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Full-Text Articles in Physical Sciences and Mathematics
Nonparametric Bayesian Deep Learning For Scientific Data Analysis, Devanshu Agrawal
Nonparametric Bayesian Deep Learning For Scientific Data Analysis, Devanshu Agrawal
Doctoral Dissertations
Deep learning (DL) has emerged as the leading paradigm for predictive modeling in a variety of domains, especially those involving large volumes of high-dimensional spatio-temporal data such as images and text. With the rise of big data in scientific and engineering problems, there is now considerable interest in the research and development of DL for scientific applications. The scientific domain, however, poses unique challenges for DL, including special emphasis on interpretability and robustness. In particular, a priority of the Department of Energy (DOE) is the research and development of probabilistic ML methods that are robust to overfitting and offer reliable …
Statistical Methods For Resolving Intratumor Heterogeneity With Single-Cell Dna Sequencing, Alexander Davis
Statistical Methods For Resolving Intratumor Heterogeneity With Single-Cell Dna Sequencing, Alexander Davis
Dissertations & Theses (Open Access)
Tumor cells have heterogeneous genotypes, which drives progression and treatment resistance. Such genetic intratumor heterogeneity plays a role in the process of clonal evolution that underlies tumor progression and treatment resistance. Single-cell DNA sequencing is a promising experimental method for studying intratumor heterogeneity, but brings unique statistical challenges in interpreting the resulting data. Researchers lack methods to determine whether sufficiently many cells have been sampled from a tumor. In addition, there are no proven computational methods for determining the ploidy of a cell, a necessary step in the determination of copy number. In this work, software for calculating probabilities from …
Multi-Omics Integration For Gene Fusion Discovery And Somatic Mutation Haplotyping In Cancer, Steven Mason Foltz
Multi-Omics Integration For Gene Fusion Discovery And Somatic Mutation Haplotyping In Cancer, Steven Mason Foltz
Arts & Sciences Electronic Theses and Dissertations
Cancer is a disease caused by changes to the genome and dysregulation of gene expression. Among many types of mutations, including point mutations, small insertions and deletions, large scale structural variants, and copy number changes, gene fusions are another category of genomic and transcriptomic alteration that can lead to cancer and which can serve as therapeutic targets. We studied gene fusion events using data from The Cancer Genome Atlas, including over 9,000 patients from 33 cancer types, finding patterns of gene fusion events and dysregulation of gene expression within and across cancer types. With data from the CoMMpass study (Multiple …