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Exploring The Impact Of Pretrained Bidirectional Language Models On Protein Secondary Structure Prediction, Dillon G. Daudert Dec 2018

Exploring The Impact Of Pretrained Bidirectional Language Models On Protein Secondary Structure Prediction, Dillon G. Daudert

Master's Theses

Protein secondary structure prediction (PSSP) involves determining the local conformations of the peptide backbone in a folded protein, and is often the first step in resolving a protein's global folded structure. Accurate structure prediction has important implications for understanding protein function and de novo protein design, with progress in recent years being driven by the application of deep learning methods such as convolutional and recurrent neural networks. Language models pretrained on large text corpora have been shown to learn useful representations for feature extraction and transfer learning across problem domains in natural language processing, most notably in instances where ...


Towards Automated Domain-Oriented Lexicon Construction And Dimension Reduction For Arabic Sentiment Analysis, Hasan A. Alshahrani Dec 2018

Towards Automated Domain-Oriented Lexicon Construction And Dimension Reduction For Arabic Sentiment Analysis, Hasan A. Alshahrani

Dissertations

Sentiment analysis is a type of text mining that uses Natural Language Processing (NLP) tools to identify and label opinionated text. There are two main approaches of sentiment analysis: lexicon-based, and statistical approach. In our research, we use the lexicon-based approach because the lexicon contains sentiment words and phrases which are the main linguistic units to express sentiments. More specifically, we work with domain-oriented lexicons as they are more efficient than general ones because the polarity is heavily driven by domains.

Arabic language has a degree of uniqueness that makes it hard to be processed with the available cross-language tools ...


Generalized Line Graphs, Mohra Abdullah Z. Alqahtani Dec 2018

Generalized Line Graphs, Mohra Abdullah Z. Alqahtani

Dissertations

With every nonempty graph, there are associated many graphs. One of the best known and most studied of these is the line graph L (G) of a graph G, whose vertices are the edges of G and where two vertices of L (G) are adjacent if the corresponding edges of G are adjacent. This concept was implicitly introduced by Whitney in 1932. Over the years, characterizations of graphs that are line graphs have been given, as well as graphs whose line graphs have some specified property. For example, Beineke characterized graphs that are line graphs by forbidding certain graphs that ...


Exploring Potential Water-Ice Occurrence On Asteroid 4 Vesta Using Orbital Radar Observations By The Dawn Mission, Elizabeth M. Palmer Dec 2018

Exploring Potential Water-Ice Occurrence On Asteroid 4 Vesta Using Orbital Radar Observations By The Dawn Mission, Elizabeth M. Palmer

Dissertations

Airless, differentiated planetesimals in the inner solar system were presumed to have been depleted of most of their initial volatile content during formation. However, water-ice has been discovered at the lunar poles (Li et al., 2018), is inferred to exist in polar craters on Mercury (e.g., Butler, Slade & Muhleman, 1993, and suggested to survive beneath the dusty regolith of objects in the main asteroid belt if buried at sufficient depths—at least one meter for small-bodies in the outer main-belt (Schorghofer, 2008). Hence, the study of volatile occurrence, past or present, on airless, desiccated small-bodies provides insights into the ...


Radiative Double Electron Capture (Rdec) By Fully-Stripped Fluorine Ions In Collisions With Nitrogen, Nuwan Sisira Kumara Dec 2018

Radiative Double Electron Capture (Rdec) By Fully-Stripped Fluorine Ions In Collisions With Nitrogen, Nuwan Sisira Kumara

Dissertations

Radiative double electron capture (RDEC) by highly-stripped ions in collisions with atomic targets is a fundamental process that can be used to study electron-electron correlation, the interaction between two electrons, in the vicinity of the Coulomb field of a bare ion. In this process two electrons from the target are captured to bound states of the projectile with the simultaneous emission of a single photon. RDEC is closely related to the well-known one-step atomic process of radiative electron capture (REC), in which a target electron is captured to the projectile and a photon is simultaneously emitted. REC and RDEC can ...


