Other Computer Sciences Commons^™

Trunctrimmer: A First Step Towards Automating Standard Bioinformatic Analysis, Z. Gunner Lawless, Dana Dittoe, Dale R. Thompson, Steven C. Ricke

Computer Science and Computer Engineering Undergraduate Honors Theses

Bioinformatic analysis is a time-consuming process for labs performing research on various microbiomes. Researchers use tools like Qiime2 to help standardize the bioinformatic analysis methods, but even large, extensible platforms like Qiime2 have drawbacks due to the attention required by researchers. In this project, we propose to automate additional standard lab bioinformatic procedures by eliminating the existing manual process of determining the trim and truncate locations for paired end 2 sequences. We introduce a new Qiime2 plugin called TruncTrimmer to automate the process that usually requires the researcher to make a decision on where to trim and truncate manually after …

A Framework To Detect The Susceptibility Of Employees To Social Engineering Attacks, Hashim H. Alneami

Doctoral Dissertations and Master's Theses

Social engineering attacks (SE-attacks) in enterprises are hastily growing and are becoming increasingly sophisticated. Generally, SE-attacks involve the psychological manipulation of employees into revealing confidential and valuable company data to cybercriminals. The ramifications could bring devastating financial and irreparable reputation loss to the companies. Because SE-attacks involve a human element, preventing these attacks can be tricky and challenging and has become a topic of interest for many researchers and security experts. While methods exist for detecting SE-attacks, our literature review of existing methods identified many crucial factors such as the national cultural, organizational, and personality traits of employees that enable …

A High-Precision Machine Learning Algorithm To Classify Left And Right Outflow Tract Ventricular Tachycardia, Jianwei Zhang, Guohua Fu, Islam Abudayyeh, Magdi Yacoub, Anthony Chang, William Feaster, Louis Ehwerhemuepha, Hesham El-Askary, Xianfeng Du, Bin He, Mingjun Feng, Yibo Yu, Binhao Wang, Jing Liu, Hai Yao, Hulmin Chu, Cyril Rakovski

Mathematics, Physics, and Computer Science Faculty Articles and Research

Introduction: Multiple algorithms based on 12-lead ECG measurements have been proposed to identify the right ventricular outflow tract (RVOT) and left ventricular outflow tract (LVOT) locations from which ventricular tachycardia (VT) and frequent premature ventricular complex (PVC) originate. However, a clinical-grade machine learning algorithm that automatically analyzes characteristics of 12-lead ECGs and predicts RVOT or LVOT origins of VT and PVC is not currently available. The effective ablation sites of RVOT and LVOT, confirmed by a successful ablation procedure, provide evidence to create RVOT and LVOT labels for the machine learning model.

Methods: We randomly sampled training, validation, and testing …

Ensemble Protein Inference Evaluation, Kyle Lee Lucke

Graduate Student Theses, Dissertations, & Professional Papers

The Protein inference problem is becoming an increasingly important tool that aids in the characterization of complex proteomes and analysis of complex protein samples. In bottom-up shotgun proteomics experiments the metrics for evaluation (like AUC and calibration error) are based on an often imperfect target-decoy database. These metrics make the inherent assumption that all of the proteins in the target set are present in the sample being analyzed. In general, this is not the case, they are typically a mix of present and absent proteins. To objectively evaluate inference methods, protein standard datasets are used. These datasets are special in …

Design Project: Smart Headband, John Michel, Jack Durkin, Noah Lewis

Williams Honors College, Honors Research Projects

Concussion in sports is a prevalent medical issue. It can be difficult for medical professionals to diagnose concussions. With the fast pace nature of many sports, and the damaging effects of concussions, it is important that any concussion risks are assessed immediately. There is a growing trend of wearable technology that collects data such as steps and provides the wearer with in-depth information regarding their performance. The Smart Headband project created a wearable that can record impact data and provide the wearer with a detailed analysis on their risk of sustaining a concussion. The Smart Headband uses accelerometers and gyroscopes …

