Exploring ant-based algorithms for gene expression data analysis

Objective: Recently, much research has been proposed using nature inspired algorithms to perform complex machine learning tasks. Ant colony optimization (ACO) is one such algorithm based on swarm intelligence and is derived from a model inspired by the collective foraging behavior of ants. Taking advantage of the ACO in traits such as self-organization and robustness, this paper investigates ant-based algorithms for gene expression data clustering and associative classification. Methods and material: An ant-based clustering (Ant-C) and an ant-based association rule mining (Ant-ARM) algorithms are proposed for gene expression data analysis. The proposed algorithms make use of the natural behavior of ants such as cooperation and adaptation to allow for a flexible robust search for a good candidate solution. Results: Ant-C has been tested on the three datasets selected from the Stanford Genomic Resource Database and achieved relatively high accuracy compared to other classical clustering methods. Ant-ARM has been tested on the acute lymphoblastic leukemia (ALL)/acute myeloid leukemia (AML) dataset and generated about 30 classification rules with high accuracy. Conclusions: Ant-C can generate optimal number of clusters without incorporating any other algorithms such as K-means or agglomerative hierarchical clustering. For associative classification, while a few of the well-known algorithms such as Apriori, FP-growth and Magnum Opus are unable to mine any association rules from the ALL/AML dataset within a reasonable period of time, Ant-ARM is able to extract associative classification rules.

Design and implementation of a multisite data repository for pediatric epilepsy

This dissertation established a software-hardware integrated design for a multisite data repository in pediatric epilepsy. A total of 16 institutions formed a consortium for this web-based application. This innovative fully operational web application allows users to upload and retrieve information through a unique human-computer graphical interface that is remotely accessible to all users of the consortium. A solution based on a Linux platform with My-SQL and Personal Home Page scripts (PHP) has been selected. Research was conducted to evaluate mechanisms to electronically transfer diverse datasets from different hospitals and collect the clinical data in concert with their related functional magnetic resonance imaging (fMRI). What was unique in the approach considered is that all pertinent clinical information about patients is synthesized with input from clinical experts into 4 different forms, which were: Clinical, fMRI scoring, Image information, and Neuropsychological data entry forms. A first contribution of this dissertation was in proposing an integrated processing platform that was site and scanner independent in order to uniformly process the varied fMRI datasets and to generate comparative brain activation patterns. The data collection from the consortium complied with the IRB requirements and provides all the safeguards for security and confidentiality requirements. An 1-MR1-based software library was used to perform data processing and statistical analysis to obtain the brain activation maps. Lateralization Index (LI) of healthy control (HC) subjects in contrast to localization-related epilepsy (LRE) subjects were evaluated. Over 110 activation maps were generated, and their respective LIs were computed yielding the following groups: (a) strong right lateralization: (HC=0%, LRE=18%), (b) right lateralization: (HC=2%, LRE=10%), (c) bilateral: (HC=20%, LRE=15%), (d) left lateralization: (HC=42%, LRE=26%), e) strong left lateralization: (HC=36%, LRE=31%). Moreover, nonlinear-multidimensional decision functions were used to seek an optimal separation between typical and atypical brain activations on the basis of the demographics as well as the extent and intensity of these brain activations. The intent was not to seek the highest output measures given the inherent overlap of the data, but rather to assess which of the many dimensions were critical in the overall assessment of typical and atypical language activations with the freedom to select any number of dimensions and impose any degree of complexity in the nonlinearity of the decision space.

Joint Analysis of Multiple Algorithms and Performance Measures

There has been an increasing interest in the development of new methods using Pareto optimality to deal with multi-objective criteria (for example, accuracy and time complexity). Once one has developed an approach to a problem of interest, the problem is then how to compare it with the state of art. In machine learning, algorithms are typically evaluated by comparing their performance on different data sets by means of statistical tests. Standard tests used for this purpose are able to consider jointly neither performance measures nor multiple competitors at once. The aim of this paper is to resolve these issues by developing statistical procedures that are able to account for multiple competing measures at the same time and to compare multiple algorithms altogether. In particular, we develop two tests: a frequentist procedure based on the generalized likelihood-ratio test and a Bayesian procedure based on a multinomial-Dirichlet conjugate model. We further extend them by discovering conditional independences among measures to reduce the number of parameters of such models, as usually the number of studied cases is very reduced in such comparisons. Data from a comparison among general purpose classifiers is used to show a practical application of our tests.