Assessing Land Deformation And Sea Encroachment In The Nile Delta: A Radar Interferometric And Modeling Approach, Esayas Gebrekidan Gebremichael Dec 2018

Assessing Land Deformation And Sea Encroachment In The Nile Delta: A Radar Interferometric And Modeling Approach, Esayas Gebrekidan Gebremichael

Dissertations

Many of the deltas of the world are experiencing land deformation, subsidence or uplift of landmass, due to natural or anthropogenic causes, or a combination of both processes and causes. These deltaic settings are densely populated and border some of our world’s largest water bodies (oceans and seas). The land deformation, especially the subsidence component, when combined with the climate change-induced sea level rise, coastal erosion, and other anthropogenic drivers, will undoubtedly impact the population and economy of coastal areas of deltas. For the Nile Delta of Egypt, the land deformation processes and the factors that control the deformation ...


Efficacy Of Deep Learning In Support Of Smart Services, Basheer Mohammed Basheer Qolomany Dec 2018

Efficacy Of Deep Learning In Support Of Smart Services, Basheer Mohammed Basheer Qolomany

Dissertations

The massive amount of streaming data generated and captured by smart service appliances, sensors and devices needs to be analyzed by algorithms, transformed into information, and minted to extract knowledge to facilitate timely actions and better decision making. This can lead to new products and services that can dramatically transform our lives. Machine learning and data analytics will undoubtedly play a critical role in enabling the delivery of smart services. Within the machine-learning domain, Deep Learning (DL) is emerging as a superior new approach that is much more effective than any rule or formula used by traditional machine learning. Furthermore ...


Computational Study Of The Nature Of Tetrel Bond, Yama Aman Aug 2018

Computational Study Of The Nature Of Tetrel Bond, Yama Aman

Master's Theses

For more than a hundred years, the type of a chemical bond has been distinguished according to the relative electronegativities of chemical units at the ends of a bond. Whereas, the bond of unequally electronegative on both ends is called a polar covalent or even ionic bond or a non-polar covalent bond in case of both equal. Regardless the type of bonded elements, the whole idea for the bond was believed to be electron driven only. In the 20th century the development of the idea, that not just the electronic relation but specific elements are also able to characterize the ...


An Investigation Of Sub-Meter Skill In Stem And Non-Stem Undergraduate Students, Laura A. Tingin Aug 2018

An Investigation Of Sub-Meter Skill In Stem And Non-Stem Undergraduate Students, Laura A. Tingin

Master's Theses

This study designed a nationally-relevant, valid, and reliable survey that measures STEM and Non-STEM undergraduate student familiarity with sub-meter metric scale and common sub-meter sized science objects. The instrument assesses scalar relationship and scalar magnitude, as explained by Cheek, LaDue, and Shipley (2017). The instrument development was based on an existing Scale of Objects Questionnaire (SOQ) instrument created by Tretter, Jones, Andre, Negishi, & Minogue (2006a) which was modified to be nationally relevant and in an electronic format in two phases: online survey development and undergraduate pilot testing. Online survey development was framed in the tailored design method described by Dillman ...


Probabilistic And Extremal Problems In Combinatorics, Sean English Aug 2018

Probabilistic And Extremal Problems In Combinatorics, Sean English

Dissertations

Graph theory as a mathematical branch has been studied rigorously for almost three centuries. In the past century, many new branches of graph theory have been proposed. One important branch of graph theory involves the study of extremal graph theory. In 1941, Turán studied one of the first extremal problems, namely trying to maximize the number of edges over all graphs which avoid having certain structures. Since then, a large body of work has been created in the study of similar problems. In this dissertation, a few different extremal problems are studied, but for hypergraphs rather than graphs. In particular ...


