Knowledge discovery using multiple sources of biological data

The primary aim of this dissertation is to develop data mining tools for knowledge discovery in biomedical data when multiple (homogeneous or heterogeneous) sources of data are available. The central hypothesis is that, when information from multiple sources of data are used appropriately and effectively, knowledge discovery can be better achieved than what is possible from only a single source. ^ Recent advances in high-throughput technology have enabled biomedical researchers to generate large volumes of diverse types of data on a genome-wide scale. These data include DNA sequences, gene expression measurements, and much more; they provide the motivation for building analysis tools to elucidate the modular organization of the cell. The challenges include efficiently and accurately extracting information from the multiple data sources; representing the information effectively, developing analytical tools, and interpreting the results in the context of the domain. ^ The first part considers the application of feature-level integration to design classifiers that discriminate between soil types. The machine learning tools, SVM and KNN, were used to successfully distinguish between several soil samples. ^ The second part considers clustering using multiple heterogeneous data sources. The resulting Multi-Source Clustering (MSC) algorithm was shown to have a better performance than clustering methods that use only a single data source or a simple feature-level integration of heterogeneous data sources. ^ The third part proposes a new approach to effectively incorporate incomplete data into clustering analysis. Adapted from K-means algorithm, the Generalized Constrained Clustering (GCC) algorithm makes use of incomplete data in the form of constraints to perform exploratory analysis. Novel approaches for extracting constraints were proposed. For sufficiently large constraint sets, the GCC algorithm outperformed the MSC algorithm. ^ The last part considers the problem of providing a theme-specific environment for mining multi-source biomedical data. The database called PlasmoTFBM, focusing on gene regulation of Plasmodium falciparum, contains diverse information and has a simple interface to allow biologists to explore the data. It provided a framework for comparing different analytical tools for predicting regulatory elements and for designing useful data mining tools. ^ The conclusion is that the experiments reported in this dissertation strongly support the central hypothesis.^

The effects of intellectual property rights on knowledge spillovers and innovation: An empirical investigation

FDI is believed to be a conduit of new technologies between countries. The first chapter of this dissertation studies the advantages of outward FDI for the home country of multinationals conducting research and development abroad. We use patent citations as a proxy for technology spillovers and we bring empirical evidence that supports the hypothesis that a U.S. subsidiary conducting research and development overseas facilitates the flow of knowledge between its host and home countries.^ The second chapter examines the impact of intellectual property rights (IPR) reforms on the technology flows between the U.S. and host countries of U.S. affiliates. We again use patent citations to examine whether the diffusion of new technology between the host countries and the U.S. is accelerated by the reforms. Our results suggest that the reforms favor innovative efforts of domestic firms in the reforming countries rather than U.S. affiliates efforts. In other words, reforms mediate the technology flows from the U.S. to the reforming countries.^ The third chapter deals with another form of IPR, open source (OS) licenses. These differ in the conditions under which licensors and OS contributors are allowed to modify and redistribute the source code. We measure OS project quality by the speed with which programming bugs are fixed and test whether the license chosen by project leaders influences bug resolution rates. In initial regressions, we find a strong correlation between the hazard of bug resolution and the use of highly restrictive licenses. However, license choices are likely to be endogenous. We instrument license choice using (i) the human language in which contributors operate and (ii) the license choice of the project leaders for a previous project. We then find weak evidence that restrictive licenses adversely affect project success.^

Source/receptor reconciliation of ambient organic fine particulate matter in Palm Beach County

