Activity Counter: New Optimization for the Dynamic Scheduling of SIMD Control Flow

Abstract SIMD or vector computers and collection-oriented languages, like C , are designed to perform the same computation on each data item or on just a subset of the data. Subsets of processors or data items are implemented via an activity bit and a stack of activity bits when subsets of subsets are supported. This method is also used in VLIW processors through if-conversion to implement parallel control flow as in SIMD computers. We present a new method of dynamic sheduling of several SIMD control flow constructions which can be nested. Our implementation of activity stacks is based on activity counters. At a given stack depth n, the number of memory bits required is log 2 n, whereas previous implementations require n bits. The local controller is of equivalent complexity in both cases. This algorithm is useful for SIMD, vector or VLIW machines and for compilers of collection-oriented languages on MIMD computers

Getting Started with Particle Metropolis-Hastings for Inference in Nonlinear Dynamical Models

This tutorial provides a gentle introduction to the particle Metropolis-Hastings (PMH) algorithm for parameter inference in nonlinear state-space models together with a software implementation in the statistical programming language R. We employ a step-by-step approach to develop an implementation of the PMH algorithm (and the particle filter within) together with the reader. This final implementation is also available as the package pmhtutorial in the CRAN repository. Throughout the tutorial, we provide some intuition as to how the algorithm operates and discuss some solutions to problems that might occur in practice. To illustrate the use of PMH, we consider parameter inference in a linear Gaussian state-space model with synthetic data and a nonlinear stochastic volatility model with real-world data.Comment: 41 pages, 7 figures. In press for Journal of Statistical Software. Source code for R, Python and MATLAB available at: https://github.com/compops/pmh-tutoria

Parallel algorithms for three dimensional electrical impedance tomography

This thesis is concerned with Electrical Impedance Tomography (EIT), an imaging technique in which pictures of the electrical impedance within a volume are formed from current and voltage measurements made on the surface of the volume. The focus of the thesis is the mathematical and numerical aspects of reconstructing the impedance image from the measured data (the reconstruction problem). The reconstruction problem is mathematically difficult and most reconstruction algorithms are computationally intensive. Many of the potential applications of EIT in medical diagnosis and industrial process control depend upon rapid reconstruction of images. The aim of this investigation is to find algorithms and numerical techniques that lead to fast reconstruction while respecting the real mathematical difficulties involved. A general framework for Newton based reconstruction algorithms is developed which describes a large number of the reconstruction algorithms used by other investigators. Optimal experiments are defined in terms of current drive and voltage measurement patterns and it is shown that adaptive current reconstruction algorithms are a special case of their use. This leads to a new reconstruction algorithm using optimal experiments which is considerably faster than other methods of the Newton type. A tomograph is tested to measure the magnitude of the major sources of error in the data used for image reconstruction. An investigation into the numerical stability of reconstruction algorithms identifies the resulting uncertainty in the impedance image. A new data collection strategy and a numerical forward model are developed which minimise the effects of, previously, major sources of error. A reconstruction program is written for a range of Multiple Instruction Multiple Data, (MIMD), distributed memory, parallel computers. These machines promise high computational power for low cost and so look promising as components in medical tomographs. The performance of several reconstruction algorithms on these computers is analysed in detail

Convocations of Empire: Public Spectacle and Ceremony in Britain, 1851-2012

Britain has long been associated with the staging of grand ceremonies, popular spectacles, massive exhibitions, state occasions, and Royal events which embody historically-informed conceptualizations of “Britishness.” To this end, significant public spectacles occurred periodically from the height of the British Empire until its decline—many of which spoke to the nature of British imperial ambition. This project traces the evolution of those key popular gatherings which relate to the shifting British imperial scene from 1851-2012, providing an in-depth accounting of the Great Exhibition of 1851, the Jubilees of Queen Victoria in 1887 and 1897, the postwar memorial movements after the First and Second World Wars, the Coronation of Elizabeth II in 1953, and the contemporary, post-imperial events between 1997 and 2012

Novel computational techniques for mapping and classifying Next-Generation Sequencing data