Application Of Handheld Ed-Xrf For High-Resolution Chemostratigraphy In Texturally Homogeneous Carbonate Mudstones: Salina A-1 Carbonate (Silurian), Michigan Basin, Matthew A. Hemenway Jun 2018

Application Of Handheld Ed-Xrf For High-Resolution Chemostratigraphy In Texturally Homogeneous Carbonate Mudstones: Salina A-1 Carbonate (Silurian), Michigan Basin, Matthew A. Hemenway

Master's Theses

Handheld energy dispersive x-ray fluorescence spectrometry (ED-XRF) is routinely used to observe elemental variability in fine-grained siliciclastics but has been applied rarely in fine-grained carbonates. Here, ED-XRF chemostratigraphy is utilized in the texturally homogenous, mudstones of the Silurian A-1 Carbonate (A-1C), Michigan Basin. Previous studies on the A-1C focused on the stratigraphic relationship with the underlying Niagaran reefs, so little is known about the geological variability in the basin center. In this study, high-resolution elemental data from nine cores were integrated with petrographic and mineralogical observations to evaluate two hypotheses: (1) Texturally homogeneous, basin-center mudstones in the A-1C have spatially ...


Synthesis And Characterization Of Fluorescent Nanojars, Vageesha Warnajith Liyana Gunawardana Jun 2018

Synthesis And Characterization Of Fluorescent Nanojars, Vageesha Warnajith Liyana Gunawardana

Master's Theses

Self-assembly is a powerful tool utilized by synthetic chemists to create large, intricate structures for a variety of applications such as drug delivery, adaptable materials and electronics. In contrast to stepwise synthesis, this process allows the formation of intricate molecular architectures starting from synthetically rudimentary building blocks. Nanojars are class of self-assembling, cyclic copper(II) pyrazolate coordination compounds that encapsulate oxoanions with negative two or three charge. The strong anion binding characteristics of nanojars have potential towards developing novel tools for detecting biologically and environmentally relevant anions such as carbonate, sulfate and phosphate.

This work addresses the design and synthesis ...


Detection Of Bedrock Fractures And Joints Beneath Cover: Geophysical Approaches To An Engineering Geology Problem, Muthanna Yousif Yaqoob Aldiney Jun 2018

Detection Of Bedrock Fractures And Joints Beneath Cover: Geophysical Approaches To An Engineering Geology Problem, Muthanna Yousif Yaqoob Aldiney

Dissertations

This research used geophysical methods to detect the presence of sub-vertical failure planes, their direction(s), and their frequency in bedrock beneath soil or glacial drift overburden. Azimuthal measurements using the seismic, electrical resistivity (ER), and electromagnetic conductivity were made to evaluate which techniques might provide the best indication of the bedrock joints, faults, or shear zones. Measurements were made at multiple sites near each of three locations: Jackson, Alpena, and Grand Ledge, Michigan. The first two are former limestone quarries and the third is underlain by sandstone. Seismic measurements began with one or two linear refraction spreads, used to ...


Nanojars: Versatile Platform For Pyrazole Synthesis And Chemistry, And Selective Extraction Of Anions, Basil Mohammed Ahmed Jun 2018

Nanojars: Versatile Platform For Pyrazole Synthesis And Chemistry, And Selective Extraction Of Anions, Basil Mohammed Ahmed

Dissertations

This work is centered around nanojars, a family of nano-sized anion-incarcerating agents. It addresses various aspects of nanojar chemistry, such as synthesis strategies (including green methodologies) for pyrazole ligands needed for the preparation of nanojars, characterization and study of the mechanism of assembly of nanojars, and selective extraction of anions from water using nanojars.

Nanojars are neutral, supramolecular coordination complexes of the general formula [anion⊂ {Cu(μ-OH)(μ-pz)}n], formed by the reaction of Cu2+, HO and pyrazolate ions (C3H2N2‒, pz) in the presence of oxoanions with large hydration energy (e.g. CO3 ...