Design and implementation of BIRDY satellite data and Radiation Payload simulators

Numerical modelling and simulations are needed to develop and test specific analysis methods by providing test data before BIRDY would be launched. This document describes the "satellite data simulator" which is a multi-sensor, multi-spectral satellite simulator produced especially for the BIRDY mission which could be used as well to analyse data from other satellite missions providing energetic particles data in the Solar system.

An Analysis of the Implementation and Perceived Effectiveness of the SchoolMAX Family Portal

ABSTRACT Title of Document: AN ANALYSIS OF THE IMPLEMENTATION AND PERCEIVED EFFECTIVENESS OF THE SCHOOLMAX FAMILY PORTAL Warren Wesley Watts, Doctor of Education, 2015 Directed By: Margaret J. McLaughlin, Ph.D. Department of Counseling, Higher Education and Special Education School districts have spent millions of dollars implementing student information systems that offer family portals with web-based access to parents and students. One of the main purposes of these systems is to improve school-to-home communication. Research has shown that when school-to-home communication is implemented effectively, parent involvement improves and student achievement increases (Epstein, 2001). The purpose of the study was to (a) understand why parents used or refrained from using the family portal and (b) determine what barriers to use might exist. To this end, this descriptive study identified the information parent users accessed in the SchoolMAX family portal, determined how frequently parents accessed the portal, and ascertained whether parents perceived an increase in communication with their children about academic matters after they began accessing the portal. Finally, the study sought to identify whether barriers existed that prevented parents from using the family portal. The inquiry employed three data sources to answer the aforementioned queries. These sources included (a) a survey sent electronically to 19,108 parents who registered online for the SchoolMAX family portal; (b) SchoolMAX portal usage data from the student information system for system usage between January 1, 2015 and June 30, 2015; and (c) a paper survey sent to 691 parents of students that had never used the SchoolMAX family portal in one elementary school, one middle school and one high school that were representative of other schools in the district. Survey results indicated that parents at all grade levels used the family portal. Usage data also confirmed that approximately 19% of the students had parents who monitored their progress through the family portal. Usage data also showed that parents were monitoring approximately 25% of students in secondary schools (6th – 12th grade) and 16% of students in elementary schools. Of the wide menu of resources available through the SchoolMAX family portal, parents used three areas most frequently: attendance, daily grades, and report cards. Approximately 70% of parents responded that their communication had improved with their children about academic matters since they started using the SchoolMAX family portal, and 90% of parents responded that the SchoolMAX family portal was an effective or somewhat effective tool. Parents also expressed interest in the addition of additional information to the SchoolMAX family portal. Specifically, the top three additions parents wanted to see included homework assignments, high stakes test scores, and graduation requirements. Parents also reported that 92% of them spoke to their children at least 2 to 3 times per week about academics. Due to the low response rate of the parent non-user survey, potential barriers to using the SchoolMAX family portal could not be addressed in this study. However, this issue may be a useful research topic in a future study. Keywords: school to home communication, student information systems, family portal, parent portal

Comprehensive economic and financial analysis of the enterprise activity: approaches, methods and implementation

