Machine Learning Approaches to Tumor Estimation of Whole Slide Images

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Description

Molecular pathology makes use of estimates of tumor content (tumor percentage) for pre-analytic and analytic purposes, such as molecular oncology testing, massive parallel sequencing, or next-generation sequencing (NGS), assessment of sample acceptability, accurate quantitation of variants, assessment of copy number

Molecular pathology makes use of estimates of tumor content (tumor percentage) for pre-analytic and analytic purposes, such as molecular oncology testing, massive parallel sequencing, or next-generation sequencing (NGS), assessment of sample acceptability, accurate quantitation of variants, assessment of copy number changes (among other applications), determination of specimen viability for testing (since many assays require a minimum tumor content to report variants at the limit of detection) may all be improved with more accurate and reproducible estimates of tumor content. Currently, tumor percentages of samples submitted for molecular testing are estimated by visual examination of Hematoxylin and Eosin (H&E) stained tissue slides under the microscope by pathologists. These estimations can be automated, expedited, and rendered more accurate by applying machine learning methods on digital whole slide images (WSI).

Date Created
2022-05
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Fluid flow in a temperature-stratified, parametrically forced regime

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Description

This project is a synthesis of the author's learning over the semesters in working with the CFD Group at Arizona State University. The incompressible Navier-Stokes equations are overviewed, starting with the derivation from the continuity equation, then non-dimensionalization, methods of

This project is a synthesis of the author's learning over the semesters in working with the CFD Group at Arizona State University. The incompressible Navier-Stokes equations are overviewed, starting with the derivation from the continuity equation, then non-dimensionalization, methods of solving and computing quantities of interest. The rest of this document is expository analysis of solutions in a confined fluid flow, building toward a parametrically forced regime that generates complex flow patterns including Faraday waves. The solutions come from recently published studies Dynamics in a stably stratified tilted square cavity (Grayer et al.) and Parametric instabilities of a stratified shear layer (Buchta et al).

Date Created
2021-05
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Parametric Forcing of Confined and Stratified Flows

Description
A continuously and stably stratified fluid contained in a square cavity subjected to harmonic body forcing is studied numerically by solving the Navier-Stokes equations under the Boussinesq approximation. Complex dynamics are observed near the onset of instability of the basic

A continuously and stably stratified fluid contained in a square cavity subjected to harmonic body forcing is studied numerically by solving the Navier-Stokes equations under the Boussinesq approximation. Complex dynamics are observed near the onset of instability of the basic state, which is a flow configuration that is always an exact analytical solution of the governing equations. The instability of the basic state to perturbations is first studied with linear stability analysis (Floquet analysis), revealing a multitude of intersecting synchronous and subharmonic resonance tongues in parameter space. A modal reduction method for determining the locus of basic state instability is also shown, greatly simplifying the computational overhead normally required by a Floquet study. Then, a study of the nonlinear governing equations determines the criticality of the basic state's instability, and ultimately characterizes the dynamics of the lowest order spatial mode by the three discovered codimension-two bifurcation points within the resonance tongue. The rich dynamics include a homoclinic doubling cascade that resembles the logistic map and a multitude of gluing bifurcations.

The numerical techniques and methodologies are first demonstrated on a homogeneous fluid contained within a three-dimensional lid-driven cavity. The edge state technique and linear stability analysis through Arnoldi iteration are used to resolve the complex dynamics of the canonical shear-driven benchmark problem. The techniques here lead to a dynamical description of an instability mechanism, and the work serves as a basis for the remainder of the dissertation.
Date Created
2019
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