We explore the application of deep learning to the disparate fields of natural language processing and computational biology. Both the sentences uttered by humans as well as the RNA and protein sequences found within the cells of their bodies can be considered formal languages in computer science, as sets of...
Intrinsically disordered proteins (IDP) are a class of proteins that lack a three-dimensional structure and their prevalence and diverse functions in the cell have only been discovered relatively recently. The intermediate chain (IC) subunit of the microtubule motor protein complex dynein contains an N-terminal disordered region, N-IC, which is central...
Designing spectral efficient, high-speed wireless links that offer high quality-
of-service and range capability has been a critical research and engineering challenge. In this thesis, we mainly address the complexity and performance issues of
channel estimation and data detection in multiple-input multiple-output (MIMO)
orthogonal frequency division multiplexing (OFDM) systems over...
Multiple-input multiple-output (MIMO) antenna technology is promising
for high-speed wireless communications without increasing the transmission band-
width. Space time coding (STC) is a scheme that employs multiple antennas to
increase transmission rate or to improve transmission quality. STC is used widely
in mobile cellular networks, wireless local area networks (WLAN)...
RNAs play important roles in the central dogma of molecular biology, and are involved in multiple biology processes such as chromatin modification, transcriptional interference and translation initiation. The functions of RNAs, especially non-coding RNAs, are highly related to its secondary structures, therefore computational methods for RNA structure prediction are of...
Maintaining the sustainability of the earth’s ecosystems has attracted much attention as these ecosystems are facing more and more pressure from human activities. Machine learning can play an important role in promoting sustainability as a large amount of data is being collected from ecosystems. There are at least three important...
The advent of deep learning models leads to a substantial improvement in a wide range of NLP tasks, achieving state-of-art performances without any hand-crafted features. However, training deep models requires a massive amount of labeled data. Labeling new data as a new task or domain emerges consumes time and efforts...
Natural Language Comprehension is a challenging domain of Natural Language Processing. To improve a model’s language comprehension/understanding, one approach would be to enrich the structure of the model to enhance its capability in learning the latent rules of the language.
In this dissertation, we will first introduce several deep models...
We present an experimental investigation of the effect of kinetic energy on the ion doping efficiency of superfluid helium droplets using cesium cations from a thermionic emission source. The kinetic energy of Cs⁺ is controlled by the bias voltage of a collection grid collinearly arranged with the droplet beam. Efficient...
The isotopic composition of water vapour provides integrated perspectives on the hydrological histories of air masses and has been widely used for tracing physical processes in hydrological and climatic studies. Over the last two decades, the infrared laser spectroscopy technique has been used to measure the isotopic composition of water...
We propose the Breathing Earth System Simulator (BESS), an upscaling approach to quantify global gross primary productivity and evapotranspiration using MODIS with a spatial resolution of 1-5 km and a temporal resolution of 8 days. This effort is novel because it is the first system that harmonizes and utilizes MODIS...
BACKGROUND: Chronic exposure to arsenic is associated with skin lesions. However, it is not known whether reducing arsenic exposure will improve skin lesions.
OBJECTIVE: We evaluated the association between reduced arsenic exposures and skin lesion recovery over time.
METHODS: A follow-up study of 550 individuals was conducted in 2009-2011 on...
Vitamin E (VitE) is necessary for vertebrate embryonic development. VitE prevents lipid peroxidation (LPO), which requires detoxification by cellular antioxidant systems subsequently involving reducing power derived from energy metabolism. Thus, VitE protects metabolic networks in the developing embryo and the integrated gene expression networks compensating for and impaired by LPO-induced...
In this dissertation, I present experimental observations of multiply charged atomic ions (MCAI) generated from interactions of atomic/molecular clusters with moderately intense nanosecond laser pulses. This process is also known as Coulomb explosion (CE) and it has been extensively studied in intense laser fields using ultrashort pulses. Several prevailing theories...
Chemistry of preparing dense film from solution deposition is explored with several cases in this thesis. Surface dense structure, conversion at melting point, and ion exchange in aqueous solution are the main topics covered here for the thin films of aluminum oxide phosphate and tin dioxide. Thin film density, optical...
Recent advances in computing, communication, and artificial intelligence (AI) technologies have made our world more interconnected and data-rich than ever with the proliferation of smart devices and sensors. As a result, we are increasingly dependent on electronic devices and sensors to automate away life’s mundane parts. For example, in business...
