Thesis (Ph. D.)--University of Wisconsin--Madison, 1980. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Includes bibliographical references (leaves 177-180).

Thesis (M.S.)--Tennessee Technological University, 2009. / Title from title page screen (viewed on Aug. 19, 2009). Bibliography: leaves 37-39.

Thesis (Ph. D.)--University of Wisconsin--Madison, 1975. / Typescript. Vita. eContent provider-neutral record in process. Description based on print version record. Bibliography: leaves 103-109.

Thesis (M.S.)--Duquesne University, 2005. / Title from document title page. Abstract included in electronic submission form. Includes bibliographical references and abstract.

Genes, the fundamental building blocks of life, act together (often through their derived proteins) in modules such as protein complexes and molecular pathways to achieve a cellular function such as DNA repair and cellular transport. A current emphasis in genomics research is to identify gene modules from gene profiles, which are measurements (such as a mutant phenotype or an expression level), associated with the individual genes under conditions of interest; genes in modules often have similar gene profiles. Clustering groups of genes with similar profiles can hence deliver candidate gene modules. Pairwise similarity measures derived from these profiles are used as input to the popular hierarchical agglomerative clustering algorithms; however, these algorithms offer little guidance on how to choose candidate modules and how to improve a clustering as new data becomes available. As an alternative, there are methods based on thresholding the similarity values to obtain a graph; such a graph can be analyzed through (probabilistic) methods developed in the social sciences. However, thresholding the data discards valuable information and choosing the threshold is difficult. Extending binary relational analysis, we exploit ranked relational data as the basis for two distinct approaches for identifying modules from genomic data, both based on the theory of random graph processes. We propose probabilistic models for ranked relational data that allow candidate modules to be accompanied by objective confidence scores and that permit an elegant integration of external information on gene-gene relationships. We first followed theoretical work by Ling to objectively select exceptionally isolated groups as candidate gene modules. Secondly, inspired by stochastic block models used in the social sciences, we construct a novel model for ranked relational data, where all genes have hidden module parameters which govern the strength of all gene-gene relationships. Adapting a classical likelihood often used for the analysis of horse races, clustering is performed by estimating the module parameters using standard Bayesian methods. The method allows the incorporation of prior information on gene-gene relationships; the utility of using prior information in the form of protein-protein interaction data in clustering of yeast mutant phenotype profiles is demonstrated. / Science, Faculty of / Statistics, Department of / Graduate

The removal of coherent noise generated by surface waves in land based seismic is a prerequisite to imaging the subsurface. These surface waves, termed as ground roll, overlay important reflector information in both the t-x and f-k domains. Standard techniques of ground roll removal commonly alter reflector information as a consequence of the ground roll removal. We propose the combined use of the curvelet domain as a sparsifying basis in which to perform signal separation techniques that can preserve reflector information while increasing ground roll removal. We examine two signal separation techniques, a block-coordinate relaxation method and a Bayesian separation method. The derivations and background for both methods are presented and the parameter sensitivity is examined. Both methods are shown to be effective in certain situations regarding synthetic data and erroneous surface wave predictions. The block-coordinate relaxation method is shown to have major weaknesses when dealing with seismic signal separation in the presence of noise and with the production of artifacts and reflector degradation. The Bayesian separation method is shown to improve overall separation for both seismic and real data. The Bayesian separation scheme is used on a real data set with a surface wave prediction containing reflector information. It is shown to improve the signal separation by recovering reflector information while improving the surface wave removal. The abstract contains a separate real data example where both the block-coordinate relaxation method and the Bayesian separation method are compared. / Science, Faculty of / Earth, Ocean and Atmospheric Sciences, Department of / Graduate