Airborne particulate matter (PM) is of environmental concern not only in urban but also rural areas that are easily inhalable and have been considered responsible, together with gaseous pollutants, for possible health effects. The objectives of this research study is to generate an extensive data set for ambient PM collected at Belle Glade and Delray Beach that ultimately was used together with published source profiles to predict the contributions of major sources to the overall airborne particle burden in Belle Glade and Delray Beach. ^ The size segregated particle sampling was conducted for one entire year. The samples collected during the months of January and May were further subjected to chemical analysis for organic compounds by Gas Chromatography-Mass Spectrometry. Additional, PM10 sampling was conducted simultaneously with size segregated particle sampling during January and May to analyze for trace elements using Instrumental Neutron Activation Analysis technique. Elements and organic marker compounds were used in Chemical Mass Balance modeling to determine the major source contribution to the ambient fine particle matter burden. ^ Size segregated particle distribution results show bimodal in both sampling sites. Sugarcane pre-harvest burning in the rural site elevated PM10 concentration by about 30% during the sugarcane harvest season compared to sugarcane growing season. Sea salt particles and Saharan dust particles accounted for the external sources. ^ The results of trace element analysis show that Al, Ca, Cs, Eu, Lu, Nd, Sc, Sm, Th, and Yb are more abundant at the rural sampling site. The trace elements Ba, Br, Ce, Cl, Cr, Fe, Gd, Hf, Na, Sb, Ta, V, and W show high abundance at the urban site due to anthropogenic activities except for Na and Cl, which are from sea salt spray. On the other hand, size segregated trace organic compounds measurements show that organic compounds mainly from combustion process were accumulated in PM0.95. ^ In conclusion, major particle sources were determined by the CMB8.2 software as follows: road dust, sugarcane leaf burning, diesel-powered and gasoline powered vehicle exhaust, leaf surface abrasion particles, and a very small fraction of meat cooking. ^

Social network structure as a critical success condition for open source software project communities

In recent years, a surprising new phenomenon has emerged in which globally-distributed online communities collaborate to create useful and sophisticated computer software. These open source software groups are comprised of generally unaffiliated individuals and organizations who work in a seemingly chaotic fashion and who participate on a voluntary basis without direct financial incentive. ^ The purpose of this research is to investigate the relationship between the social network structure of these intriguing groups and their level of output and activity, where social network structure is defined as (1) closure or connectedness within the group, (2) bridging ties which extend outside of the group, and (3) leader centrality within the group. Based on well-tested theories of social capital and centrality in teams, propositions were formulated which suggest that social network structures associated with successful open source software project communities will exhibit high levels of bridging and moderate levels of closure and leader centrality. ^ The research setting was the SourceForge hosting organization and a study population of 143 project communities was identified. Independent variables included measures of closure and leader centrality defined over conversational ties, along with measures of bridging defined over membership ties. Dependent variables included source code commits and software releases for community output, and software downloads and project site page views for community activity. A cross-sectional study design was used and archival data were extracted and aggregated for the two-year period following the first release of project software. The resulting compiled variables were analyzed using multiple linear and quadratic regressions, controlling for group size and conversational volume. ^ Contrary to theory-based expectations, the surprising results showed that successful project groups exhibited low levels of closure and that the levels of bridging and leader centrality were not important factors of success. These findings suggest that the creation and use of open source software may represent a fundamentally new socio-technical development process which disrupts the team paradigm and which triggers the need for building new theories of collaborative development. These new theories could point towards the broader application of open source methods for the creation of knowledge-based products other than software. ^

Adaptation in knowledge-based teams: An examination of team composition, leader sensegiving, and cognitive, behavioral, and motivational mechanisms