The need for less toxic quantum dots (QDs) has led to a significant number of investigations related to copper indium sulfide (CIS) QDs. Lower toxicity and broad band absorbance width makes CIS QDs appealing for light emitting diodes (LEDs), lasers, sensors, bio-imaging, solar cells, and computing. The optical and electronic...
DNA has a well-defined structural transition-the denaturation of its double-stranded form into two single strands-that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA denaturation, one can engineer DNA 'heattronic' devices that have a rapidly increasing thermal conductance over a narrow temperature...
Melanoma is the deadliest form of skin cancer, arising from malignant transformation of pigment-producing melanocytes. The primary risk factor for melanoma and other skin cancers is DNA damage resulting from unprotected solar ultraviolet radiation (UVR). If incorrectly repaired, this damage can result in incorporation of mutations that cause aberrant cell...
Gender relations as well as the social situation of Manchu women have long been ignored in studies of the cultural evolution of the Manchu. By setting the discussion of Manchu women in the context of cultural adaptation, this study reintroduces gender and women's problems into the research on the Manchu...
The demand for the development of sustainable energy is an all time high as we burn through limited fossil fuel reserves and as environmental concerns rise every year. Renewable energy sources such as wind and solar power have limitations due to inconsistent power supply that cannot meet the regular needs...
This dissertation proposes the use of advanced time-varying approaches for modeling the dynamics of the multipath channel in wireless communication networks. These advanced time-varying approaches include linear Kalman innovation models in observable block companion form, and neural network-based models. The e˙ectiveness of these type of models is evaluated through three...
The variety of natural disasters provide different sets of characteristics and properties with unique challenges. One significant difference between hazard types is prewarning lead time, the amount of time individuals have from a potential warning to the disaster occurring. Rapid onset disasters may not provide an official warning about a...
Dynamic bipedal locomotion is among the most difficult and yet relevant problems in modern robotics. While a multitude of classical control methods for bipedal locomotion exist, they are often brittle or limited in capability. In recent years, work in applying reinforcement learning to robotics has lead to superior performance across...
Copper antimony sulfide (CAS) is a ternary material that is of research interest for thin film photovoltaic applications due to its high absorption coefficient and tunable bandgap. The material is also ideal for sustainable manufacturing due the constituent elements being earth-abundant and less toxic than solar cell absorbers like gallium...
This thesis studies cooperative techniques that rely on femtocell user diversity to improve the downlink communication quality of macrocell users. We analytically analyze and evaluate the achievable performance of these techniques in the downlink of Rayleigh fading channels. We provide an approximation of both the bit-error rate (BER) and the...
The dissertation focuses on the engineering of light-matter interaction using plasmonic nanoparticles and metamaterials to achieve enhanced luminescence and based on which to improve the performance of biosensing and light-emitting technologies. We designed and fabricated a spectrum of nanostructures to exhibit particular dispersion relations capable of controlling the spontaneous emission...
In this dissertation, I describe the experimental investigation in electron diffraction of molecules in superfluid helium droplets. The project is part of an overall scheme called ‘single molecule serial electron diffraction imaging’ (SS-EDI), with the ultimate goal of building an apparatus to determine atomic structures from oriented macromolecules. In SS-EDI,...
Laser Powder Bed Fusion (LPBF) is a process commonly used to create additively manufactured metal parts. The flexibility and complexity allowed by the LPBF process provides opportunity for significant advancement in multiple industries as parts can be customized in shape and function for specific needs. These benefits can be compounded...
This paper addresses the high model complexity and overconfident frame labeling of state-of-the-art (SOTA) action segmenters. Their complexity is typically justified by the need to sequentially refine action segmentation through multiple stages of a deep architecture. However, this multistage refinement does not take into account uncertainty of frame labeling predicted...
Back pain is the leading cause of disability worldwide, entailing a significant socioeconomic impact. A primary source of back pain can be attributed to intervertebral disc (IVD) degeneration allowing nerve ingrowth, facet joint arthritis, disc bulging, and osteophyte formations that press on nearby nerve roots or the spinal cord. While...
Deep learning is becoming the latest trend in sensitive applications, such as healthcare, criminal justice, and finance. As these new applications emerge, adversaries are circumventing them.