Exploring Information For Quantum Machine Learning Models, Michael Telahun

Electronic Theses and Dissertations

Quantum computing performs calculations by using physical phenomena and quantum mechanics principles to solve problems. This form of computation theoretically has been shown to provide speed ups to some problems of modern-day processing. With much anticipation the utilization of quantum phenomena in the field of Machine Learning has become apparent. The work here develops models from two software frameworks: TensorFlow Quantum (TFQ) and PennyLane for machine learning purposes. Both developed models utilize an information encoding technique amplitude encoding for preparation of states in a quantum learning model. This thesis explores both the capacity for amplitude encoding to provide enriched state …

Coevolution, Dynamics And Allostery Conspire In Shaping Cooperative Binding And Signal Transmission Of The Sars-Cov-2 Spike Protein With Human Angiotensin-Converting Enzyme 2, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Binding to the host receptor is a critical initial step for the coronavirus SARS-CoV-2 spike protein to enter into target cells and trigger virus transmission. A detailed dynamic and energetic view of the binding mechanisms underlying virus entry is not fully understood and the consensus around the molecular origins behind binding preferences of SARS-CoV-2 for binding with the angiotensin-converting enzyme 2 (ACE2) host receptor is yet to be established. In this work, we performed a comprehensive computational investigation in which sequence analysis and modeling of coevolutionary networks are combined with atomistic molecular simulations and comparative binding free energy analysis of …

Analyzing Yankees And Red Sox Sentiment Over The Course Of A Season, Connor Koch

Honors Projects in Data Science

This paper investigates data collected on twitter which references the Yankees or Red Sox during the 2020 Major League Baseball (MLB) season. The objective is to analyze the sentiment of tweets referencing the Yankees and Red Sox over the course of the season. In addition, an investigation of the networks within the data and the topics that were prevalent will be conducted. The 2020 MLB season was started late because of the COVID-19 pandemic and was a season like no other. The expectation of a dataset revolving around baseball is that the topics discussed would be about baseball. The findings …

Espade: An Efficient And Semantically Secure Shortest Path Discovery For Outsourced Location-Based Services, Bharath K. Samanthula, Divyadharshini Karthikeyan, Boxiang Dong, K. Anitha Kumari

Department of Computer Science Faculty Scholarship and Creative Works

With the rapid growth of smart devices and technological advancements in tracking geospatial data, the demand for Location-Based Services (LBS) is facing a constant rise in several domains, including military, healthcare and transportation. It is a natural step to migrate LBS to a cloud environment to achieve on-demand scalability and increased resiliency. Nonetheless, outsourcing sensitive location data to a third-party cloud provider raises a host of privacy concerns as the data owners have reduced visibility and control over the outsourced data. In this paper, we consider outsourced LBS where users want to retrieve map directions without disclosing their location information. …

Exploring The Eating Disorder Examination Questionnaire, Clinical Impairment Assessment, And Autism Quotient To Identify Eating Disorder Vulnerability: A Cluster Analysis, Natalia Stewart Rosenfield, Erik Linstead

Engineering Faculty Articles and Research

Eating disorders are very complicated and many factors play a role in their manifestation. Furthermore, due to the variability in diagnosis and symptoms, treatment for an eating disorder is unique to the individual. As a result, there are numerous assessment tools available, which range from brief survey questionnaires to in-depth interviews conducted by a professional. One of the many benefits to using machine learning is that it offers new insight into datasets that researchers may not previously have, particularly when compared to traditional statistical methods. The aim of this paper was to employ k-means clustering to explore the Eating Disorder …

A Fortran-Keras Deep Learning Bridge For Scientific Computing, Jordan Ott, Mike Pritchard, Natalie Best, Erik Linstead, Milan Curcic, Pierre Baldi

Engineering Faculty Articles and Research

Implementing artificial neural networks is commonly achieved via high-level programming languages such as Python and easy-to-use deep learning libraries such as Keras. These software libraries come preloaded with a variety of network architectures, provide autodifferentiation, and support GPUs for fast and efficient computation. As a result, a deep learning practitioner will favor training a neural network model in Python, where these tools are readily available. However, many large-scale scientific computation projects are written in Fortran, making it difficult to integrate with modern deep learning methods. To alleviate this problem, we introduce a software library, the Fortran-Keras Bridge (FKB). This two-way …

