Physical Sciences and Mathematics Commons^™

Improving A Mesh Segmentation Algorithm Based On Non-Negative Matrix Factorization, Jisun Kang

Open Access Theses

3D Mesh segmentation is used in various applications such as object recognition, reconstruction, and analyzing structure of meshes. The method for 3D mesh segmentation based on sparse non-negative matrix factorization (NMF) was previously proposed. It represents a novel, and conceptually simpler, method than other comparable algorithms. However, this method still has potential to improve performance, results could have better consistency and uniqueness with faster computation time than the prior proposed algorithm. This study introduced several approaches to enhance the performance of the algorithm comprehensively: applying dierent update rule and initialization of factor matrices, and imposing sparseness to the factor matrices …

Video Annotation By Crowd Workers With Privacy-Preserving Local Disclosure, Apeksha Dipak Kumavat

Open Access Theses

Advancements in computer vision are still not reliable enough for detecting video content including humans and their actions. Microtask crowdsourcing on task markets such as Amazon Mechnical Turk and Upwork can bring humans into the loop. However, engaging crowd workers to annotate non-public video footage risks revealing the identities of people in the video who may have a right to anonymity.

This thesis demonstrates how we can engage untrusted crowd workers to detect behaviors and objects, while robustly concealing the identities of all faces. We developed a web-based system that presents obfuscated videos to crowd workers, and provides them with …

Mathematical Analysis Of Feedback Targets Of Bmp Signaling In Drosophila Embryonic Development, Yan Luo

Open Access Theses

Bone morphogenetic proteins (BMPs) drive a range of cellular processes especially in the early stages of embryonic development. This family of proteins acts as one of the most important extracellular signals in development pattern formation across the animal kingdom. Cells in embryos differentiate into different cell types in response to the concentration level of BMP. This complex process is regulated by multiple regulators that serve to tune the signal response.

Extensive experimental and computational research has been performed to analyze BMP regulation in Drosophila, a widely studied model organism, and has advanced our understanding of animal development. Because of …

A Small-Scale Testbed For Large-Scale Reliable Computing, Jason R. St. John

Open Access Theses

High performance computing (HPC) systems frequently suffer errors and failures from hardware components that negatively impact the performance of jobs run on these systems. We analyzed system logs from two HPC systems at Purdue University and created statistical models for memory and hard disk errors. We created a small-scale error injection testbed—using a customized QEMU build, libvirt, and Python—for HPC application programmers to test and debug their programs in a faulty environment so that programmers can write more robust and resilient programs before deploying them on an actual HPC system. The deliverables for this project are the fault injection program, …

Computational Environment For Modeling And Analysing Network Traffic Behaviour Using The Divide And Recombine Framework, Ashrith Barthur

Open Access Dissertations

There are two essential goals of this research. The first goal is to design and construct a computational environment that is used for studying large and complex datasets in the cybersecurity domain. The second goal is to analyse the Spamhaus blacklist query dataset which includes uncovering the properties of blacklisted hosts and understanding the nature of blacklisted hosts over time.

The analytical environment enables deep analysis of very large and complex datasets by exploiting the divide and recombine framework. The capability to analyse data in depth enables one to go beyond just summary statistics in research. This deep analysis is …

A Framework For The Statistical Analysis Of Mass Spectrometry Imaging Experiments, Kyle Bemis

Open Access Dissertations

Mass spectrometry (MS) imaging is a powerful investigation technique for a wide range of biological applications such as molecular histology of tissue, whole body sections, and bacterial films , and biomedical applications such as cancer diagnosis. MS imaging visualizes the spatial distribution of molecular ions in a sample by repeatedly collecting mass spectra across its surface, resulting in complex, high-dimensional imaging datasets. Two of the primary goals of statistical analysis of MS imaging experiments are classification (for supervised experiments), i.e. assigning pixels to pre-defined classes based on their spectral profiles, and segmentation (for unsupervised experiments), i.e. assigning pixels to newly …

Visual Analytics Of Location-Based Social Networks For Decision Support, Junghoon Chae