Further, there have been concerns about the possibility of bias and discrimination in predictive applications.
In order to address these issues, we propose an...
Today nano scale materials are being used for wide range of applications. One promising topic in nano scale materials is using them for reinforcement of different polymeric materials to reach desirable stiffness properties. The stiffness of these materials is mostly found experimentally because the nanocomposite community lacks a decent analytical...
This dissertation addresses the problem of semantic labeling of image pixels. In the course of our work, we considered different types of semantic labels, including object classes (e.g., car, person), 3D depth values (in the range 0 to 80 meters), and affordance classes (e.g., walkable, sittable). Semantic pixel labeling is...
Herbs have been used for many centuries in diverse civilizations for the treatment of heart disease. Only a few natural supplements claim to have direct cardiovascular actions including hawthorn (Crataegus spp.) and berberine derived from the Berberidaceae family. Several different studies indicate important cardiovascular effects of hawthorn and berberine. For...
We describe a series of novel computational models, CERENKOV (Computational Elucidation of the REgulatory NonKOding Variome) and its successors CERENKOV2, CERENKOV3, and Convolutional CERENKOV3, for discriminating regulatory single nucleotide polymorphisms (rSNPs) from non-regulatory SNPs within non-coding genetic loci. The CERENKOV models are designed for recognizing rSNPs in the context of...
Wheat (Triticum aestivum L.) is one of the most important crops in the world. It has been and continues to be one of the main sources of food for humans and animals. Although traditional wheat breeding has contributed greatly to the improvement of wheat both in productivity and biotic/abiotic stress...
Emerging data showing the presence of atmospheric microplastics (MPs) has recently raised awareness surrounding the potential of human nanoplastics (NPs) exposure. Due to factors such as weathering, UV exposure, and other biodegradation processes, plastic pollution in the environment breaks down over time into micro (<5 micrometers) and nanoscale (<1000nm) particles....
Cyanobacterial harmful algae blooms (cyanoHABs) are a growing concern worldwide due to damage of ecosystems and threats to human health. Previous research indicates that plant humics from aquatic and wetland vascular plants are effective inhibitors of cyanobacterial metabolism and growth and may be useful as control agents for mitigating cyanoHABs....
Autonomous robotic agents are on their way to becoming in-home personal assistants, construction assistants, and warehouse workers. The degree of autonomy of such systems is reflected by the manner in which we specify goals to them; the abstraction of low-level commands to high-level goals goes hand-in-hand with increased autonomy. In...
The utility of high-throughput, computational screening has become an invaluable asset to the field of materials science. In the hierarchy of computational methods, the most accurate methods are often the most computationally expensive. However, as both the efficiency and fidelity of numerical techniques advance, high-quality screening of large materials datasets...
Learning to recognize objects is a fundamental and essential step in human perception and understanding of the world. Accordingly, research of object discovery across diverse modalities plays a pivotal role in the context of computer vision. This field not only contributes significantly to enhancing our understanding of visual information but...
The Va nationality, despite its small population compared
to other nationalities in China, has preserved most of its
traditions largely due to limits placed by historical
circumstances and geographical isolation. To non-Chinese
anthropologists, the Va people still remain unknown, as there
is little or no information about them in English...
Coniferous trees are a major North American crop that has been intensively managed for its commercial value, while also serving as critical habitat for abundant wildlife and as carbon sinks. Having diverse functions, North American temperate coniferous forests have become a research hotspot for numerous scientific studies aiming to integrate...
In this dissertation, I describe the experimental investigation of catching ions in superfluid helium droplets. The ultimate goal of our project is to build a coherent electron diffraction apparatus for atomic structure determination from oriented single macromolecules. This involves generating protein ions from electrospray ionization (ESI) and doping them in...
This thesis studies the problem of structured prediction (SP), where the agent needs to predict a structured output for a given structured input (e.g., Part-of-Speech tagging sequence for an input sentence). Many important applications including machine translation in natural language processing (NLP) and image interpretation in computer vision can be...
Intrinsically disordered proteins (IDPs), protein regions (IDRs), and protein complexes continue to emerge at the forefront of protein science. Proteins and protein regions lacking specific structure are found in all organisms, and often have vital roles in numerous biological processes. Breaking the well-known structure-function paradigm, the understanding of disorder-based functionality...