This thesis intends to analyse the performance and the efficiency of companies and to identify the key factors that may explain it. A comprehensive analysis based on a set of economic and financial ratios was studied as an instrument which provides information on enterprise performance and its efficiency. It was selected a sample with 15 enterprises: 7 Portuguese and 8 Ukrainian ones, belonging to several industries. Financial and non-financial data was collected for 6 years, during the period of 2009 to 2014. Research questions that guided this work were: Are the enterprises efficient/profitable? What factors influence enterprises’ efficiency/performance? Is there any difference between Ukrainian and Portuguese enterprises’ efficiency/performance, which factors have more influence? Which industrial sector is represented by more efficient/profitable enterprises? The main results showed that in average enterprises were efficient; comparing by states Ukrainian enterprises are more efficient; industries have similar level of efficiency. Among factors that influence ATR positively are fixed and current assets turnover ratios, ROA; negatively influencing are EBITDA margin and liquidity ratio. There is no significant difference between models by country. Concerning profitability, enterprises have low performance level but in comparison of countries Ukrainian enterprises have better profitability in average. Regarding the industry sector, paper industry is the most profitable. Among factors influencing ROA are profit margin, fixed asset turnover ratio, EBITDA margin, Debt to equity ratio and the country. In case of profitability both countries have different models. For Ukrainian enterprises is suggested to pay attention on factors of Short-term debt to total debt, ROA, Interest coverage ratio in order to be more efficient; Profit margin and EBITDA margin to make their performance better. For Portuguese enterprises for improving efficiency the observation and improvement of fixed assets turnover ratio, current assets turnover ratio, Short-term financial debt to total debt, Leverage Ratio, EBITDA margin is suggested; for improving higher profitability track fixed assets turnover ratio, current assets turnover ratio, Debt to equity ratio, Profit margin and Interest coverage ratio is suggested.

Algorithms and tools of big data: A bibliographic review

66 p.

On cluster analysis of complex and heterogeneous data

3rd SMTDA Conference Proceedings, 11-14 June 2014, Lisbon Portugal.

Private cloud computing platforms. Analysis and implementation in a Higher Education Institution

The constant evolution of the Internet and its increasing use and subsequent entailing to private and public activities, resulting in a strong impact on their survival, originates an emerging technology. Through cloud computing, it is possible to abstract users from the lower layers to the business, focusing only on what is most important to manage and with the advantage of being able to grow (or degrades) resources as needed. The paradigm of cloud arises from the necessity of optimization of IT resources evolving in an emergent and rapidly expanding and technology. In this regard, after a study of the most common cloud platforms and the tactic of the current implementation of the technologies applied at the Institute of Biomedical Sciences of Abel Salazar and Faculty of Pharmacy of Oporto University a proposed evolution is suggested in order adorn certain requirements in the context of cloud computing.

Design and implementation of a behaviorally typed programming system for web services

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do Grau de Mestre em Engenharia Informática.

Towards a GIS-T database design and implementation for public transit planning: the case study of Dar-Es-salaam metropolitan city, Tanzania.

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

Acquisition and data analysis related to changes in some forest soils properties after prescribed fire action

Controlled fires in forest areas are frequently used in most Mediterranean countries as a preventive technique to avoid severe wildfires in summer season. In Portugal, this forest management method of fuel mass availability is also used and has shown to be beneficial as annual statistical reports confirm that the decrease of wildfires occurrence have a direct relationship with the controlled fire practice. However prescribed fire can have serious side effects in some forest soil properties. This work shows the changes that occurred in some forest soils properties after a prescribed fire action. The experiments were carried out in soil cover over a natural site of Andaluzitic schist, in Gramelas, Caminha, Portugal, that had not been burn for four years. The composed soil samples were collected from five plots at three different layers (0-3cm, 3-6cm and 6-18cm) during a three-year monitoring period after the prescribed burning. Principal Component Analysis was used to reach the presented conclusions.

Vertex component analysis GPU-based implementation for hyperspectral unmixing

Endmember extraction (EE) is a fundamental and crucial task in hyperspectral unmixing. Among other methods vertex component analysis ( VCA) has become a very popular and useful tool to unmix hyperspectral data. VCA is a geometrical based method that extracts endmember signatures from large hyperspectral datasets without the use of any a priori knowledge about the constituent spectra. Many Hyperspectral imagery applications require a response in real time or near-real time. Thus, to met this requirement this paper proposes a parallel implementation of VCA developed for graphics processing units. The impact on the complexity and on the accuracy of the proposed parallel implementation of VCA is examined using both simulated and real hyperspectral datasets.

Relationship between national culture, democracy and environmental performance: A panel data analysis

This paper demonstrates the significance of culture in examining the relationshipbetween democratic capital and environmental performance.The aim is to examine the relationship among scores on the Environmental Performance Index and the two dimensions of cross cultural variation suggested by Ronald Inglehart and Christian Welzel. Significantional interrelationships among democracy, cultural and environmental sustaintability measures could be found, following the regression results. Firstly, higher levels of democratic capital stock are associated with better environmental performance. Secondly importance to distinguish between cultural groups could be confirmed.