Modelling complex systems such as how the white rhinoceros Ceratotherium simum simum uses a landscape requires innovative and multi-disciplinary approaches. Bayesian networks have been shown to provide a dynamic, easily interpretable framework to represent real-world problems. This, together with advances in remote sensor technology to easily quantify environmental variables, make non-intrusive techniques for understanding and inference of ecological processes more viable than ever. However, when modelling an animal’s use of a landscape we only have access to presence locations. These data are also extremely susceptible to both temporal and spatial sampling bias in that animal presence locations often originate from aerial surveys or from individual rhinos fitted with tracking collars. In modelling species’ presence, little recognition is given to finding quantifiable drivers and managing confounding variables. Here we use presence-unlabelled modelling to construct Bayesian networks for rhino presence with remotely sensed covariates and show how it can provide an understanding of a complex system in a temporal and spatial context. We find that strategic unlabelled data sampling is important to counter sampling biases and discretisation of covariate data needs to be well considered in the tradeoff between computational efficiency and data accuracy. We show how learned Bayesian networks can be used to not only reveal interesting relations between drivers of rhino presence, but also to perform inference. Having temporally aware environmental variables such as soil moisture and distance to fire, allowed us to infer rhino presences for the following time step with incomplete evidence. We confirmed that in general, white rhinos tend to be close to surface water, rivers and previously burned areas with a preference for warm slopes. These relationships between drivers shift notably when modelling for individuals. We anticipate our dissertation to be a starting point for more sophisticated models of complex systems specifically investigating its use to model individual behaviour. / Dissertation (MEng)--University of Pretoria, 2020. / Industrial and Systems Engineering / MEng (Industrial Engineering) / Unrestricted

Bayesian inverse modelling provides a top-down technique of verifying emissions and uptake of carbon dioxide (CO₂) from both natural and anthropogenic sources. It relies on accurate measurements of CO₂ concentrations at appropriately placed sites and "best-guess" initial estimates of the biogenic and anthropogenic emissions, together with uncertainty estimates. The Bayesian framework improves current estimates of CO₂ fluxes based on independent measurements of CO₂ concentrations while being constrained by the initial estimates of these fluxes. Monitoring, reporting and verification (MRV) is critical for establishing whether emission reducing activities to mitigate the effects of climate change are being effective, and the Bayesian inverse modelling approach of correcting CO₂ flux estimates provides one of the tools regulators and researchers can use to refine these emission estimates. South Africa is known to be the largest emitter of CO₂ on the African continent. The first major objective of this research project was to carry out such an optimal network design for South Africa. This study used fossil fuel emission estimates from a satellite product based on observations of night-time lights and locations of power stations (Fossil Fuel Data Assimilations System (FFDAS)), and biogenic productivity estimates from a carbon assessment carried out for South Africa to provide the initial CO₂ flux estimates and their uncertainties. Sensitivity analyses considered changes to the covariance matrix and spatial scale of the inversion, as well as different optimisation algorithms, to assess the impact of these specifications on the optimal network solution. This question was addressed in Chapters 2 and 3. The second major objective of this project was to use the Bayesian inverse modelling approach to obtain estimates of CO₂ fluxes over Cape Town and surrounding area. I collected measurements of atmospheric CO₂ concentrations from March 2012 until July 2013 at Robben Island and Hangklip lighthouses. CABLE (Community Atmosphere Biosphere Land Exchange), a land-atmosphere exchange model, provided the biogenic estimates of CO₂ fluxes and their uncertainties. Fossil fuel estimates and uncertainties were obtained by means of an inventory analysis for Cape Town. As an inventory analysis was not available for Cape Town, this exercise formed an additional objective of the project, presented in Chapter 4. A spatially and temporally explicit, high resolution surface of fossil fuel emission estimates was derived from road vehicle, aviation and shipping vessel count data, population census data, and industrial fuel use statistics, making use of well-established emission factors. The city-scale inversion for Cape Town solved for weekly fluxes of CO₂ emissions on a 1 km × 1 km grid, keeping fossil fuel and biogenic emissions as separate sources. I present these results for the Cape Town inversion under the proposed best available configuration of the Bayesian inversion framework in Chapter 5. Due to the large number of CO₂ sources at this spatial and temporal resolution, the reference inversion solved for weekly fluxes in blocks of four weeks at a time. As the uncertainties around the biogenic flux estimates were large, the inversion corrected the prior fluxes predominantly through changes to the biogenic fluxes. I demonstrated the benefit of using a control vector with separate terms for fossil fuel and biogenic flux components. Sensitivity analyses, solving for average weekly fluxes within a monthly inversion, as well as solving for separate weekly fluxes (i.e. solving in one week blocks) were considered. Sensitivity analyses were performed which focused on how changes to the prior information and prior uncertainty estimates and the error correlations of the fluxes would impact on the Bayesian inversion solution. The sensitivity tests are presented in Chapter 6. These sensitivity analyses indicated that refining the estimates of biogenic fluxes and reducing their uncertainties, as well as taking advantage of spatial correlation between areas of homogeneous biota would lead to the greatest improvement in the accuracy and precision of the posterior fluxes from the Cape Town metropolitan area.