Open Access Dissertations

Recent advances in technology have enabled people to add location information to social networks called Location-Based Social Networks (LBSNs) where people share their communication and whereabouts not only in their daily lives, but also during abnormal situations, such as crisis events. However, since the volume of the data exceeds the boundaries of human analytical capabilities, it is almost impossible to perform a straightforward qualitative analysis of the data. The emerging field of visual analytics has been introduced to tackle such challenges by integrating the approaches from statistical data analysis and human computer interaction into highly interactive visual environments. Based on …

Combinatorial Algorithms For Perturbation Theory And Application On Quantum Computing, Yudong Cao

Open Access Dissertations

Quantum computing is an emerging area between computer science and physics. Numerous problems in quantum computing involve quantum many-body interactions. This dissertation concerns the problem of simulating arbitrary quantum many-body interactions using realistic two-body interactions. To address this issue, a general class of techniques called perturbative reductions (or perturbative gadgets) is adopted from quantum complexity theory and in this dissertation these techniques are improved for experimental considerations. The idea of perturbative reduction is based on the mathematical machinery of perturbation theory in quantum physics. A central theme of this dissertation is then to analyze the combinatorial structure of the perturbation …

Hybrid Stm/Htm For Nested Transactions In Java, Keith G. Chapman

Open Access Dissertations

Transactional memory (TM) has long been advocated as a promising pathway to more automated concurrency control for scaling concurrent programs running on parallel hardware. Software TM (STM) has the benefit of being able to run general transactional programs, but at the significant cost of overheads imposed to log memory accesses, mediate access conflicts, and maintain other transaction metadata. Recently, hardware manufacturers have begun to offer commodity hardware TM (HTM) support in their processors wherein the transaction metadata is maintained “for free” in hardware. However, HTM approaches are only best-effort: they cannot successfully run all transactional programs, whether because of hardware …

Exploring The Potential Impacts Of Climate Change On North America's Laurentian Great Lakes Tourism Sector, Natalie Chin

Open Access Dissertations

Climate change is one of the major challenges facing the global hospitality and tourism sector in the coming century and, given the important role that weather and climate play in all aspects of the tourism experience, tourism businesses owners need to start thinking about and enacting climate change adaptation strategies now. This work has utilized a combination of social science and physical science methods to (1) understand how the Great Lakes tourism sector could be impacted by climate change and (2) provide some insights into how researchers can help business owners prepare for these potential impacts. Overall, the results of …

Low Rank Methods For Optimizing Clustering, Yangyang Hou

Open Access Dissertations

Complex optimization models and problems in machine learning often have the majority of information in a low rank subspace. By careful exploitation of these low rank structures in clustering problems, we find new optimization approaches that reduce the memory and computational cost.

We discuss two cases where this arises. First, we consider the NEO-K-Means (Non-Exhaustive, Overlapping K-Means) objective as a way to address overlapping and outliers in an integrated fashion. Optimizing this discrete objective is NP-hard, and even though there is a convex relaxation of the objective, straightforward convex optimization approaches are too expensive for large datasets. We utilize low …

Effective Memory Management For Mobile Environments, Ahmed Mohamed Abd-Elhaffiez Hussein

Open Access Dissertations

Smartphones, tablets, and other mobile devices exhibit vastly different constraints compared to regular or classic computing environments like desktops, laptops, or servers. Mobile devices run dozens of so-called “apps” hosted by independent virtual machines (VM). All these VMs run concurrently and each VM deploys purely local heuristics to organize resources like memory, performance, and power. Such a design causes conflicts across all layers of the software stack, calling for the evaluation of VMs and the optimization techniques specific for mobile frameworks.