Organizations are increasingly relying on teams to do the work that has traditionally been done by individuals. At the same time, the environments in which these organizations and teams operate have been becoming progressively more complex and uncertain. These trends raise important questions about the factors that enable teams to adapt. In response to these questions, the current study sought to identify the cognitive, behavioral, and motivational processes and emergent states that promote a team's adaptation to unforeseen changes and novel events, and the team compositional characteristics and leadership processes that enabled these processes and emergent states. Two hundred twenty two undergraduate students from a large Southeastern University composed 74 3-person teams, and participated in a computerized decision-making simulation where each team formed the governing body (i.e., Mayor's cabinet) for two separate simulated cities, and made strategic decisions about city operations. Participants were randomly assigned to one of three roles, distributing expertise and creating mutual interdependence. External team leader sensegiving was manipulated through video recorded communications from an external team leader. Results indicate that team cognitive ability, achievement striving, and psychological collectivism, as well as external team leader sensegiving, were all related to the similarity and quality of team members' strategy-focused mental models (cognitive emergent states), and to the amount of information sharing among members (behavioral process). In turn, teams with more similar and higher quality mental models, and who shared greater levels of information, were found to have a greater ability to react and adapt to environmental changes, and to have greater levels of decision-making effectiveness. Results indicate a pattern of relationships consistent with hypotheses, and have important implications for organizations and knowledge-based teams charged with management responsibilities. Organizations should staff teams with the compositional characteristics that enable the development of similar and high quality mental models, and that promote information sharing among teammates. Similarly, organizations which train and develop leaders to engage in sensegiving behaviors enable team adaptability and promote enhanced decision-making effectiveness when faced with unforeseen changes and novel situations.

Effect of performance feedback on perceived knowledge and likelihood to pursue continuing education

The purpose of this study was to assess the effect of performance feedback on Athletic Trainers’ (ATs) perceived knowledge (PK) and likelihood to pursue continuing education (CE). The investigation was grounded in the theories of “the definition of the situation” (Thomas & Thomas, 1928) and the “illusion of knowing,” (Glenberg, Wilkinson, & Epstein, 1982) suggesting that PK drives behavior. This investigation measured the degree to which knowledge gap predicted CE seeking behavior by providing performance feedback designed to change PK. A pre-test post-test control-group design was used to measure PK and likelihood to pursue CE before and after assessing actual knowledge. ATs (n=103) were randomly sampled and assigned to two groups, with and without performance feedback. Two independent samples t-tests were used to compare groups on the difference scores of the dependent variables. Likelihood to pursue CE was predicted by three variables using multiple linear regression: perceived knowledge, pre-test likelihood to pursue CE, and knowledge gap. There was a 68.4% significant difference (t101=2.72, p=0.01, ES=0.45) between groups in the change scores for likelihood to pursue CE because of the performance feedback (Experimental group=13.7% increase; Control group=4.3% increase). The strongest relationship among the dependent variables was between pre-test and post-test measures of likelihood to pursue CE (F2,102=56.80, p<0.01, r=0.73, R2=0.53). The pre- and post-test predictive relationship was enhanced when group was included in the model. In this model [YCEpost=0.76XCEpre-0.34 Xgroup+2.24+E], group accounted for a significant amount of unique variance in predicting CE while the pre-test likelihood to pursue CE variable was held constant (F3,102=40.28, p<0.01, r=0.74, R2=0.55). Pre-test knowledge gap, regardless of group allocation, was a linear predictor of the likelihood to pursue CE (F1,102=10.90, p=.01, r=.31, R2=.10). In this investigation, performance feedback significantly increased participants’ likelihood to pursue CE. Pre-test knowledge gap was a significant predictor of likelihood to pursue CE, regardless if performance feedback was provided. ATs may have self-assessed and engaged in internal feedback as a result of their test-taking experience. These findings indicate that feedback, both internal and external, may be necessary to trigger CE seeking behavior.

The Influence of Purchase Confidence on Information Source Selection: Implications for Hospitality Industry

Whether the product of choice is a restaurant, vacation resort or hotel, it is important for hospitality marketers to understand how consumers treat purchase decisions and the influence purchase confidence and situation play on that decision. This study investigated the role purchase confidence plays with knowledge in the selection of sources of information during purchase decisions. The results indicate sources of information are perceived differently by consumers and depending on the purchase situation, subjective knowledge is influenced by purchase confidence affecting the source of information considered when making a purchase decision. The results also indicated that those with high purchase confidence and subjective knowledge will rely on themselves as a source when making a purchase rather than a retail clerk or published material.

