Computer Sciences Commons^™

Multidimensional Feature Engineering For Post-Translational Modification Prediction Problems, Norman Mapes Jr.

Doctoral Dissertations

Protein sequence data has been produced at an astounding speed. This creates an opportunity to characterize these proteins for the treatment of illness. A crucial characterization of proteins is their post translational modifications (PTM). There are 20 amino acids coded by DNA after coding (translation) nearly every protein is modified at an amino acid level. We focus on three specific PTMs. First is the bonding formed between two cysteine amino acids, thus introducing a loop to the straight chain of a protein. Second, we predict which cysteines can generally be modified (oxidized). Finally, we predict which lysine amino acids are …

Cmos Compatible Memristor Networks For Brain-Inspired Computing, Can Li

Doctoral Dissertations

In the past decades, the computing capability has shown an exponential growth trend, which is observed as Moore’s law. However, this growth speed is slowing down in recent years mostly because the down-scaled size of transistors is approaching their physical limit. On the other hand, recent advances in software, especially in big data analysis and artificial intelligence, call for a break-through in computing hardware. The memristor, or the resistive switching device, is believed to be a potential building block of the future generation of integrated circuits. The underlying mechanism of this device is different from that of complementary metal-oxide-semiconductor (CMOS) …

Righting Web Development, John Vilk

Doctoral Dissertations

The web browser is the most important application runtime today, encompassing all types of applications on practically every Internet-connected device. Browsers power complete office suites, media players, games, and augmented and virtual reality experiences, and they integrate with cameras, microphones, GPSes, and other sensors available on computing devices. Many apparently native mobile and desktop applications are secretly hybrid apps that contain a mix of native and browser code. History has shown that when new devices, sensors, and experiences appear on the market, the browser will evolve to support them. Despite the browser's importance, developing web applications is exceedingly difficult. Web …

Data Stream Algorithms For Large Graphs And High Dimensional Data, Hoa Vu

Doctoral Dissertations

In contrast to the traditional random access memory computational model where the entire input is available in the working memory, the data stream model only provides sequential access to the input. The data stream model is a natural framework to handle large and dynamic data. In this model, we focus on designing algorithms that use sublinear memory and a small number of passes over the stream. Other desirable properties include fast update time, query time, and post processing time. In this dissertation, we consider different problems in graph theory, combinatorial optimization, and high dimensional data processing. The first part of …

System Support For Managing Risk In Cloud Computing Platforms, Supreeth Shastri

Doctoral Dissertations

Cloud platforms sell computing to applications for a price. However, by precisely defining and controlling the service-level characteristics of cloud servers, they expose applications to a number of implicit risks throughout the application’s lifecycle. For example, user’s request for a server may be denied, leading to rejection risk; an allocated resource may be withdrawn, resulting in revocation risk; an acquired cloud server’s price may rise relative to others, causing price risk; a cloud server’s performance may vary due to external factors, triggering valuation risk. Though these risks are implicit, the costs they bear on the applications are not. While some …

Leveraging Eye Structure And Motion To Build A Low-Power Wearable Gaze Tracking System, Addison Mayberry

Doctoral Dissertations

Clinical studies have shown that features of a person's eyes can function as an effective proxy for cognitive state and neurological function. Technological advances in recent decades have allowed us to deepen this understanding and discover that the actions of the eyes are in fact very tightly coupled to the operation of the brain. Researchers have used camera-based eye monitoring technology to exploit this connection and analyze mental state across across many different metrics of interest. These range from simple things like attention and scene processing, to impairments such as a fatigue or substance use, and even significant mental disorders …

Integration Of Robotic Perception, Action, And Memory, Li Yang Ku

Doctoral Dissertations

In the book "On Intelligence", Hawkins states that intelligence should be measured by the capacity to memorize and predict patterns. I further suggest that the ability to predict action consequences based on perception and memory is essential for robots to demonstrate intelligent behaviors in unstructured environments. However, traditional approaches generally represent action and perception separately---as computer vision modules that recognize objects and as planners that execute actions based on labels and poses. I propose here a more integrated approach where action and perception are combined in a memory model, in which a sequence of actions can be planned based on …

Parallel Algorithms For Time Dependent Density Functional Theory In Real-Space And Real-Time, James Kestyn

Doctoral Dissertations

Density functional theory (DFT) and time dependent density functional theory (TDDFT) have had great success solving for ground state and excited states properties of molecules, solids and nanostructures. However, these problems are particularly hard to scale. Both the size of the discrete system and the number of needed eigenstates increase with the number of electrons. A complete parallel framework for DFT and TDDFT calculations applied to molecules and nanostructures is presented in this dissertation. This includes the development of custom numerical algorithms for eigenvalue problems and linear systems. New functionality in the FEAST eigenvalue solver presents an additional level of …

