Optimizing I/O cost and managing memory for composition vector method based on correlation matrix calculation in bioinformatics

The generation of a correlation matrix for set of genomic sequences is a common requirement in many bioinformatics problems such as phylogenetic analysis. Each sequence may be millions of bases long and there may be thousands of such sequences which we wish to compare, so not all sequences may fit into main memory at the same time. Each sequence needs to be compared with every other sequence, so we will generally need to page some sequences in and out more than once. In order to minimize execution time we need to minimize this I/O. This paper develops an approach for faster and scalable computing of large-size correlation matrices through the maximal exploitation of available memory and reducing the number of I/O operations. The approach is scalable in the sense that the same algorithms can be executed on different computing platforms with different amounts of memory and can be applied to different bioinformatics problems with different correlation matrix sizes. The significant performance improvement of the approach over previous work is demonstrated through benchmark examples.

K-tree : large scale document clustering

We introduce K-tree in an information retrieval context. It is an efficient approximation of the k-means clustering algorithm. Unlike k-means it forms a hierarchy of clusters. It has been extended to address issues with sparse representations. We compare performance and quality to CLUTO using document collections. The K-tree has a low time complexity that is suitable for large document collections. This tree structure allows for efficient disk based implementations where space requirements exceed that of main memory.

Attention and memory bias for body image and health related information using an Emotional Stroop task in a non-clinical sample

It has been proposed that body image disturbance is a form of cognitive bias wherein schemas for self-relevant information guide the selective processing of appearancerelated information in the environment. This threatening information receives disproportionately more attention and memory, as measured by an Emotional Stroop and incidental recall task. The aim of this thesis was to expand the literature on cognitive processing biases in non-clinical males and females by incorporating a number of significant methodological refinements. To achieve this aim, three phases of research were conducted. The initial two phases of research provided preliminary data to inform the development of the main study. Phase One was a qualitative exploration of body image concerns amongst males and females recruited through the general community and from a university. Seventeen participants (eight male; nine female) provided information on their body image and what factors they saw as positively and negatively impacting on their self evaluations. The importance of self esteem, mood, health and fitness, and recognition of the social ideal were identified as key themes. These themes were incorporated as psycho-social measures and Stroop word stimuli in subsequent phases of the research. Phase Two involved the selection and testing of stimuli to be used in the Emotional Stroop task. Six experimental categories of words were developed that reflected a broad range of health and body image concerns for males and females. These categories were high and low calorie food words, positive and negative appearance words, negative emotion words, and physical activity words. Phase Three addressed the central aim of the project by examining cognitive biases for body image information in empirically defined sub-groups. A National sample of males (N = 55) and females (N = 144), recruited from the general community and universities, completed an Emotional Stroop task, incidental memory test, and a collection of psycho-social questionnaires. Sub-groups of body image disturbance were sought using a cluster analysis, which identified three sub-groups in males (Normal, Dissatisfied, and Athletic) and four sub-groups in females (Normal, Health Conscious, Dissatisfied, and Symptomatic). No differences were noted between the groups in selective attention, although time taken to colour name the words was associated with some of the psycho-social variables. Memory biases found across the whole sample for negative emotion, low calorie food, and negative appearance words were interpreted as reflecting the current focus on health and stigma against being unattractive. Collectively these results have expanded our understanding of processing biases in the general community by demonstrating that the processing biases are found within non-clinical samples and that not all processing biases are associated with negative functionality

Understanding the Main Phases of Developing a Maturity Assessment Model

Practitioners and academics have developed numerous maturity models for many domains in order to measure competency. These initiatives have often been influenced by the Capability Maturity Model. However, an accumulative effort has not been made to generalize the phases of developing a maturity model in any domain. This paper proposes such a methodology and outlines the main phases of generic model development. The proposed methodology is illustrated with the help of examples from two advanced maturity models in the domains of Business Process Management and Knowledge Management.

Two main challenges in service description : Web service tunnel vision and semantic myopia

Through media such as newspapers, letterbox flyers, corporate brochures and television we are regularly confronted with descriptions for conventional (bricks 'n' mortar style) services. These representations vary in the terminology utilised, the depth of the description, the aspects of the service that are characterised and their applicability to candidate service requestors. Existing service catalogues (such as the Yellow Pages) provide little relief for service requestors from the burdensome task of discovering, comparing and substituting services. Add to this environment the rapidly evolving area of web services with its associated surfeit of standards, and the result is a considerably fragmented approach to the description of services. It leaves the reality of the Semantic Web somewhat clouded. --------- Let's consider service description briefly, before discussing our concerns with existing approaches to description. The act of describing is performed prior to advertising. This simple fact provides an interesting paradox as services cannot be described exactly before advertisement. This doesn't mean they can't be described comprehensively. By "exactly", we are referring to the fact that context provided by a service requestor (and their service needs) will alter the description of the service that is presented to the discoverer. For example, a service provider who operates a cinema wants to describe the price of their service. Let's say the advertised price is $15. They also want to state that a pensioner discount and a student discount is available which provides a 50% discount. A customer (i.e. service requestor) uses the cinema web site to purchase tickets online. They find the movie of their choice at a time that suits. However, its not until some context is provided by the requestor that the exact price is determined. The requestor might state that they are a pensioner. The same is applicable for a service requestor who purchases multiple tickets perhaps on behalf of other people. The disconnect between when the service is described and when a requestor provides context introduces challenges to the description process. A service provider would be ill-advised to offer independent descriptions that represent all the permutations possible for a single service. The descriptive effort would be prohibitive.

