acase@tulane.edu / The technological advances of past decades have led to the accumulation of large amounts of genomic and neuroimaging data, enabling novel strategies in precision medicine. These largely rely on machine learning algorithms and modern statistical methods for big biological datasets, which are data-driven rather than hypothesis-driven. These methods often lack guarantees on the validity of the research findings. Because it can be a matter of life and death, when computational methods are deployed in clinical practice in medicine, establishing guarantees on the validity of the results is essential for the advancement of precision medicine. This thesis proposes several novel sparse regression and sparse canonical correlation analysis techniques, which by design include guarantees on the false discovery rate in variable selection. Variable selection on biomedical data is essential for many areas of healthcare, including precision medicine, population stratification, drug development, and predictive modeling of disease phenotypes. Predictive machine learning models can directly affect the patient when used to aid diagnosis, and therefore they need to be thoroughly evaluated before deployment. We present a novel approach to validly reuse the test data for performance evaluation of predictive models. The proposed methods are validated in the application on large genomic and neuroimaging datasets, where they confirm results from previous studies and also lead to new biological insights. In addition, this work puts a focus on making the proposed methods widely available to the scientific community though the release of free and open-source scientific software. / 1 / Alexej Gossmann

The availability of large-scale data on the Web motivates the development of automatic algorithms to analyze topics and to identify relationships between topics. Various approaches have been proposed in the literature. Most focus on specific topics, mainly those representing people, with little attention to topics of other kinds. They are also less flexible in how they represent topics. In this thesis we study existing methods as well as describe a different approach, based on profiles, for representing topics. A Topic Profile is analogous to a synopsis of a topic and consists of different types of features. Profiles are flexible to allow different combinations of features to be emphasized and are extensible to support new features to be incorporated without having to change the underlying logic. More generally, topic profiles provide an abstract framework that can be used to create different types of concrete representations for topics. Different options regarding the number of documents considered for a topic or types of features extracted can be decided based on requirements of the problem as well as the characteristics of the data. Topic profiles also provide a framework to explore relationships between topics. We compare different methods for building profiles and evaluate them in terms of their information content and their ability to predict relationships between topics. We contribute new methods in term weighting and for identifying relevant text segments in web documents. In this thesis, we present an application of our profile-based approach to explore social networks of US senators generated from web data and compare with networks generated from voting data. We consider both general networks as well as issue-specific networks. We also apply topic profiles for identifying and ranking experts given topics of interest, as part of the 2007 TREC Expert Search task. Overall, our results show that topic profiles provide a strong foundation for exploring different topics and for mining relationships between topics using web data. Our approach can be applied to a wide range of web knowledge discovery problems, in contrast to existing approaches that are mostly designed for specific problems.

In the fight against disease and illness, nature has provided mankind some of our best therapeutics in the form of secondary metabolites. The plant, fungi and animal phyla inhabiting the Earth produce diverse and unique chemistry that can be used in our fight against disease. In the growing threat of drug resistance and pathogen evolution, the field of natural products chemistry strives to explore new biological and chemical diversity sources, and develop innovative methodology to identify and isolate new chemistry faster than ever. The dissertation herein presented is one such effort to find new, bioactive chemistry from the marine environments. New biodiversity sources, from the tropical Floridian mangrove forests to the cold waters of the Antarctic oceans, were evaluated for the new, unique chemistry they produce. A large-scale screening of epigenetically modulated mangrove fungi was undertaken, producing a large, biologically and chemically diverse extract library. New methodology was developed in order to evaluate these extracts, leading to rapid identification and isolation of known and new bioactive metabolites. From the Southern Oceans, a collection of sponges was studied, and a new, highly unique peptide was isolated and characterized. These efforts were undertaken in the continued effort to isolate new, unique lead compounds.