In this dissertation, we study the design of managed runtime systems for mobile platforms. More specifically, we deepen the …

Securing Cloud-Based Data Analytics: A Practical Approach, Julian James Stephen

Open Access Dissertations

The ubiquitous nature of computers is driving a massive increase in the amount of data generated by humans and machines. The shift to cloud technologies is a paradigm change that offers considerable financial and administrative gains in the effort to analyze these data. However, governmental and business institutions wanting to tap into these gains are concerned with security issues. The cloud presents new vulnerabilities and is dominated by new kinds of applications, which calls for new security solutions. In the direction of analyzing massive amounts of data, tools like MapReduce, Apache Storm, Dryad and higher-level scripting languages like Pig Latin …

Gonadal Intersex In Teleosts: Mechanisms, Molecular Biomarkers And Diagnostic Assays, Ahmed M.E. Abdel-Moneim Mohamed

Open Access Dissertations

Natural and synthetic estrogenic and androgenic compounds are continuously released into aquatic ecosystems. Exposure of teleost fishes to these contaminants can negatively impact sex differentiation and reproductive output. Specifically, development of gonadal intersex in gonochoristic (fixed sex) fish species has been studied extensively in relation to exposure to this class of compounds. The main objectives of this dissertation were to: 1) conduct field and laboratory studies to investigate the molecular signaling pathways behind the development of gonadal intersex; and 2) establish molecular biomarkers and assays for testing the ability of environmental pollutants to develop this condition using a battery of …

Ambient Ionization - Mass Spectrometry: Advances Toward Intrasurgical Cancer Detection, Alan Keith Jarmusch

Open Access Dissertations

My dissertation research has focused on the development of ambient ionization – mass spectrometry (MS) for clinical measurements, specifically intrasurgical cancer detection. The molecular differences between normal and cancerous tissue were detected via direct tissue analysis in vitro by touch spray ionization (TS) or by analyzing sectioned or smeared tissue using desorption electrospray ionization (DESI). The physical form of the tissue, e.g. in vitro sampling, sectioned, or smeared, was inconsequential in differentiating normal from cancerous tissue; however, the spectra acquired by TS and DESI differed due to differences in ionization processes. We envision that TS-MS and DESI-MS could impact diagnostic …

Gravity-Assist Trajectories To Venus, Mars, And The Ice Giants: Mission Design With Human And Robotic Applications, Kyle M. Hughes

Open Access Dissertations

Gravity-assist trajectories to Uranus and Neptune are found (with the allowance of impulsive maneuvers using chemical propulsion) for launch dates ranging from 2024 to 2038 for Uranus and 2020 to 2070 for Neptune. Solutions are found using a patched conic model with analytical ephemeris via the Satellite Tour Design Program (STOUR), originally developed at the Jet Propulsion Laboratory (JPL). Delivered payload mass is computed for all solutions for select launch vehicles, and attractive solutions are identified as those that deliver a specified amount of payload mass into orbit at the target body in minimum time. The best cases for each …

Redox-Active Ligand Uranium Complexes For Approaches To Multi-Electron Chemistry, John J. Kiernicki

Open Access Dissertations

While transition metal complexes are known to participate in multi-electron redox chemistry to facilitate important organometallic transformations, actinides, due to their low redox potentials, have a propensity to perform single electron chemistry. Because of its highly reducing nature, the ability to control the electronics of low-valent uranium is highly sought after as this may lead to unprecedented reactivity. Our lab has specifically been interested in mediating multi-electron transformations at uranium by employing redox-active ligands. Redox-active ligands can be used to facilitate multi-electron processes such as oxidative addition and reductive elimination at single metal centers. Using primarily 2,6-((Mes)N=CMe)2C5H3N) ( MesPDIMe) as …

Plasmonic Devices Based On Transparent Conducting Oxides For Near Infrared Applications, Kim Jongbum

Open Access Dissertations

In the past decade, there have been many breakthroughs in the field of plasmonics and nanophotonics that have enabled optical devices with unprecedented functionalities. Even though remarkable demonstration of at photonic devices has been reported, constituent materials are limited to the noble metals such as gold (Au) and silver (Ag) due to their abundance of free electrons which enable the support of plasmon resonances in the visible range. With the strong demand for extension of the optical range of plasmonic applications, it is now a necessity to explore and develop alternative materials which can overcome intrinsic issues of noble metals …