Synergistic Use Of Remote Sensing And Modeling For Estimating Net Primary Productivity In The Red Sea With Vgpm, Eppley-Vgpm, And Cbpm Models Intercomparison, Wenzhao Li, Surya Prakash Tiwari, Hesham El-Askary, Mohamed Ali Qurban, Vassilis Amiridis, K. P. Manikandan, Michael J. Garay, Olga V. Kalashnikova, Thomas C. Piechota, Daniele C. Struppa

Mathematics, Physics, and Computer Science Faculty Articles and Research

Primary productivity (PP) has been recently investigated using remote sensing-based models over quite limited geographical areas of the Red Sea. This work sheds light on how phytoplankton and primary production would react to the effects of global warming in the extreme environment of the Red Sea and, hence, illuminates how similar regions may behave in the context of climate variability. study focuses on using satellite observations to conduct an intercomparison of three net primary production (NPP) models--the vertically generalized production model (VGPM), the Eppley-VGPM, and the carbon-based production model (CbPM)--produced over the Red Sea domain for the 1998-2018 time period. …

Knot Flow Classification And Its Applications In Vehicular Ad-Hoc Networks (Vanet), David Schmidt

Electronic Theses and Dissertations

Intrusion detection systems (IDSs) play a crucial role in the identification and mitigation for attacks on host systems. Of these systems, vehicular ad hoc networks (VANETs) are difficult to protect due to the dynamic nature of their clients and their necessity for constant interaction with their respective cyber-physical systems. Currently, there is a need for a VANET-specific IDS that meets this criterion. To this end, a spline-based intrusion detection system has been pioneered as a solution. By combining clustering with spline-based general linear model classification, this knot flow classification method (KFC) allows for robust intrusion detection to occur. Due its …

Storage Management Strategy In Mobile Phones For Photo Crowdsensing, En Wang, Zhengdao Qu, Xinyao Liang, Xiangyu Meng, Yongjian Yang, Dawei Li, Weibin Meng

Department of Computer Science Faculty Scholarship and Creative Works

In mobile crowdsensing, some users jointly finish a sensing task through the sensors equipped in their intelligent terminals. In particular, the photo crowdsensing based on Mobile Edge Computing (MEC) collects pictures for some specific targets or events and uploads them to nearby edge servers, which leads to richer data content and more efficient data storage compared with the common mobile crowdsensing; hence, it has attracted an important amount of attention recently. However, the mobile users prefer uploading the photos through Wifi APs (PoIs) rather than cellular networks. Therefore, photos stored in mobile phones are exchanged among users, in order to …

Ordinal Hyperplane Loss, Bob Vanderheyden

Doctor of Data Science and Analytics Dissertations

This research presents the development of a new framework for analyzing ordered class data, commonly called “ordinal class” data. The focus of the work is the development of classifiers (predictive models) that predict classes from available data. Ratings scales, medical classification scales, socio-economic scales, meaningful groupings of continuous data, facial emotional intensity and facial age estimation are examples of ordinal data for which data scientists may be asked to develop predictive classifiers. It is possible to treat ordinal classification like any other classification problem that has more than two classes. Specifying a model with this strategy does not fully utilize …

Incorporating Word Order Explicitly In Glove Word Embedding, Brandon Cox

Computer Science and Computer Engineering Undergraduate Honors Theses

Word embedding is the process of representing words from a corpus of text as real number vectors. These vectors are often derived from frequency statistics from the source corpus. In the GloVe model as proposed by Pennington et al., these vectors are generated using a word-word cooccurrence matrix. However, the GloVe model fails to explicitly take into account the order in which words appear within the contexts of other words. In this paper, multiple methods of incorporating word order in GloVe word embeddings are proposed. The most successful method involves directly concatenating several word vector matrices for each position in …

Predicting Switch-Like Behavior In Proteins Using Logistic Regression On Sequence-Based Descriptors, Benjamin Strauss

Master's Projects

Ligands can bind at specific protein locations, inducing conformational changes such as those involving secondary structure. Identifying these possible switches from sequence, including homology, is an important ongoing area of research. We attempt to predict possible secondary structure switches from sequence in proteins using machine learning, specifically a logistic regression approach with 48 N-acetyltransferases as our learning set and 5 sirtuins as our test set. Validated residue binary assignments of 0 (no change in secondary structure) and 1 (change in secondary structure) were determined (DSSP) from 3D X-ray structures for sets of virtually identical chains crystallized under different conditions. Our …

Identifying Depression In The National Health And Nutrition Examination Survey Data Using A Deep Learning Algorithm, Jihoon Oh, Kyongsik Yun, Uri Maoz, Tae-Suk Kim, Jeong-Ho Chae

Psychology Faculty Articles and Research

Background

As depression is the leading cause of disability worldwide, large-scale surveys have been conducted to establish the occurrence and risk factors of depression. However, accurately estimating epidemiological factors leading up to depression has remained challenging. Deep-learning algorithms can be applied to assess the factors leading up to prevalence and clinical manifestations of depression.