With the increasing amount of valuable data that companies have access to the need for tools visualizing this data have reached a wider group of users, many of which are not tech-savvy. Self-service Business Intelligence applications aim to meet this need and many guidelines regarding the general design of Business Intelligence have been produced in recent years. In this thesis some of these guidelines are interpreted and applied during the development of a Qlik Sense application for the Device Connection Platform department at Ericsson. The purpose of this thesis is to produce more specific guidelines that aim to complement existing general guidelines on Self-service Business Intelligence design; guidelines that should be taken into account when developing Qlik Sense applications. As a result, five guidelines that concerns conditional dimensions, screen resolutions, naming conventions for master items, the data layer and Qlik Sense conventions for visualizations are presented. Pros and cons regarding these guidelines are discussed along with alternative approaches. The conclusion states that the general guidelines interpreted in this project work were helpful for the workflow and readability of the application, but that more specific guidelines such as the ones presented in the result could be well needed when it comes to customizabil ity and flexibility for end users. / Allt eftersom mängden värdefull data som företag har tillgång till ökar har behovet av verktyg som visualiserar dessa data nått en bredare grupp användare, där många är mindre tekniskt kunniga. Self-service Business Intelligence applikationer syftar till att möta detta behov och många generella riktlinjer för hur sådana applikationer ska designas har tagits fram under senare år. I denna rapport blir dessa riktlinjer tolkade och därefter applicerade under tiden av skapandet av en Self-service Business Intelligence applikation i mjukvaran Qlik Sense och för Ericsson Device Connection Platform. Syftet med rapporten är att utforma och presentera specifika riktlinjer för Qlik Sense att användas som komplement till de existerande och mer generella riktlinjerna för design av Self-service Business Intelligence i allmänhet. Rapportens resultat består av fem riktlinjer som avser villkorliga dimensioner, skärmupplösning, namnkonventioner för original, datalagret och Qlik Sense egna konventioner för visualiseringar. Föroch nackdelar med de framtagna riktlinjerna diskuteras tillsammans med alternativa tillvägagångssätt. Vi drar slutsatsen att de generella riktlinjerna som tolkats genom projektet i denna rapport var speciellt hjälpfulla för att uppnå läsbarhet och ett bra arbetsflöde för slutanvändaren i applikationen. Vidare konstateras att fler mjukvaruspecifika riktlinjer kan vara välbehövliga när det kommer till anpassningsbarhet av applikationer och flexibilitet för slutanvändare.

When Captain James Cook sailed into Botany Bay in Australia for the first time in 1770, his botanist Joseph Banks described the behaviour of the Aboriginals to be 'totally unmovd' and 'totally engagd'.During this same few days Cook named the place Stingray Bay. Within eight days the name was changed by Cook to Botany Bay. Banks' phrases generate oscillating perceptions and Cook's name change poses questions. The perceptions documented in Banks' journal, refer to an invisibility of the Aboriginals themselves. The name 'Stingray' and its change to 'Botany' raises political questions about the necessity for the change. The change also sheds light on a viewpoint at odds with its subject. The events that occurred during the eight days Cook was anchored in Botany Bay will be discussed firstly in the framework of an analysis of the implications of the terms 'totally unmovd' and 'totally engagd' in Banks' journal, and secondly in a discussion about the various historical notions concerning the name change. Did these curly histories and viewpoints render the indigenous culture invisible? Can these inscriptions made by Cook and Banks and the subsequent mythologies surrounding them, including those about the actual place, be a metaphor for 'further understanding'? / Master of Arts (Hons) (Visual Arts)