Includes bibliographical references (pages. 379-400). / This dissertation responds to the need for integration between researchers and decision-makers who are dealing with complex social-ecological system sustainability and decision-making challenges. To this end, we propose a new approach, called Bayesian Participatory-based Decision Analysis (BPDA), which makes use of graphical causal maps and Bayesian networks to facilitate integration at the appropriate scales and levels of descriptions. The BPDA approach is not a predictive approach, but rather, caters for a wide range of future scenarios in anticipation of the need to adapt to unforeseeable changes as they occur. We argue that the graphical causal models and Bayesian networks constitute an evolutionary, adaptive formalism for integrating research and decision-making for sustainable development. The approach was implemented in a number of different interdisciplinary case studies that were concerned with social-ecological system scale challenges and problems, culminating in a study where the approach was implemented with decision-makers in Government. This dissertation introduces the BPDA approach, and shows how the approach helps identify critical cross-scale and cross-sector linkages and sensitivities, and addresses critical requirements for understanding system resilience and adaptive capacity.

Perception relies on the integration of numerous noisy inputs (cues). Cue combination has been relatively understudied in somatosensation, compared to vision and audition. Here, we investigated whether haptic cutaneous and hand configuration cues are combined optimally to discriminate between coin-sized discs of different sizes. When the hand is open such that the thumb and index fingers span the diameter of a disc to contact its perimeter, cutaneous cues occur from the indentation of the skin caused by the curvature of the disc (smaller discs cause greater indentation). Simultaneously, the hand configuration cue (relating to the perceived distance between fingers), provides an additional cue to size. These cues may vary in their reliability. In three experiments involving 34 participants, we measured these cues and considered three hypotheses for how humans may use them: humans rely solely on the least noisy cue (Winner-Take-All Model), humans combine cues based on a simple average (Average-Measurement Model), or humans combine cues via an optimal weighted average (Optimally-Weighted Model). Each experiment tested participants using a two-interval forced-choice (2IFC) paradigm with 3D printed disc stimuli. On each trial, under occluded vision, participants felt two discs sequentially and responded which felt larger. Participants were tested with each finger’s cutaneous cue alone, the hand configuration cue alone, and all cues together. In two experiments, the presented discs were both circular. In a third experiment, unknown to participants, some of the presented discs were oval-like cue conflict stimuli. Participant performance was compared to predictions of the cue combination models. We conclude that humans may combine haptic cutaneous and hand configuration cues optimally to judge the size of held objects. / Thesis / Doctor of Philosophy (PhD) / The sense of touch is understudied compared to the senses of sight and hearing. But simply reaching for a coin without looking involves complex calculations and decision-making. We studied how the brain may approach tasks like this. We were interested in how well the brain deals with multiple sources of information that do not always agree with each other. We investigated these questions in computer simulations and in experiments with undergraduate participants. Using carefully designed 3D-printed discs, we tested dozens of participants across 3 different experiments. Our results show that humans may use information in the best possible way and applications relevant to VR and robot-assisted surgery.