Methods

Customized deep-neural-network and machine-learning classifiers were assessed using survey data from 19,725 participants from the NHANES database (from 1999 through 2014) and 4949 from the South Korea NHANES (K-NHANES) database in 2014.

Results

A deep-learning algorithm showed area under the receiver operating characteristic curve (AUCs) …

The Effects Of Finite Precision On The Simulation Of The Double Pendulum, Rebecca Wild

Senior Honors Projects, 2010-2019

We use mathematics to study physical problems because abstracting the information allows us to better analyze what could happen given any range and combination of parameters. The problem is that for complicated systems mathematical analysis becomes extremely cumbersome. The only effective and reasonable way to study the behavior of such systems is to simulate the event on a computer. However, the fact that the set of floating-point numbers is finite and the fact that they are unevenly distributed over the real number line raises a number of concerns when trying to simulate systems with chaotic behavior. In this research we …

Orca Travel Grant Recipient An Interview With Emily Hoard, Emily Hoard

Steeplechase: An ORCA Student Journal

No abstract provided.

Extending Set Functors To Generalised Metric Spaces, Adriana Balan, Alexander Kurz, Jiří Velebil

Mathematics, Physics, and Computer Science Faculty Articles and Research

For a commutative quantale V, the category V-cat can be perceived as a category of generalised metric spaces and non-expanding maps. We show that any type constructor T (formalised as an endofunctor on sets) can be extended in a canonical way to a type constructor T_V on V-cat. The proof yields methods of explicitly calculating the extension in concrete examples, which cover well-known notions such as the Pompeiu-Hausdorff metric as well as new ones.

Conceptually, this allows us to to solve the same recursive domain equation X ≅ TX in different categories (such as sets and metric spaces) and …

Snap Scholar: The User Experience Of Engaging With Academic Research Through A Tappable Stories Medium, Ieva Burk

CMC Senior Theses

With the shift to learn and consume information through our mobile devices, most academic research is still only presented in long-form text. The Stanford Scholar Initiative has explored the segment of content creation and consumption of academic research through video. However, there has been another popular shift in presenting information from various social media platforms and media outlets in the past few years. Snapchat and Instagram have introduced the concept of tappable “Stories” that have gained popularity in the realm of content consumption.

To accelerate the growth of the creation of these research talks, I propose an alternative to video: …

Absorption Calculator: A Cross-Platform Application For Portable Data Analysis, Annmarie Kolbl

Williams Honors College, Honors Research Projects

Traditional spectrometers are expensive and non-portable, making them inaccessible to the public. This application will be used in conjunction with spectrometer hardware developed by Erie Open Systems. The hardware itself is 3D printed and, in addition to being portable, enables data to be collected easily. The purpose of this project is to create a cross-platform application capable of reading the output from the spectrometer hardware, calculating the absorbance levels of the sample against the control, and recording the data in tables stored on the cloud. The end result will be an application that runs on iOS and Android, and is …

A Multi-Task Approach To Incremental Dialogue State Tracking, Anh Duong Trinh, Robert J. Ross, John D. Kelleher

Conference papers

Incrementality is a fundamental feature of language in real world use. To this point, however, the vast majority of work in automated dialogue processing has focused on language as turn based. In this paper we explore the challenge of incremental dialogue state tracking through the development and analysis of a multi-task approach to incremental dialogue state tracking. We present the design of our incremental dialogue state tracker in detail and provide evaluation against the well known Dialogue State Tracking Challenge 2 (DSTC2) dataset. In addition to a standard evaluation of the tracker, we also provide an analysis of the Incrementality …

Topographic Maps: Image Processing And Path-Finding, Calin Washington

Master's Theses

Topographic maps are an invaluable tool for planning routes through unfamiliar terrain. However, accurately planning routes on topographic maps is a time- consuming and error-prone task. One factor is the difficulty of interpreting the map itself, which requires prior knowledge and practice. Another factor is the difficulty of making choices between possible routes that have different trade-offs between length and the terrain they traverse.