A 3d Simulation Of Leukocyte Adhesion In Blood Flow, Tai-Hsien Wu Jun 2018

A 3d Simulation Of Leukocyte Adhesion In Blood Flow, Tai-Hsien Wu

Dissertations

It has been widely acknowledged that further understanding about the dynamics between blood cells and blood flow can help us gain more knowledge about the causes of diseases and discover more effective treatments. Examples of such dynamics include red blood cell (RBC, or erythrocyte) aggregation, white blood cell (WBC, or leukocyte) margination, and WBC extravasation. WBC extravasation is an important multiple-step process in the inflammatory response and therefore has drawn considerable attention over the past two decades. In this multiple-step process, a WBC undergoes at least four steps, including capture, rolling, firm adhesion, and transmigration, and each step is influenced ...


Induced Graph Colorings, Ian Hart Jun 2018

Induced Graph Colorings, Ian Hart

Dissertations

An edge coloring of a nonempty graph G is an assignment of colors to the edges of G. In an unrestricted edge coloring, adjacent edges of G may be colored the same. If every two adjacent edges of G are colored differently, then this edge coloring is proper and the minimum number of colors in a proper edge coloring of G is the chromatic index χ/(G) of G. A proper vertex coloring of a nontrivial graph G is an assignment of colors to the vertices of G such that every two adjacent vertices of G are colored differently. The ...


Graceful Colorings And Connection In Graphs, Alexis D. Byers Jun 2018

Graceful Colorings And Connection In Graphs, Alexis D. Byers

Dissertations

For a graph G of size m, a graceful labeling of G is an injective function f : V (G) {0, 1, . . . , m} that gives rise to a bijective function f 1 : E(G) {1, 2, . . . , m} defined by f 1(uv) = |f (u) f (v)|. A graph is graceful if it has a graceful labeling. Over the years, a number of variations of graceful labelings have been introduced, some of which have been described in terms of colorings.

A proper (vertex) coloring of a graph G is an assignment of colors to the vertices of G such that adjacent vertices ...


A Comparison Of Frankenbrew And Traditionally Manufactured Brewing Equipment, Daniel King Apr 2018

A Comparison Of Frankenbrew And Traditionally Manufactured Brewing Equipment, Daniel King

Honors Theses

Opening a new business can be a daunting task. Between the legal paperwork, securing the best perceived location, hiring new employees, the investment can require the use of a life savings. In the brewing industry, this investment can be amplified by the cost of purchasing production scale brewing equipment. Because of this, many start-up brewing operations have turned to the use of Frankenbrew equipment within their brewing process. The term “Frankenbrew” was coined by Tom Hennessy of Colorado Boy Pub & Brewery. The term refers to any equipment incorporated into a brewery that was not originally intended for that purpose, but ...


Lee Honors College Mobile Application, James Ward Apr 2018

Lee Honors College Mobile Application, James Ward

Honors Theses

In the spring of 2018 three Computer Science students Benjamin Campbell, James Ward, and Peter Shutt created a mobile application. This app was developed over the span of two semesters for their senior design project; a capstone to their degrees.

Their client, The Lee Honors College at Western Michigan University --referred to as LHC and WMU respectively hereafter-- has a plethora of academic and social information, and a large demand for access to it. This information includes building hours, contact information, health resources, a LHC specific course catalog, social media posts, event descriptions, and much more. The volume of information ...


The Proton Veto Project At Wmu/Msu, Justin Swaim Apr 2018

The Proton Veto Project At Wmu/Msu, Justin Swaim

Honors Theses

The Proton Veto Wall (VW) is a charged particle detector designed and built at Western Michigan University for use at the National Superconducting Cyclotron Laboratory at Michigan State University. The VW assists the Large Area Neutron Array (LANA) with discriminating between charged particles detected via proton recoil in the scintillating material and charged particles detected from heavy ion collisions produced in the laboratory. Twenty five Eljen-200 plastic organic scintillators are arranged in a vertical position with photomultiplier tubes (PMTs) mounted to either end. The detector sits directly in front of LANA on a large stand that was assembled using T-slotted ...