The dual problem space model of writing (Scardamalia, Bereiter and Steinbach, 1984) shows how writers develop their knowledge and understanding of the world by reflecting on problems of substance and problems of presentation in planning a composition. Reflective thought is attributed to a two-way communication between a content problem space and a rhetorical problem space. The content space involves the development of ideas, while the rhetorical space is concerned with achieving various purposes in composition. This thesis reports an instructional experiment comparing alternative approaches to teaching the self-regulatory strategies required for the two-way process of reflection. The experiment compared the dialogue approach of current practice, which relies on the teacher to provide the linking operations between the two problem spaces, with two experimental approaches which promote development of self-regulatory strategies of reflection, so that students are able to sustain such a two-way process independently. The experimental approaches are described as a guided discovery approach proposed by Evans (1991) and an approach described as cognitive apprenticeship developed by Scardamalia, Bereiter and Steinbach (1984). Three instructional programs were prepared by the author to represent the three alternative approaches examined in the present study. The control program utilised the dialogue approach of current practice in which the dialectical process is carried on between teacher and student. The two experimental programs focused on promoting processes of self-questioning rather than questioning by an external agent such as a teacher. The guided discovery program consisted of activities which prompted self-questioning processes. The cognitive apprenticeship program employed scaffolding in the form of procedural facilitation cues to stimulate the self-questioning process. A pre-test and post-test control group design was used involving three groups, two experimental (guided discovery and cognitive apprenticeship) and one control (dialogue), with instructional method as the independent variable and rated reflectiveness of writing as the dependent variable. Instruction was concentrated on teaching the two-way problem formulating and problem solving strategies of the reflective process for opinion essays and factual exposition essays. The experiment compared the effectiveness of programs by measuring changes in overall reflectiveness of writing. Significant improvements were obtained for the experimental teaching methods withrespect to opinion essays. This research provided some support for the hypothesis that instruction which fosters self-regulation of the planning process through processes of reflection results in more reflective writing than instruction in which such regulation is prompted by the teacher.

With the advent of portable devices (e.g., smartphones) and the advances in wireless networking technologies (e.g., WLAN, GPRS, UMTS), the vision of ubiquitous computing is becoming a reality. It aims to facilitate user tasks through the seamless utilization of heterogeneous computing and communication capabilities (represented as services) available in the environment. Service discovery, which is necessary for achieving the above goal, must be aware of the service's non-functional properties due to the challenges posed by ubiquitous computing, such as device portability and mobility. This thesis proposes an overall solution that supports QoS-aware service discovery in ubiquitous computing environments. Our contribution lies in substantiating QoS awareness in the following three aspects. Firstly, during the process of discovering services, the expiring wireless links resulting from device mobility are identified and avoided since they cause service failures and thus hamper service reliability. Secondly, as mu tiple services can be discovered, a comprehensive utility function is proposed to evaluate services in terms of their various non-functional properties, meanwhile taking into account the service user's preferences among them, for the purpose of selecting the best one. Thirdly, to avoid untrustworthy services, a distributed reputation mechanism is proposed to facilitate the evaluation of the service host's trustworthiness. The above three proposed solutions are extensively evaluated respectively, based on analysis and simulation. They are further incorporated into a middleware that supports QoS aware Web service discovery in ubiquitous computing environments. A prototype implementing the middleware is deployed and evaluated. The results show that the overhead introduced by QoS awareness seems reasonable.

<p>The process of drug discovery from natural products starts with the selection of study object. In this project recent knowledge and methods are incorporated to investigate the process of such selection for pharmacognostic investigations. As the model and object of study mistletoes and their content of the small cytotoxic peptides thionins are chosen.</p><p>The thionins are compared in silico to other proposed plant innate defense peptides. Utilizing analysis of amino acid sequences and secondary structures, the thionins are shown to be one of eight distinct groups of cystein-rich plant polypeptides analysed. Common features of thionins are exploited in an investigation of isolation methods, where a simple acidic extraction is equally efficient to isolate thionins as the laborious methods hitherto used. </p><p>An effort to study the relationships of the order Santalales was done. To infer phylogenetic relationships from DNA sequences, we increased the taxon sampling for utilized genes and regions such as <i>rbcL</i>, <i>atpB</i> and ribosomal 18S and 26S rDNA sequences within the Santalales. Analysing these together with published sequences for other tricolpate taxa a position for Santalales as sister to caryophyllids and basal to asterids is implied. This indication is supported by chemical characters such as the presence of cyclopeptide alkaloids of a kind only known from Gentianales.</p><p>To validate the chemosystematic implications from thionin distribution extracts of mistletoes collected in Panama, Taiwan and Madagascar, and the relative <i>Osyris alba</i> (Santalaceae) collected in Spain, were screened with the established fluorescence microculture cytotoxicity assay using the thionin-sensitive human lymphoma cell-line U937GTB. Bioassay guided isolation concludes that the cytotoxic compounds in Loranthaceae may however constitute another group of peptides.</p><p>In conclusion this work shows that the incorporation of informatic techniques may aid prediction and decision making when planning pharmacognostic research.</p>