To alleviate these difficulties, this thesis presents a system to automate the process of finding routes on scanned images of topographic maps. The system allows users to select any two points on a topographic map and …

Stress Levels Of Cs1 Students During Programming- Measurement And A Cause And Effect Analysis, Gopi Satya Sainadh Raju Sarikonda

Theses and Dissertations

Stress is a kind of feeling we experience when we are under pressure. Stress is the word that we use when we feel that we are overloaded mentally in our thoughts and wonder whether we can cope with those placed upon us. The effects of stress are different for different people when we take their age, profession, gender and other aspects into consideration. Many studies show that stress in a learning environment impacts learning negatively.

In this thesis, the role of stress on students in an introductory programming course (CS1) at CSU has been explored. Introductory programming course has a …

Understanding Natural Keyboard Typing Using Convolutional Neural Networks On Mobile Sensor Data, Travis Siems

Computer Science and Engineering Theses and Dissertations

Mobile phones and other devices with embedded sensors are becoming increasingly ubiquitous. Audio and motion sensor data may be able to detect information that we did not think possible. Some researchers have created models that can predict computer keyboard typing from a nearby mobile device; however, certain limitations to their experiment setup and methods compelled us to be skeptical of the models’ realistic prediction capability. We investigate the possibility of understanding natural keyboard typing from mobile phones by performing a well-designed data collection experiment that encourages natural typing and interactions. This data collection helps capture realistic vulnerabilities of the security …

Automating Data Analysis For Two-Dimensional Gas Chromatography/Time-Of-Flight Mass Spectrometry Non-Targeted Analysis Of Comparative Samples, Ivan A. Titaley, O. Maduka Ogba, Leah Chibwe, Eunha Hoh, Paul H.-Y. Cheong, Staci L. Massey Simonich

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Non-targeted analysis of environmental samples, using comprehensive two‐dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC/ToF-MS), poses significant data analysis challenges due to the large number of possible analytes. Non-targeted data analysis of complex mixtures is prone to human bias and is laborious, particularly for comparative environmental samples such as contaminated soil pre- and post-bioremediation. To address this research bottleneck, we developed OCTpy, a Python™ script that acts as a data reduction filter to automate GC × GC/ToF-MS data analysis from LECO^® ChromaTOF^® software and facilitates selection of analytes of interest based on peak area …

Expression Of The Microrna-143/145 Cluster Is Decreased In Hepatitis B Virus-Associated Hepatocellular Carcinoma And May Serve As A Biomarker For Tumorigenesis In Patients With Chronic Hepatitis B, Qi Zhao, Xiangfei Sun, Chao Liu, Tao Li, Juan Cui, Chengyong Qin

School of Computing: Faculty Publications

The aims of the present study were to identify the expression profile of microRNA (miR)‑143/145 in hepatitis B virus (HBV)‑associated hepatocellular carcinoma (HCC), explore its association with prognosis and investigate whether the serum miR‑143/145 expression levels may serve as a diagnostic indicator of HBV‑associated HCC. The microRNA (miRNA) chromatin immunoprecipitation dataset was obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus databases, and analyzed using the Wilcoxon signed‑rank test. It was observed that the expression of miR‑143 and miR‑145 was decreased 1.5‑fold in HBV‑associated HCC samples compared with non‑tumor tissue in the TCGA and the GSE22058 datasets …

A Practical And Efficient Algorithm For The K-Mismatch Shortest Unique Substring Finding Problem, Daniel Robert Allen

EWU Masters Thesis Collection

This thesis revisits the k-mismatch shortest unique substring (SUS) finding problem and demonstrates that a technique recently presented in the context of solving the k-mismatch average common substring problem can be adapted and combined with parts of the existing solution, resulting in a new algorithm which has expected time complexity of O(n log^k n), while maintaining a practical space complexity at O(kn), where n is the string length. When k > 0, which is the hard case, the new proposal significantly improves the any-case O(n²) time complexity of the prior best method for k-mismatch SUS finding. Experimental study …