Statistical Properties Of Population Stability Index, Bilal Yurdakul Apr 2018

Statistical Properties Of Population Stability Index, Bilal Yurdakul

Dissertations

Population stability is an important concept in model management. It is crucial to monitor whether the current population has changed from the population used during development of a model. For example, has the distribution of credit scores changed, and is the existing credit score model still valid? Population change may occur for many reasons–change in the economic environment, strategic change in the business, policy changes within the company, or changes in regulatory environment.

The population stability index (PSI) is a statistic that measures how much a variable has shifted over time, and is used to monitor applicability of a ...


Using Agent-Based Implementation Of Active Data Bundles For Protecting Privacy In Healthcare Information Systems, Raed M. Salih Apr 2018

Using Agent-Based Implementation Of Active Data Bundles For Protecting Privacy In Healthcare Information Systems, Raed M. Salih

Dissertations

Sharing healthcare information—including electronic health/medical records (EHRs/EMRs)—among healthcare information systems is necessary for improving the quality of healthcare. However, facilitating data exchange increases privacy threats—due to easier copying and dissemination of healthcare information.

We propose a solution that provides privacy protection for patients’ EHRs/EMRs disseminated among different authorized healthcare information systems. Our solution builds upon the existing construct named an Active Data Bundle (ADB). In the proposed solution, ADBs keep EHRs/EMRs as sensitive data; include metadata describing sensitive data and prescribing their use; and encompass a policy enforcement engine (called a virtual machine ...


Statistical Models For Correlated Data, Xiaomeng Niu Apr 2018

Statistical Models For Correlated Data, Xiaomeng Niu

Dissertations

Correlated data arise frequently in many studies where multiple response variables or repeatedly measured responses within subjects are correlated. My dissertation topic lies broadly in developing various statistical methodologies for correlated types of data such as longitudinal data, clustered data, and multivariate data.

Multiple response variables might be relevant within subjects. A univariate procedure fitting each response separately does not take into account the correlation among responses. To improve estimation efficiency for the regression parameter, this study proposes two estimation procedures by accommodating correlations among the response variables. The proposed procedures do not require knowledge of the true correlation structure ...


A Holistic Computational Approach To Boosting The Performance Of Protein Search Engines, Majdi Ahmad Mosa Maabreh Apr 2018

A Holistic Computational Approach To Boosting The Performance Of Protein Search Engines, Majdi Ahmad Mosa Maabreh

Dissertations

Despite availability of several proteins search engines, due to the increasing amounts of MS/MS data and database sizes, more efficient data analysis and reduction methods are important. Improving accuracy and performance of protein identification is a main goal in the community of proteomic research. In this research, a holistic solution for improvement in search performance is developed.

Most current search engines apply the SEQUEST style of searching protein databases to define MS/MS spectra. SEQUEST involves three main phases: (i) Indexing the protein databases, (ii) Matching and Ranking the MS/MS spectra and (iii) Filtering the matches and reporting ...


Support Assurance-Based Software Development For Mission Critical Domains Using The Model Driven Architecture, Chung-Ling Lin Apr 2018

Support Assurance-Based Software Development For Mission Critical Domains Using The Model Driven Architecture, Chung-Ling Lin

Dissertations

In the past decades, software development for mission critical applications has drawn great attention not only in various mission critical communities but also software engineering communities. One of the important reasons is that the failure of these systems can lead to some serious consequences such as huge financial loss and even loss of life. Therefore, software certification has become an important activity for mission critical applications in that software assurance for such a system should be certified. With the increasing complexity of a software system in mission critical sectors, certifiers have found hard time to understand how a software system ...


Edge Induced Weightings Of Uniform Hypergraphs And Related Problems, Laars C. Helenius Apr 2018

Edge Induced Weightings Of Uniform Hypergraphs And Related Problems, Laars C. Helenius

Dissertations

The starting point of the research is the so called 1-2-3 Conjecture formulated in 2004 by Karoński, Luczak, and Thomason. Roughly speaking it says that the edges of any graph can be weighted from {1, 2, 3} so that the induced vertex coloring (as the sum of weights adjacent to a given vertex) is proper. The conjecture has attracted a lot of interest from researchers over the last decade but is still unanswered. More recently, the conjecture has been studied for hypergraphs.