As one of the most popular data types, the point cloud is widely used in various appli- cations, including computer vision, computer graphics and robotics. The capability to directly measure 3D point clouds is invaluable in those applications as depth information could remove a lot of the segmentation ambiguities in...
In recent years, many studies have focused on the molecular and biochemical mechanisms regulating the development of wine grapes. The course of grape berry development is directed by genetic design and is mediated by phytohormones, which regulate grape berry growth and development by orchestrating a complex network of interacting genes,...
The ability of Propionibacterium shermanii to produce
growth metabolites which were inhibitory to food spoilage
indicator organisms was investigated. Asperqillus niqer,
a Pseudomonas species and Kluyveromyces fraqilis were the
spoilage indicators chosen to represent molds, gram
negative psychrotrophic bacteria and yeasts, respectively.
Supplementation of milk or whey based media was...
Hub proteins bind a large number of partners to facilitate structural changes and downstream protein interactions. LC8, a highly conserved protein homodimer, is a unique hub that regulates the activity of proteins in a wide range of cellular processes by binding to intrinsically disordered regions. With many of these systems,...
The goal of this dissertation was to improve our abilities in acquiring critical in vivo data by establishing embryo-larva zebrafish as an exemplary model to quantitatively evaluate cancer progression. The living environment that encompasses a tumor has a significant effect on how cancer develops, grows and metastasizes. In order to...
As a group of promising semiconductor materials, metal chalcogenides in thin film form have been widely used in electronics and optoelectronics applications, such as solar cell devices and photon sensors. Unfortunately, the film size and product throughput are limited by the current vacuum-based thin film deposition techniques. Solution-based thin film...
Interest in nanomaterials is motivated partly by their potential for sensor arrays to detect
different gases. Nanowires in particular are of interest because their high surface-to-volume
ratio promises the possibility of high sensitivity. However, because of their discrete
quasi-one-dimensional geometry, electrical integration of nanowires into photolithographically
defined devices and circuits...
The focus of this thesis is to design, characterize, and apply novel computational methods and molecular systems to interrogate heterogeneous human gut microbiome-related phenomena. In Chapter 2, I design, implement, and characterize a method for embedding co-occurrence patterns derived from massive 16s amplicon datasets. I use this method to 1....
The scarcity of wireless spectrum resources and the overwhelming demand for wireless broadband resources have prompted industry, government agencies and academia within the wireless communities to develop and come up with effective solutions that can make additional spectrum available for broadband data. As part of these ongoing efforts, cognitive radio...
Emergence of highly accurate Convolutional Neural Networks (CNNs) with the capability to process large datasets, has led to their popularity in many applications, including safety/security-sensitive (e.g. disease recognition, self-driving cars). Despite the high accuracy of convolutional neural networks, they have been found to be susceptible to adversarial noise added to...
My work has focused on using density functional theory to elucidate mechanisms of organocatalytic and transition metal catalyzed reactions by considering competing mechanisms. In each of the three presented studies computational investigation complemented experimental work by predicting stereoselectivity or revealing origins of stereo, regio, or chemoselectivity.
A study on the...
This thesis consists of two major components. The first part is concerned with video object instance segmentation (VOS), which is the task of assigning per-pixel labels perframe of a video sequence to indicate foreground object instance membership, given the first frame ground truth mask. VOS has myriad applications, from video...
Legged robots have consistently captured our collective imagination through various forms of media, from Hollywood films, anime, and viral Youtube videos of robots accomplishing incredible feats of acrobatics. These robots have the potential to navigate our environments, capable of completing tasks that would otherwise require human intervention. However, developing controls...
Electrodeposition is a versatile polymer deposition technique to create nano-microscale materials using an electrical field generated from a charged droplet of solution and a grounded collector. Electrospinning or electrospraying can occur during electrodeposition, leading to the creation of nanofibers or bead-like materials depending on the process parameters. Photopolymerization of the...
Machine Translation, the task of automatically translating between human languages has been studied for decades. This task is used to be solved by count-based statistical models, e.g. Phrase-based Statistical Machine Translation (PBSMT), which solves the translation problem by separately training a statistical language model and a translation model. Recently, Neural...
