de inmigrantes, por lo que también proporciona un contexto de investigación para criticar las prácticas transnacionales y la interacción social. La estrategia de estudio se desarrolló a partir de dos principios metodológicos clave. El primero desarrolla la investigación del espacio abierto como una integración de la forma, el tejido y la práctica cultural, permitiendo que el estudio vincule patrones sociales con el diseño físico del ámbito público. El segundo pone en primer plano los métodos de narración de cuentos para provocar la complejidad de la interacción social, permitiendo la investigación de influencias intangibles, como las normas sociales, las normas de género, la religión y la etnicidad. Se utilizó un enfoque de estudio de caso cualitativo para investigar las prácticas culturales de los usuarios y las experiencias de los espacios públicos. Los métodos utilizados en este estudio fueron una revisión de documentos y mapas, encuestas de coches, observaciones y entrevistas en el sitio. Era fundamental desarrollar una tipología de espacio abierto para cumplir con la diversidad de uso en una selección de estudio de caso específica para un contexto de la región del Golfo. El presente estudio tiene el potencial de hacer una contribución importante a la investigación académica sobre el valor y los roles del espacio abierto en la vida social y la interacción. El enfoque en los espacios abiertos de Arabia Saudita es raro, y contribuye a abordar el sesgo occidental y del norte de Europa en la literatura académica. Las implicaciones prácticas del estudio también son importantes, ya que resalta la necesidad de desarrollar el diseño, la planificación y la gestión de espacios abiertos para satisfacer mejor las necesidades sociales de los residentes. Sin embargo, a pesar de las numerosas debilidades de la provisión de espacios abiertos en Jiddah, el estudio confirma el potencial de la creación de fuertes relaciones sociales entre los residentes de Jiddah cuando se les proporciona espacios públicos que los atraen y satisfacen sus necesidades y expectativas.Postprint (published version

The impact of open spaces in the social life : the case of Jeddah, Saudi Arabia

This study discusses social life in public open spaces within an urban context of Jeddah city, by examining the quality and design of these spaces. Jeddah is a multicultural city, with a high proportion of immigrant people, so also provides a research context for critiquing transnational practices and social interaction. The study strategy was developed from two key methodological principles. The first develops investigation of open space as an integration of form, fabric and cultural practice, allowing the study to link social patterns with the physical design of the public realm. The second foregrounds storytelling methods to elicit complexity of social interaction, enabling investigation of intangible influences, such as social norms, gender norms, religion and ethnicity. A qualitative case study approach was used to investigate users’ cultural practices and experiences of public spaces. The methods used in this study were a review of documents and maps, car surveys, observations and on-site interviews. It was fundamental to develop an open space typology to meet the diversity of use in a case study selection specific to a Gulf region context. The present study has the potential to make an important contribution to academic research on the value and roles of open space in social life and interaction. The focus on Saudi Arabian open spaces is rare, and contributes to address the Western and North European bias in academic literature. The practical implications of the study are also important, as it highlights the necessity to develop open spaces design, planning, and management in order to better meet residents’ social needs. However, despite the numerous weaknesses of the open space provision in Jeddah, the study confirms the potential of creation of strong social relations between the residents of Jeddah when they are provided public spaces that attract them and meet their needs and expectations.Este estudio discute la vida social en espacios públicos abiertos dentro de un contexto urbano de la ciudad de Jiddah, examinando la calidad y el diseño de estos espacios. Jiddah es una ciudad multicultural, con una alta proporción de inmigrantes, por lo que también proporciona un contexto de investigación para criticar las prácticas transnacionales y la interacción social. La estrategia de estudio se desarrolló a partir de dos principios metodológicos clave. El primero desarrolla la investigación del espacio abierto como una integración de la forma, el tejido y la práctica cultural, permitiendo que el estudio vincule patrones sociales con el diseño físico del ámbito público. El segundo pone en primer plano los métodos de narración de cuentos para provocar la complejidad de la interacción social, permitiendo la investigación de influencias intangibles, como las normas sociales, las normas de género, la religión y la etnicidad. Se utilizó un enfoque de estudio de caso cualitativo para investigar las prácticas culturales de los usuarios y las experiencias de los espacios públicos. Los métodos utilizados en este estudio fueron una revisión de documentos y mapas, encuestas de coches, observaciones y entrevistas en el sitio. Era fundamental desarrollar una tipología de espacio abierto para cumplir con la diversidad de uso en una selección de estudio de caso específica para un contexto de la región del Golfo. El presente estudio tiene el potencial de hacer una contribución importante a la investigación académica sobre el valor y los roles del espacio abierto en la vida social y la interacción. El enfoque en los espacios abiertos de Arabia Saudita es raro, y contribuye a abordar el sesgo occidental y del norte de Europa en la literatura académica. Las implicaciones prácticas del estudio también son importantes, ya que resalta la necesidad de desarrollar el diseño, la planificación y la gestión de espacios abiertos para satisfacer mejor las necesidades sociales de los residentes. Sin embargo, a pesar de las numerosas debilidades de la provisión de espacios abiertos en Jiddah, el estudio confirma el potencial de la creación de fuertes relaciones sociales entre los residentes de Jiddah cuando se les proporciona espacios públicos que los atraen y satisfacen sus necesidades y expectativas