WICKRAMARATHNE, T. L. (M.S., Electrical and Computer Engineering) A Belief Theoretic Approach for Automated Collaborative Filtering (May 2008) Abstract of a thesis at the University of Miami. Thesis supervised by Professor Kamal Premaratne. No. of pages in text. (84) Automated Collaborative Filtering (ACF) is one of the most successful strategies available for recommender systems. Application of ACF in more sensitive and critical applications however has been hampered by the absence of better mechanisms to accommodate imperfections (ambiguities and uncertainties in ratings, missing ratings, etc.) that are inherent in user preference ratings and propagate such imperfections throughout the decision making process. Thus one is compelled to make various "assumptions" regarding the user preferences giving rise to predictions that lack sufficient integrity. With its Dempster-Shafer belief theoretic basis, CoFiDS, the automated Collaborative Filtering algorithm proposed in this thesis, can (a) represent a wide variety of data imperfections; (b) propagate the partial knowledge that such data imperfections generate throughout the decision-making process; and (c) conveniently incorporate contextual information from multiple sources. The "soft" predictions that CoFiDS generates provide substantial exibility to the domain expert. Depending on the associated DS theoretic belief-plausibility measures, the domain expert can either render a "hard" decision or narrow down the possible set of predictions to as smaller set as necessary. With its capability to accommodate data imperfections, CoFiDS widens the applicability of ACF, from the more popular domains, such as movie and book recommendations, to more sensitive and critical problem domains, such as medical expert support systems, homeland security and surveillance, etc. We use a benchmark movie dataset and a synthetic dataset to validate CoFiDS and compare it to several existing ACF systems.

An array of ship types was used during the European Age of Expansion (early 15th to early 17th centuries), but one vessel in particular emerges from the historical records as a harbinger of discovery: the caravel. The problem is that little is known about these popular ships of discovery, despite the fair amount of historical evidence that has been uncovered. How big were they? How many men did it take to operate such a vessel? What kind of sailing characteristics did they have? How and by whom were they designed? Where did they originate and how did they develop? These questions cannot be answered by looking at the historical accounts alone. For this reason, scholars must take another approach for learning about caravels by examining additional sources, namely ancient shipbuilding treatises, archaeological evidence, surviving archaic shipbuilding techniques, and iconographic representations from the past. Information gained from the available sources reveals many of the caravel’s characteristics through time. This ship type outclassed its contemporaries during the age of exploration because of its highly adaptive characteristics. These traits were, principally, its shallow draught, speed, maneuverability, and ability to sail close to the wind. This combination of attributes made the caravel the ideal ship for reconnaissance along the rocky African coastline, as well as for making the transatlantic voyages to the New World. It was built in a Mediterranean way during its post-medieval phases, a method that still survives in some parts of the world today. During the Age of Discovery (ca. 1430 to 1530), the caravel sat low in the water, had one sterncastle, and was either lateen-rigged or had a combination of square and lateen sails. This vessel reflects the advanced shipbuilding technology that existed in Europe at this time, and played and important role in the voyages which allowed the Europeans to expand their territories around the world. The results of the studies presented in this thesis provide a history and development of the caravel, which was gradual and often obscure. What has been gained from this work is a body of information that can be applied to other studies about ancient seafaring, and can serve as a starting point for further research.