The use of board games for teaching introductory computer science is a promising recent avenue of research. The goal is to introduce computing concepts through their use in the implementations of simple games, thereby keeping students engaged through their learning process. However, there is a gap between students' algorithmic descriptions...
The purpose of this research was to investigate the optoelectronic properties of the
Ge doped biosilica, mainly focused on the photoluminescence (PL) properties of
diatom frustules of N. frustulum that contain metabolically inserted germanium
oxide produced by a two-stage photobioreactor cultivation process. In order to
explain the observed PL intensity...
In this thesis, maximum likelihood Doppler frequency estimation and phase noise suppression algorithms for Orthogonal Frequency Division Multiplexing (OFDM) systems are presented. A novel handover decision algorithm for wireless systems, called predictive base station switching (PBSS), is also introduced.
The maximum Doppler Frequency is the ratio of the speed of...
Orthogonal frequency division multiplexing (OFDM), which has been very attractive for future high rate wireless communications, is very robust to channel multipath fading effect while providing high transmission data rate with high spectral efficiency.
Multiple antennas can be combined with OFDM to increase diversity gain and to improve spectral efficiency...
Analysis of observations on sequential events over time is common in real life. Sequential measurements over time describing the behavior of systems are usually called time series data, which have been collected in a wide range of disciplines. Over the years there have been multiple research areas in studying stochastic...
Multiagent approaches are well suited to designing autonomous solutions for systems that feature complex interactions between many individuals such as in autonomous traffic systems and multi-robot exploration systems. However, creating autonomous agents that function effectively in these systems is a challenging task. In these complex environments, agents need informative reward...
Aerogels are interesting material systems with outstanding properties such as low density, high surface area, and low thermal conductivity. They can be used for a variety of applications, such as solar cells, sensors, or catalysts. Additionally they provide a unique model system to study the properties of small particles. Cellulose...
Crystals of an incongruent-melting compound, Ba₃MgSi₂O₈, were grown by the flux method and its structure was determined by single crystal X-ray diffraction methods. Ba₃MgSi₂O₈ crystallizes in trigonal space group P-3[bar]m1 with a = 5.6123(3) Å, c = 7.2667(9) Å and Z = 1. Eu²⁺ ions prefer one crystallographic Ba site...
Besides enabling an enhanced mobile broadband access, fifth-generation (5G) wireless mobile networks are envisioned to support the connectivity of massive, heterogeneous Internet of Things (IoT) devices. Connecting these devices through 5G systems and providing them with their needed data rates require huge amounts of spectrum and power resources, thus calling...
Advances in low-power digital integration and microelectro-mechanical systems (MEMS) have paved the way for micro-sensors. These sensors are equipped with data processing capabilities along with sensory circuits. Sensor data are processed on these individual sensors and transmitted to the target (sink). Lowcost integration and small sizes of these sensors have...
This dissertation delves into understanding, characterizing, and addressing dataset shift in deep learning, a pervasive issue for deployed machine learning systems. Integral aspects of the problem are examined: We start with the use of counterfactual explanations in order to characterize the behavior of deep reinforcement learning agents in visual input...
Grid-scale energy storage systems are urgently needed to increase the flexibility and rigidity of the grid for modern society and take full advantage of the renewable green energy resources such as solar energy and wind energy. Na-ion batteries (NIBs) and K-ion batteries (KIBs) have been emerged as one of the...
Most of today’s Internet of Things (IoT) applications assume that data will be moved offdevices into centralized cloud platforms. While existing IoT systems leverage cloud-based analytics for meaningful data reasoning, the assumption that data should always be moved off the devices is problematic. The amount of data to be moved...
Interactions between proteins are essential to life, driving and regulating a majority of processes within all living cells. Study of protein-protein interactions reveals that some proteins act as hubs within networks of interactions, binding to many partner proteins. These hubs therefore are of particular importance to understanding protein function, interwoven...
In weak supervision learning, label information can be provided at different levels of granularity. For example, in multi-instance multi-label learning, samples are organized into bags and labels for each class are provided at the bag level. For small datasets, this approach offers means of reducing the labeling efforts. However, in...
Metabolic syndrome is a problem affecting people around the world. In a number of studies, soy intake has been documented to possess antidiabetic and anticardiovascular effect. My project is focused on the impact of the intake of compounds found within soy, the isoflavones, their impact on metabolic syndrome symptoms, and...
