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Phylogenetic analyses that were conducted in the past didn't have the ability or functionality to inform and implement useful public health decisions while using clustering. Models can be constructed to conduct any further analyses for the result of meaningful data to be used in the future of public health informatics.

Phylogenetic analyses that were conducted in the past didn't have the ability or functionality to inform and implement useful public health decisions while using clustering. Models can be constructed to conduct any further analyses for the result of meaningful data to be used in the future of public health informatics. A phylogenetic tree is considered one of the best ways for researchers to visualize and analyze the evolutionary history of a certain virus. The focus of this study was to research HIV phylodynamic and phylogenetic methods. This involved identifying the fast growing HIV transmission clusters and rates for certain risk groups in the US. In order to achieve these results an HIV database was required to retrieve real-time data for implementation, alignment software for multiple sequence alignment, Bayesian analysis software for the development and manipulation of models, and graphical tools for visualizing the output from the models created. This study began by conducting a literature review on HIV phylogeographies and phylodynamics. Sequence data was then obtained from a sequence database to be run in a multiple alignment software. The sequence that was obtained was unaligned which is why the alignment was required. Once the alignment was performed, the same file was loaded into a Bayesian analysis software for model creation of a phylogenetic tree. When the model was created, the tree was edited in a tree visualization software for the user to easily interpret. From this study the output of the tree resulted the way it did, due to a distant homology or the mixing of certain parameters. For a further continuation of this study, it would be interesting to use the same aligned sequence and use different model parameter selections for the initial creation of the model to see how the output changes. This is because one small change for the model parameter could greatly affect the output of the phylogenetic tree.
ContributorsNandan, Meghana (Author) / Scotch, Matthew (Thesis director) / Liu, Li (Committee member) / Biomedical Informatics Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
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Artificial intelligence is one of the biggest topics being discussed in the realm of Computer Science and it has made incredible breakthroughs possible in so many different industries. One of the largest issues with utilizing computational resources in the health industry historically is centered around the quantity of data, the

Artificial intelligence is one of the biggest topics being discussed in the realm of Computer Science and it has made incredible breakthroughs possible in so many different industries. One of the largest issues with utilizing computational resources in the health industry historically is centered around the quantity of data, the specificity of conditions for accurate results, and the general risks associated with being incorrect in an analysis. Although these all have been major issues in the past, the application of artificial intelligence has opened up an entirely different realm of possibilities because accessing massive amounts of patient data, is essential for generating an extremely accurate model in machine learning. The goal of this project is to analyze tools and algorithm design techniques used in recent times to accelerate data processing in the realm of healthcare, but one of the most important discoveries is that the standardization of conditioned data being fed into the models is almost more important than the algorithms or tools being used combined.

ContributorsJanes, Jacob (Author) / Bansal, Ajay (Thesis director) / Baron, Tyler (Committee member) / Barrett, The Honors College (Contributor) / Software Engineering (Contributor)
Created2022-05
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Description

Electron Multiplying Charge Coupled Device (EMCCD) cameras are widely used for fluorescence microscopy experiments. However, the quantitative determination of biological parameters uniquely depends on characteristics of the unavoidably inhomogenous illumination profile as it gives rise to an image. It is therefore of interest to learn this inhomogenous illumination profiles that

Electron Multiplying Charge Coupled Device (EMCCD) cameras are widely used for fluorescence microscopy experiments. However, the quantitative determination of biological parameters uniquely depends on characteristics of the unavoidably inhomogenous illumination profile as it gives rise to an image. It is therefore of interest to learn this inhomogenous illumination profiles that can dramatically vary across images alongside the camera parameters though a detailed camera model. In this manuscript we create a detailed model to learn inhomogeneous illumination profiles as well as learn all associated camera parameters. We achieve this within a Bayesian paradigm allowing us to determine full distributions over the unknowns.

ContributorsBryan, Eric (Author) / Presse, Steve (Thesis director) / Fazel, Mohammed (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Physics (Contributor)
Created2022-05