Hydrocode Modeling Of Oblique Impacts Into Terrestrial Planets, Jordan D. Kendall

Open Access Dissertations

The abundance of moderately siderophile elements (“iron-loving”; e.g., Co, Ni) in the Earth’s mantle is 10 to 100 times larger than predicted by chemical equilibrium between silicate melt and iron at low pressure, but it does match expectation for equilibrium at high pressure and temperature. Recent studies of differentiated planetesimal impacts assume that planetesimal cores survive the impact intact as concentrated masses that passively settle from a zero initial velocity and undergo turbulent entrainment in a global magma ocean; under these conditions, cores greater than 10 km in diameter do not fully mix without a sufficiently deep magma ocean. I …

Quantifying Terrestrial Ecosystem Carbon Dynamics With Mechanistically-Based Biogeochemistry Models And In Situ And Remotely Sensed Data, Shaoqing Liu

Open Access Dissertations

Terrestrial ecosystem plays a critical role in the global carbon cycle and climate system. Therefore, it is important to accurately quantify the carbon dynamics of terrestrial ecosystem under future climatic change condition. This dissertation evaluates the regional carbon dynamics by using upscaling approach, mechanistically-based biogeochemistry models and in situ and remotely sensed data.

The upscaling studies based on FLUXNET network has provided us the spatial and temporal pattern of the carbon fluxes but it fails to consider the atmospheric CO2 effect given its important physiological role in carbon assimilation. In the second chapter, we consider the effect of atmospheric CO2 …

The Cloud-Radiative Forcing Of The U.S. Landfalling Atmospheric Rivers, Qianwen Luo

Open Access Dissertations

Atmospheric rivers (ARs) are narrow channels in the atmosphere that transport an enormous amount of moisture from the tropics to the higher latitudes. Streaks of highly reflective clouds are observed along with the ARs in satellite imagery. These clouds both influence the moisture transport of ARs, as well as modify the Earth-Atmospheric energy budget through pathways such as cloud-radiative forcing (CRF). This dissertation studies the CRF of the U.S. Landfalling ARs in weather and climate scales. Three crucial questions are addressed. First, how do clouds produced by the ARs modulate the moisture and heat balance of the Earth-Atmospheric system? Even …

What Broke Where For Distributed And Parallel Applications — A Whodunit Story, Subrata Mitra

Open Access Dissertations

Detection, diagnosis and mitigation of performance problems in today's large-scale distributed and parallel systems is a difficult task. These large distributed and parallel systems are composed of various complex software and hardware components. When the system experiences some performance or correctness problem, developers struggle to understand the root cause of the problem and fix in a timely manner. In my thesis, I address these three components of the performance problems in computer systems. First, we focus on diagnosing performance problems in large-scale parallel applications running on supercomputers. We developed techniques to localize the performance problem for root-cause analysis. Parallel applications, …

Functional Regression Models In The Frame Work Of Reproducing Kernel Hilbert Space, Simeng Qu

Open Access Dissertations

The aim of this thesis is to systematically investigate some functional regression models for accurately quantifying the effect of functional predictors. In particular, three functional models are studied: functional linear regression model, functional Cox model, and function-on-scalar model. Both theoretical properties and numerical algorithms are studied in depth. The new models find broad applications in many areas.

For the functional linear regression model, the focus is on testing the nullity of the slope function, and a generalized likelihood ratio test based on easily implementable data-driven estimate is proposed. The quality of the test is measured by the minimal distance between …

Graphlet Based Network Analysis, Mahmudur Rahman

Open Access Dissertations

The majority of the existing works on network analysis, study properties that are related to the global topology of a network. Examples of such properties include diameter, power-law exponent, and spectra of graph Laplacians. Such works enhance our understanding of real-life networks, or enable us to generate synthetic graphs with real-life graph properties. However, many of the existing problems on networks require the study of local topological structures of a network.