The goal of many machine learning problems can be formalized as the creation of a function that can properly classify an input vector, given a set of examples of that function. While this formalism has produced a number of success stories, there are notable situations in which it fails. One...
Ultra-wideband (UWB) communication has emerged as a very promising
technology for short-range wireless applications, including
high-speed multimedia transmissions and sensor networks. UWB
system designs involve many different aspects covering analog and
digital processing, channel estimation and modeling, and
modulation and demodulation. Although UWB still faces many
challenges, significant progress has...
Gamma Ray Bursts (GRBs) are the most energetic explosions in the Universe, producing up to $\sim10^{53}$ ergs of energy in the first few seconds of their emission -- the so-called prompt phase that is dominated by high energy X-ray and $\gamma$-ray photons. The very large luminosities released in these events...
Software systems are becoming an essential part of the lives of both individuals and organizations, and as a consequence, these systems are getting bigger and more complex. Because of this, the tasks of maintaining the quality in these complex software systems are becoming increasingly difficult. Furthermore, these systems are subject...
Machine learning (ML) and deep learning (DL) models impact our daily lives with applications in natural language modeling, image analysis, healthcare, genomics, and bioinformatics. The exponential growth of biological sequence data necessitates accompanying advances in computational methods. Although deep learning is highly effective for detecting and classifying biological sequences, challenges...
Cells represent microcosms of spatial and temporal structural organization, with the achievement of internal spatial organization relying upon a collection of macromolecular motor complexes to transport and localize components throughout the cell. Cytoplasmic dynein is one such motor complex, and is the principal ATP-dependent motor for retrograde transport along microtubules...
This dissertation presents novel, field-activated smart material systems for the actuation and control of autonomous robots. Smart materials, a type of material whose properties can be changed with an external stimuli, represent a promising direction to expand upon existing robotic control and actuation methods, particularly in the sub-fields of soft...
Ecological domains seeking to understand the environment and the behavior of species have received little attention in machine learning (ML), despite the fact that environmental changes have a significant impact on humans as well as ecosystems. Some ecological problems can be formulated similarly to other common ML applications, but there...
In this dissertation we consider two application specific flow and transport models in porous media at multiple scales: 1) methane gas transport models for hydrate formation and dissociation in the subsurface under two-phase conditions, and 2) coupled flow and biomass-nutrient model for biofilm growth in complex geometries with biofilm, and...
The environmental health science community recognizes polycyclic aromatic hydrocarbons (PAHs) as a re-emerging class of environmental pollutants due to their persistence and prominence in mixtures of concern. Due to their widespread distribution in the environment, exposure to PAHs often occur as complex chemical mixtures. Exposures are linked to numerous adverse...
The rising global trend to reduce dependence on fossil fuels has provided significant motivation toward the development of alternative energy conversion methods and new technologies to improve their efficiency. Recently, oscillating energy harvesters have shown promise as highly efficient and scalable turbines, which can be implemented in areas where traditional...
The interactions of chemical species with a solid surface play a role in many everyday applications such as heterogeneous catalysis, corrosion, and degradation reactions. Understanding the reaction kinetics and thermodynamics via rate constants and equilibrium constants, which require knowledge of the adsorbed species’ entropy, is essential for tuning these surface...
The United States Department of Energy has identified the pebble-bed reactor as a high priority for US research with the end goal of licensing a pebble-bed reactor (PBR) for operation in the United States. Before this can be accomplished significant research must be done regarding the safety of the pebble-bed...
Functional control at the nanoscale forms the foundation of biological systems. These work at the cellular level by manipulating ions and molecules. Nanoscale devices that give functional control at this scale are also becoming an important component in diverse fields such as electronics, medicine, engineering, and manufacturing. Moreover, scientific advances...
The objective of this dissertation is to enhance the monitoring of forest ecosystems through the utilization of remotely sensed data to address the exigencies posed by the Anthropocene. On a global scale, rising temperatures and fluctuating precipitation patterns have strained forests and produced shifts in natural disturbance regimes. Additionally, the...
This is a bibliography of doctoral dissertations and masters' theses in forestry and related topics issued during the period from July 1981 through June 1990. The colleges and universities included are all accredited by the Society of American Foresters. The actual listings were supplied by the individual institutions. Topics covered...