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Full-Text Articles in Physical Sciences and Mathematics
Bayesian Networks To Assess The Newborn Stool Microbiome, William E. Bennett Jr.
Bayesian Networks To Assess The Newborn Stool Microbiome, William E. Bennett Jr.
McKelvey School of Engineering Theses & Dissertations
In human stool, a large population of bacterial genes and transcripts from hundreds of genera coexist with host genes and transcripts. Assessments of the metagenome and transcriptome are particularly challenging, since there is a great deal of sequence overlap among related species and related genes. We sequenced the total RNA content from stool samples in a neonate using previously-described methods. We then performed stepwise alignment of different populations of RNA sequence reads to different indices, including ribosomal databases, the human genome, and all sequenced bacterial genomes. Each pool of RNA at each alignment step was subjected to compression to assess …
Shortest Path Based Decision Making Using Probabilistic Inference, Akshat Kumar
Shortest Path Based Decision Making Using Probabilistic Inference, Akshat Kumar
Research Collection School Of Computing and Information Systems
We present a new perspective on the classical shortest path routing (SPR) problem in graphs. We show that the SPR problem can be recast to that of probabilistic inference in a mixture of simple Bayesian networks. Maximizing the likelihood in this mixture becomes equivalent to solving the SPR problem. We develop the well known Expectation-Maximization (EM) algorithm for the SPR problem that maximizes the likelihood, and show that it does not get stuck in a locally optimal solution. Using the same probabilistic framework, we then address an NP-Hard network design problem where the goal is to repair a network of …