Graphlets which are induced small subgraphs capture the local topological structure of a network effectively. They are becoming increasingly popular for characterizing large networks in recent years. Graphlet based …

The Search For Dark Matter In Xenon: Innovative Calibration Strategies And Novel Search Channels, Shayne Edward Reichard

Open Access Dissertations

The direct detection dark matter experiment XENON1T became operational in early 2016, heralding the era of tonne-scale dark matter detectors. Direct detection experiments typically search for elastic scatters of dark matter particles off target nuclei. XENON1T's larger xenon target provides the advantage of stronger dark matter signals and lower background rates compared to its predecessors, XENON10 and XENON100; but, at the same time, calibration of the detector's response to backgrounds with traditional external sources becomes exceedingly more difficult.

A 220Rn source is deployed on the XENON100 dark matter detector in order to address the challenges in calibration of tonne-scale liquid …

Convicted By Memory: Automatically Recovering Spatial-Temporal Evidence From Memory Images, Brendan D. Saltaformaggio

Open Access Dissertations

Memory forensics can reveal “up to the minute” evidence of a device’s usage, often without requiring a suspect’s password to unlock the device, and it is oblivious to any persistent storage encryption schemes, e.g., whole disk encryption. Prior to my work, researchers and investigators alike considered data-structure recovery the ultimate goal of memory image forensics. This, however, was far from sufficient, as investigators were still largely unable to understand the content of the recovered evidence, and hence efficiently locating and accurately analyzing such evidence locked in memory images remained an open research challenge.

In this dissertation, I propose breaking from …

Modeling The Impact Of Land Surface Feedbacks On Post Landfall Tropical Cyclones, Subashini Subramanian

Open Access Dissertations

The land surface is an important component of numerical models. The land surface models are modules that control energy partitioning, compute surface exchange coefficients and form the only physical boundary in a regional scale numerical model. Thus, an accurate representation of land surface is critical to compute surface fluxes, represent the boundary layer evolution and affect changes in weather systems. Land surface can affect landfalling tropical cyclones in two ways: (i) when the cyclone is offshore and land can influence cyclones by introducing dry (or moist) air that can weaken (or strengthen) the organized convective structure of cyclones, and (ii) …

Differentially Private Data Publishing For Data Analysis, Dong Su

Open Access Dissertations

In the information age, vast amounts of sensitive personal information are collected by companies, institutions and governments. A key technological challenge is how to design mechanisms for effectively extracting knowledge from data while preserving the privacy of the individuals involved. In this dissertation, we address this challenge from the perspective of differentially private data publishing. Firstly, we propose PrivPfC, a differentially private method for releasing data for classification. The key idea underlying PrivPfC is to privately select, in a single step, a grid, which partitions the data domain into a number of cells. This selection is done using the exponential …

Dynamic Holography In Semiconductors And Biomedical Optics, Hao Sun

Open Access Dissertations

Three-dimensional scanning and display are rapidly-advancing new technologies with important commercial drivers such as 3D printing and remote imaging for big data applications. Holography is a natural approach to recording and displaying three-dimensional information because it uses phase-sensitive interferometry to record interference patterns when a reference beam encounters coherent light arriving from an object. The 3D information is contained in the values of wave optics. Holography is a broad field that goes beyond recording and displaying. For instance, holographic optical elements, which take advantage of holographic imaging principles, perform the functions of lenses, gratings or mirrors. Holographic interferometry is also …

Characterizing The Effects Of Repetitive Head Trauma In Female Soccer Athletes For Prevention Of Mild Traumatic Brain Injury, Diana Otero Svaldi

Open Access Dissertations

As participation in women’s soccer continues to grow and the longevity of female athletes’ careers continues to increase, prevention of mTBI in women’s soccer has become a major concern for female athletes as the long-term risks associated with a history of mTBI are well documented. Among women’s sports, soccer exhibits the highest concussion rates, on par with those of men’s football at the collegiate level. Head impact monitoring technology has revealed that “concussive hits” occurring directly before symptomatic injury are not predictive of mTBI, suggesting that the cumulative effect of repetitive head impacts experienced by collision sport athletes should be …