Inexact And Nonlinear Extensions Of The Feast Eigenvalue Algorithm, Brendan E. Gavin

Doctoral Dissertations

Eigenvalue problems are a basic element of linear algebra that have a wide variety of applications. Common examples include determining the stability of dynamical systems, performing dimensionality reduction on large data sets, and predicting the physical properties of nanoscopic objects. Many applications require solving large dimensional eigenvalue problems, which can be very challenging when the required number of eigenvalues and eigenvectors is also large. The FEAST algorithm is a method of solving eigenvalue problems that allows one to calculate large numbers of eigenvalue/eigenvector pairs by using contour integration in the complex plane to divide the large number of desired pairs …

Run-Time Program Phase Detection And Prediction, Meng-Chieh Chiu

Doctoral Dissertations

It is well-known that programs tend to have multiple phases in their execution. Because phases have impact on micro-architectural features such as caches and branch predictors, they are relevant to program performance (Xian et al., 2007; Roh et al., 2009; Gu and Verbrugge, 2008) and energy consumption. They are also relevant to detecting whether a program is executing as expected or is encountering unusual or exceptional conditions, a software engineering and program monitoring concern (Peleg and Mendelson, 2007; Singer and Kirkham, 2008; Pirzadeh et al., 2011; Benomar et al., 2014). We present methods for real-time phase change detection and phase …

Hybrid Black-Box Solar Analytics And Their Privacy Implications, Dong Chen

Doctoral Dissertations

The aggregate solar capacity in the U.S. is rising rapidly due to continuing decreases in the cost of solar modules. For example, the installed cost per Watt (W) for residential photovoltaics (PVs) decreased by 6X from 2009 to 2018 (from $8/W to $1.2/W), resulting in the installed aggregate solar capacity increasing 128X from 2009 to 2018 (from 435 megawatts to 55.9 gigawatts). This increasing solar capacity is imposing operational challenges on utilities in balancing electricity's real-time supply and demand, as solar generation is more stochastic and less predictable than aggregate demand. To address this problem, both academia and utilities have …

Machine Learning Methods For Activity Detection In Wearable Sensor Data Streams, Roy Adams

Doctoral Dissertations

Wearable wireless sensors have the potential for transformative impact on the fields of health and behavioral science. Recent advances in wearable sensor technology have made it possible to simultaneously collect multiple streams of physiological and context data from individuals in natural environments; however, extracting reliable high-level inferences from these raw data streams remains a key data analysis challenge. In this dissertation, we address three challenges that arise when trying to perform activity detection from wearable sensor streams. First, we address the challenge of learning from small amounts of noisy data by proposing a class of conditional random field models for …

Transfer Learning With Mixtures Of Manifolds, Thomas Boucher

Doctoral Dissertations

Advances in scientific instrumentation technology have increased the speed of data acquisition and the precision of sampling, creating an abundance of high-dimensional data sets. The ability to combine these disparate data sets and to transfer information between them is critical to accurate scientific analysis. Many modern-day instruments can record data at many thousands of channels, far greater than the actual degrees of freedom in the sample data. This makes manifold learning, a class of methods that exploit the observation that high-dimensional data tend to lie on lower-dimensional manifolds, especially well-suited to this transfer learning task. Existing manifold-based transfer learning methods …

Supporting Scientific Analytics Under Data Uncertainty And Query Uncertainty, Liping Peng

Doctoral Dissertations

Data management is becoming increasingly important in many applications, in particular, in large scientific databases where (1) data can be naturally modeled by continuous random variables, and (2) queries can involve complex predicates and/or be difficult for users to express explicitly. My thesis work aims to provide efficient support to both the "data uncertainty" and the "query uncertainty". When data is uncertain, an important class of queries requires query answers to be returned if their existence probabilities pass a threshold. I start with optimizing such threshold query processing for continuous uncertain data in the relational model by (i) expediting selections …

Using Latent Variable Models To Improve Causal Estimation, Huseyin Oktay

Doctoral Dissertations

Estimating the causal effect of a treatment from data has been a key goal for a large number of studies in many domains. Traditionally, researchers use carefully designed randomized experiments for causal inference. However, such experiments can not only be costly in terms of time and money but also infeasible for some causal questions. To overcome these challenges, causal estimation methods from observational data have been developed by researchers from diverse disciplines and increasingly studies using such methods account for a large share in empirical work. Such growing interest has also brought together two arguably separate fields: machine learning and …

On The Performance Of Adaptive Bitrate Streaming And Parallel Cloud Applications, Cong Wang

Doctoral Dissertations

As shown in recent studies, video streaming is by far the biggest category of backbone Internet traffic in the US. As a measure to reduce the cost of highly over-provisioned physical infrastructures while remaining the quality of video services, many streaming service providers started to use cloud services, where physical resources can be dynamically allocated based on current demand. In this dissertation, we seek to evaluate and improve the performance for both Adaptive Bitrate (ABR) video streaming and cloud applications. First, we present a set of measurement studies for ABR streaming applications. Using the data from the application, network, and …