Since their emergence around 2006, Next-Generation Sequencing technologies have been revolutionizing biological and medical research. Quickly obtaining an extensive amount of short or long reads of DNA sequence from almost any biological sample enables detecting genomic variants, revealing the composition of species in a metagenome, deciphering cancer biology, decoding the evolution of living or extinct species, or understanding human migration patterns and human history in general. The pace at which the throughput of sequencing technologies is increasing surpasses the growth of storage and computer capacities, which creates new computational challenges in NGS data processing. In this thesis, we present novel computational techniques for read mapping and taxonomic classification. With more than a hundred of published mappers, read mapping might be considered fully solved. However, the vast majority of mappers follow the same paradigm and only little attention has been paid to non-standard mapping approaches. Here, we propound the so-called dynamic mapping that we show to significantly improve the resulting alignments compared to traditional mapping approaches. Dynamic mapping is based on exploiting the information from previously computed alignments, helping to improve the mapping of subsequent reads. We provide the first comprehensive overview of this method and demonstrate its qualities using Dynamic Mapping Simulator, a pipeline that compares various dynamic mapping scenarios to static mapping and iterative referencing. An important component of a dynamic mapper is an online consensus caller, i.e., a program collecting alignment statistics and guiding updates of the reference in the online fashion. We provide Ococo, the first online consensus caller that implements a smart statistics for individual genomic positions using compact bit counters. Beyond its application to dynamic mapping, Ococo can be employed as an online SNP caller in various analysis pipelines, enabling SNP calling from a stream without saving the alignments on disk. Metagenomic classification of NGS reads is another major topic studied in the thesis. Having a database with thousands of reference genomes placed on a taxonomic tree, the task is to rapidly assign a huge amount of NGS reads to tree nodes, and possibly estimate the relative abundance of involved species. In this thesis, we propose improved computational techniques for this task. In a series of experiments, we show that spaced seeds consistently improve the classification accuracy. We provide Seed-Kraken, a spaced seed extension of Kraken, the most popular classifier at present. Furthermore, we suggest ProPhyle, a new indexing strategy based on a BWT-index, obtaining a much smaller and more informative index compared to Kraken. We provide a modified version of BWA that improves the BWT-index for a quick k-mer look-up

Fashioning social aspiration: lower-middle-class rational recreational leisure participation and the evolution of popular rational recreational leisure clothing c.1880-1950

Supervisors: Becky Conekin and Elizabeth Wilso

Online gaming and addiction: a psychosocial investigation using mixed methods

Online virtual worlds known as Massively Multiplayer Online Role-Playing Games (MMORPGs) have gained increased popularity over the last decade. MMORPGs provide a sophisticated environment that enables complete immersion within the virtual world to the extent that it may become an alternative reality to its users. Some researchers have suggested that online gaming addiction is growing in prevalence among adolescents and adult gamers. It has been proposed that research is needed to establish the incidence and prevalence of MMORPG addiction. The aim of this body of research was to examine the impact of MMORPGs (psychologically and socially) on peoples' lives for the purpose of providing an empirical research base on which future research in the area can build. Using a mixed methods approach for data collection and analysis, an online scoping study, interview study and two questionnaire studies were conducted. The thesis provides a detailed conceptualisation of the psychological processes involved in MMORPG playing. The thesis was directed by previous research into video games, online gaming and addiction which provided a substantive picture of the psychosocial effects of online gaming. The findings showed that there were both positive and negative effects associated with online gaming; gamers used MMORPGs to alleviate negative feelings and to meet new people, learn about new cultures, and build friendships. Gamers also provided detailed descriptions of personal problems that had arisen due to playing MMORPGs. A small percentage of gamers (3.6%) were classified as addicted to MMORPGs, these gamers may find it difficult to control their game playing behaviour. However, there are still gaps in our knowledge of MMORPGs. Overall, the research has shown that the psychology of MMORPGs is an important topic that requires further in-depth investigation. The present research has revealed valuable information about the impact of MMORPGs on the lives of gamers that can be built upon by other researchers. Implications of the findings regarding excessive playing and addiction to MMORPGs, and social responsibility were discussed, and recommendations for future research studies were proposed

JTEC panel report on machine translation in Japan

The goal of this report is to provide an overview of the state of the art of machine translation (MT) in Japan and to provide a comparison between Japanese and Western technology in this area. The term 'machine translation' as used here, includes both the science and technology required for automating the translation of text from one human language to another. Machine translation is viewed in Japan as an important strategic technology that is expected to play a key role in Japan's increasing participation in the world economy. MT is seen in Japan as important both for assimilating information into Japanese as well as for disseminating Japanese information throughout the world. Most of the MT systems now available in Japan are transfer-based systems. The majority of them exploit a case-frame representation of the source text as the basis of the transfer process. There is a gradual movement toward the use of deeper semantic representations, and some groups are beginning to look at interlingua-based systems