Strategy for the development of investment decision-making framework for road asset management for queensland department of main roads

The aim of this project is to develop a systematic investment decision-making framework for infrastructure asset management by incorporation economic justification, social and environmental consideration in the decision-making process. This project assesses the factors that are expected to provide significant impacts on the variability of expenditures. A procedure for assessing risk and reliability for project investment appraisals will be developed. The project investigates public perception, social and environmental impacts on road infrastructure investment. This research will contribute to the debate about how important social and environmental issues should be incorporated into the investment decision-making process for infrastructure asset management.

Situated case-based reasoning as a constructive memory model for design reasoning

This paper describes an extended case-based reasoning model that addresses the notion of situatedness in designing through constructive memory. The model is illustrated through an application for predicting the corrosion rate for a specific material on a specific building.

Data mining on prices of highway project main material based on WEB

The management of main material prices of provincial highway project quota has problems of lag and blindness. Framework of provincial highway project quota data MIS and main material price data warehouse were established based on WEB firstly. Then concrete processes of provincial highway project main material prices were brought forward based on BP neural network algorithmic. After that standard BP algorithmic, additional momentum modify BP network algorithmic, self-adaptive study speed improved BP network algorithmic were compared in predicting highway project main prices. The result indicated that it is feasible to predict highway main material prices using BP NN, and using self-adaptive study speed improved BP network algorithmic is the relatively best one.

Measuring episodic memory: A novel approach with an indefinite number of alternative forms

Both clinical practice and clinical research settings can require successive administrations of a memory test, particularly when following the trajectory of suspected memory decline in older adults. However, relatively few verbal episodic memory tests have alternative forms. We set out to create a broad based memory test to allow for the use of an essentially unlimited number of alternative forms. Four tasks for inclusion in such a test were developed. These tasks varied the requirement for recall as opposed to recognition, the need to form an association between unrelated words, and the need to discriminate the most recent list from earlier lists, all of which proved useful. A total of 115 participants completed the battery of tests and were used to show that the test could differentiate between older and younger adults; a sub-sample of 73 participants completed alternative forms of the tests to determine test-retest reliability and the amount of learning to learn.

Event-related potential (ERP) correlates of impaired visuospatial memory in schizophrenia

Previous studies have reported that patients with schizophrenia demonstrate impaired performance during working memory (WM) tasks. The current study aimed to determine whether WM impairments in schizophrenia are accompanied by reduced slow wave (SW) activity during on-line maintenance of mnemonic information. Event-related potentials were obtained from patients with schizophrenia and well controls as they performed a visuospatial delayed response task. On 50% of trials, a distractor stimulus was introduced during the delay. Compared with controls, patients with schizophrenia produced less SW memory negativity, particularly over the right hemisphere, together with reduced frontal enhancement of SW memory negativity in response to distraction. The results indicate that patients with schizophrenia generate less maintenance phase neuronal activity during WM performance, especially under conditions of distraction.

Working memory correlates of three symptom clusters in schizophrenia

Examined whether discrete working memory deficits underlie positive, negative and disorganised symptoms of schizophrenia. 52 outpatients (mean age 37.5 yrs) with schizophrenia were studied using items drawn from the Positive and Negative Syndrome Scale (PANSS). Linear regression and correlational analyses were conducted to examine whether symptom dimension scores were related to performance on several tests of working memory function. Severity of negative symptoms correlated with reduced production of words during a verbal fluency task, impaired ability to hold letter and number sequences on-line and manipulate them simultaneously, reduced performance during a dual task, and compromised visuospatial working memory under distraction-free conditions. Severity of disorganisation symptoms correlated with impaired visuospatial working memory under conditions of distraction, failure of inhibition during a verbal fluency task, perseverative responding on a test of set-shifting ability, and impaired ability to judge the veracity of simple declarative statements. The present study provides evidence that the positive, negative and disorganised symptom dimensions of the PANSS constitute independent clusters, associated with unique patterns of working memory impairment.

Eye-movements and visual imagery : a working memory approach to the treatment of post-traumatic stress disorder

It has been claimed that the symptoms of post-traumatic stress disorder (PTSD) can be ameliorated by eye-movement desensitization-reprocessing therapy (EMD-R), a procedure that involves the individual making saccadic eye-movements while imagining the traumatic event. We hypothesized that these eye-movements reduce the vividness of distressing images by disrupting the function of the visuospatial sketchpad (VSSP) of working memory, and that by doing so they reduce the intensity of the emotion associated with the image. This hypothesis was tested by asking non-PTSD participants to form images of neutral and negative pictures under dual task conditions. Their images were less vivid with concurrent eye-movements and with a concurrent spatial tapping task that did not involve eye-movements. In the first three experiments, these secondary tasks did not consistently affect participants' emotional responses to the images. However, Expt 4 used personal recollections as stimuli for the imagery task, and demonstrated a significant reduction in emotional response under the same dual task conditions. These results suggest that, if EMD-R works, it does so by reducing the vividness and emotiveness of traumatic images via the VSSP of working memory. Other visuospatial tasks may also be of therapeutic value.