A Study Of High Performance Multiple Precision Arithmetic On Graphics Processing Units, Niall Emmart

Doctoral Dissertations

Multiple precision (MP) arithmetic is a core building block of a wide variety of algorithms in computational mathematics and computer science. In mathematics MP is used in computational number theory, geometric computation, experimental mathematics, and in some random matrix problems. In computer science, MP arithmetic is primarily used in cryptographic algorithms: securing communications, digital signatures, and code breaking. In most of these application areas, the factor that limits performance is the MP arithmetic. The focus of our research is to build and analyze highly optimized libraries that allow the MP operations to be offloaded from the CPU to the GPU. …

Mitigation Of Environmental Hazards Of Sulfide Mineral Flotation With An Insight Into Froth Stability And Flotation Performance, Muhammad Badar Hayat

Doctoral Dissertations

"Today's major challenges facing the flotation of sulfide minerals involve constant variability in the ore composition; environmental concerns; water scarcity and inefficient plant performance. The present work addresses these challenges faced by the flotation process of complex sulfide ore of Mississippi Valley type with an insight into the froth stability and the flotation performance. The first project in this study was aimed at finding the optimum conditions for the bulk flotation of galena (PbS) and chalcopyrite (CuFeS₂) through Response Surface Methodology (RSM). In the second project, an attempt was made to replace toxic sodium cyanide (NaCN) with the biodegradable chitosan …

Security Risk Assessment In Cloud Computing Domains, Amartya Sen

Doctoral Dissertations

"Cyber security is one of the primary concerns persistent across any computing platform. While addressing the apprehensions about security risks, an infinite amount of resources cannot be invested in mitigation measures since organizations operate under budgetary constraints. Therefore the task of performing security risk assessment is imperative to designing optimal mitigation measures, as it provides insight about the strengths and weaknesses of different assets affiliated to a computing platform.

The objective of the research presented in this dissertation is to improve upon existing risk assessment frameworks and guidelines associated to different key assets of Cloud computing domains - infrastructure, applications, …

Mining And Analysis Of Real-World Graphs, Armita Abedijaberi

Doctoral Dissertations

"Networked systems are everywhere - such as the Internet, social networks, biological networks, transportation networks, power grid networks, etc. They can be very large yet enormously complex. They can contain a lot of information, either open and transparent or under the cover and coded. Such real-world systems can be modeled using graphs and be mined and analyzed through the lens of network analysis. Network analysis can be applied in recognition of frequent patterns among the connected components in a large graph, such as social networks, where visual analysis is almost impossible. Frequent patterns illuminate statistically important subgraphs that are usually …

Machine Learning Techniques Implementation In Power Optimization, Data Processing, And Bio-Medical Applications, Khalid Khairullah Mezied Al-Jabery

Doctoral Dissertations

"The rapid progress and development in machine-learning algorithms becomes a key factor in determining the future of humanity. These algorithms and techniques were utilized to solve a wide spectrum of problems extended from data mining and knowledge discovery to unsupervised learning and optimization. This dissertation consists of two study areas. The first area investigates the use of reinforcement learning and adaptive critic design algorithms in the field of power grid control. The second area in this dissertation, consisting of three papers, focuses on developing and applying clustering algorithms on biomedical data. The first paper presents a novel modelling approach for …

Dragline Excavation Simulation, Real-Time Terrain Recognition And Object Detection, Godfred Somua-Gyimah

Doctoral Dissertations

"The contribution of coal to global energy is expected to remain above 30% through 2030. Draglines are the preferred excavation equipment in most surface coal mines. Recently, studies toward dragline excavation efficiency have focused on two specific areas. The first area is dragline bucket studies, where the goal is to develop new designs which perform better than conventional buckets. Drawbacks in the current approach include operator inconsistencies and the inability to physically test every proposed design. Previous simulation models used Distinct Element Methods (DEM) but they over-predict excavation forces by 300% to 500%. In this study, a DEM-based simulation model …

Detecting Cells And Analyzing Their Behaviors In Microscopy Images Using Deep Neural Networks, Yunxiang Mao

Doctoral Dissertations

"The computer-aided analysis in the medical imaging field has attracted a lot of attention for the past decade. The goal of computer-vision based medical image analysis is to provide automated tools to relieve the burden of human experts such as radiologists and physicians. More specifically, these computer-aided methods are to help identify, classify and quantify patterns in medical images. Recent advances in machine learning, more specifically, in the way of deep learning, have made a big leap to boost the performance of various medical applications. The fundamental core of these advances is exploiting hierarchical feature representations by various deep learning …