Social Network Structure as a Critical Success Condition for Open Source Software Project Communities

In recent years, a surprising new phenomenon has emerged in which globally-distributed online communities collaborate to create useful and sophisticated computer software. These open source software groups are comprised of generally unaffiliated individuals and organizations who work in a seemingly chaotic fashion and who participate on a voluntary basis without direct financial incentive. The purpose of this research is to investigate the relationship between the social network structure of these intriguing groups and their level of output and activity, where social network structure is defined as 1) closure or connectedness within the group, 2) bridging ties which extend outside of the group, and 3) leader centrality within the group. Based on well-tested theories of social capital and centrality in teams, propositions were formulated which suggest that social network structures associated with successful open source software project communities will exhibit high levels of bridging and moderate levels of closure and leader centrality. The research setting was the SourceForge hosting organization and a study population of 143 project communities was identified. Independent variables included measures of closure and leader centrality defined over conversational ties, along with measures of bridging defined over membership ties. Dependent variables included source code commits and software releases for community output, and software downloads and project site page views for community activity. A cross-sectional study design was used and archival data were extracted and aggregated for the two-year period following the first release of project software. The resulting compiled variables were analyzed using multiple linear and quadratic regressions, controlling for group size and conversational volume. Contrary to theory-based expectations, the surprising results showed that successful project groups exhibited low levels of closure and that the levels of bridging and leader centrality were not important factors of success. These findings suggest that the creation and use of open source software may represent a fundamentally new socio-technical development process which disrupts the team paradigm and which triggers the need for building new theories of collaborative development. These new theories could point towards the broader application of open source methods for the creation of knowledge-based products other than software.

Effect of Performance Feedback on Perceived Knowledge and Likelihood to Pursue Continuing Education

The purpose of this study was to assess the effect of performance feedback on Athletic Trainers’ (ATs) perceived knowledge (PK) and likelihood to pursue continuing education (CE). The investigation was grounded in the theories of “the definition of the situation” (Thomas & Thomas, 1928) and the “illusion of knowing,” (Glenberg, Wilkinson, & Epstein, 1982) suggesting that PK drives behavior. This investigation measured the degree to which knowledge gap predicted CE seeking behavior by providing performance feedback designed to change PK. A pre-test post-test control-group design was used to measure PK and likelihood to pursue CE before and after assessing actual knowledge. ATs (n=103) were randomly sampled and assigned to two groups, with and without performance feedback. Two independent samples t-tests were used to compare groups on the difference scores of the dependent variables. Likelihood to pursue CE was predicted by three variables using multiple linear regression: perceived knowledge, pre-test likelihood to pursue CE, and knowledge gap. There was a 68.4% significant difference (t101= 2.72, p=0.01, ES=0.45) between groups in the change scores for likelihood to pursue CE because of the performance feedback (Experimental group=13.7% increase; Control group= 4.3% increase). The strongest relationship among the dependent variables was between pre-test and post-test measures of likelihood to pursue CE (F2,102=56.80, p<0.01, r=0.73, R2=0.53). The pre- and post-test predictive relationship was enhanced when group was included in the model. In this model [YCEpost=0.76XCEpre-0.34 Xgroup+2.24+E], group accounted for a significant amount of unique variance in predicting CE while the pre-test likelihood to pursue CE variable was held constant (F3,102=40.28, p<0.01,: r=0.74, R2=0.55). Pre-test knowledge gap, regardless of group allocation, was a linear predictor of the likelihood to pursue CE (F1,102=10.90, p=.01, r=.31, R2=.10). In this investigation, performance feedback significantly increased participants’ likelihood to pursue CE. Pre-test knowledge gap was a significant predictor of likelihood to pursue CE, regardless if performance feedback was provided. ATs may have self-assessed and engaged in internal feedback as a result of their test-taking experience. These findings indicate that feedback, both internal and external, may be necessary to trigger CE seeking behavior.