The main result of this dissertation shows in particular that an analogous conjecture holds for almost all uniform ...


Mapping And Interpreting The Glacial Geology Of Pictured Rocks National Lakeshore, Michigan, Sarah M. Vandermeer Apr 2018

Mapping And Interpreting The Glacial Geology Of Pictured Rocks National Lakeshore, Michigan, Sarah M. Vandermeer

Dissertations

Pictured Rocks National Lakeshore is among the most popular parks in Michigan, yet prior to this study, it was the only National Park that lacked a detailed surficial geology map characterizing the distribution of sediments and landforms. Additionally, much of the landscape remained unexplored. These factors prevented thorough interpretations of landscape development and evolution. This research aims to map and further explore the relationship of glacial sediments and landforms throughout Pictured Rocks to refine and expand the current understanding of glacial events that shaped this landscape.

A new, detailed (1:24,000-scale) surficial geology map of the ten 7.5-minute ...


Mapping Bedrock Topography Of The Portage And Schoolcraft Nw 7.5’ Quadrangles, Kalamazoo Co. Mi, Using The Hvsr Passive Seismic Method, Benjamin B. Seiderman Apr 2018

Mapping Bedrock Topography Of The Portage And Schoolcraft Nw 7.5’ Quadrangles, Kalamazoo Co. Mi, Using The Hvsr Passive Seismic Method, Benjamin B. Seiderman

Master's Theses

This study utilizes the Horizontal to Vertical Spectral Ratio (HVSR) technique to map bedrock topography in the Portage and Schoolcraft NW quadrangles, Kalamazoo Co., MI, looking for buried bedrock valleys. Glacial sediment-landform assemblages dominate the study area, due to multiple advances of the Laurentide Ice Sheet (LIS). Tunnel valleys, which are one type of buried valley, are eroded by subglacial meltwater and commonly filled with the coarser varieties of glacial outwash, making them potential aquifers. The HVSR technique measures the ratio of horizontal to vertical ground motion, excited by ambient seismic noise, resulting in a peak at the resonance frequency ...


Determinants Of Household Water Use In The City Of Kalamazoo, Michigan: The Role Of Climate And Socioeconomic Factors, Danielle Molenaar Apr 2018

Determinants Of Household Water Use In The City Of Kalamazoo, Michigan: The Role Of Climate And Socioeconomic Factors, Danielle Molenaar

Master's Theses

Located in the Great Lakes Watershed, the City of Kalamazoo can be considered “water rich”. Therefore, the area has been absent from water use studies. Water use studies are beneficial in all locations; as they can aid city planners, water resource managers, and utility companies. This study examines how household monthly water use in the City of Kalamazoo is impacted by both climate and socioeconomic variables over the period 2006-2016. Household level data were aggregated into census tracts to obtain monthly tract averages for the eleven-year period. Ordinary least squares regression (OLS) was used to determine which variables impact the ...


Organocatalyzed Synthesis Of Epoxides From Chalcones Utilizing Amino Acids, Sabrina N. Kegeler Apr 2018

Organocatalyzed Synthesis Of Epoxides From Chalcones Utilizing Amino Acids, Sabrina N. Kegeler

Master's Theses

The epoxide functional group is important throughout the chemical and pharmaceutical industries, as well as in nature. In the chemical industry, epoxides are present in resins and fragrances. In the pharmaceutical industry, epoxide-containing compounds are used as intermediates in the manufacturing of drugs. In nature, many natural products contain epoxide groups and are used for medicinal purposes, and for models to create synthetic molecules.

One approach to epoxide synthesis involves the use of an alkene precursor, a base, and an oxidizing agent. This is where my investigations began. The first step was to optimize the epoxidation reaction, examining substrate scope ...