Data Science Commons^™

Molecular Understanding And Design Of Deep Eutectic Solvents And Proteins Using Computer Simulations And Machine Learning, Usman Lame Abbas

Theses and Dissertations--Chemical and Materials Engineering

Hydrophobic deep eutectic solvents (DESs) have emerged as excellent extractants. A major challenge is the lack of an efficient tool to discover DES candidates. Currently, the search relies heavily on the researchers’ intuition or a trial-and-error process, which leads to a low success rate or bypassing of promising candidates. DES performance depends on the heterogeneous hydrogen bond environment formed by multiple hydrogen bond donors and acceptors. Understanding this heterogeneous hydrogen bond environment can help develop principles for designing high performance DESs for extraction and other separation applications. This work investigates the structure and dynamics of hydrogen bonds in hydrophobic DESs …

An Enhanced Deep Autoencoder For Flight Delay Prediction, Desmond B. Bisandu, Dan Andrei Soviani-Sitoiu, Irene Moulitsas

Journal of Aviation/Aerospace Education & Research

Accurate and timely flight delay prediction cannot be overemphasized because of the ever-increasing demand for air travel and its importance in deploying intelligent transportation systems. Nonetheless, there has not been a universal solution to the problem, as more intelligent flight decision systems are required for the aviation industry's future growth. Existing flight delay classification and prediction approaches are mainly shallow traffic models and do not satisfy many applications in the real world. Our motivation to rethink the deep architecture model for predicting flight delays emanates from the problem. In this research, we proposed a technique that modified stacked autoencoder architecture …

Deapsecure Computational Training For Cybersecurity: Progress Toward Widespread Community Adoption, Wirawan Purwanto, Bahador Dodge, Karina Arcaute, Masha Sosonkina, Hongyi Wu

Electrical & Computer Engineering Faculty Publications

The Data-Enabled Advanced Computational Training Program for Cybersecurity Research and Education (DeapSECURE) is a non-degree training consisting of six modules covering a broad range of cyberinfrastructure techniques, including high performance computing, big data, machine learning and advanced cryptography, aimed at reducing the gap between current cybersecurity curricula and requirements needed for advanced research and industrial projects. Since 2020, these lesson modules have been updated and retooled to suit fully-online delivery. Hands-on activities were reformatted to accommodate self-paced learning. In this paper, we summarize the four years of the project comparing in-person and on-line only instruction methods as well as outlining …

A Benchmark Framework For Data Visualization And Explainable Ai (Xai), Murat Kuzlu, Gokcen Ozdemir, Umut Ozdemir

Engineering Technology Faculty Publications

This research introduces a benchmark framework, called EDUMX, designed for machine learning (ML)-based forecasting and XAI tasks, leveraging the Streamlit open-source Python library. The framework offers a comprehensive suite of functionalities, including data loading, feature selection, relationship analysis, data preprocessing, model selection, metric evaluation, training, and real-time monitoring. Users can easily upload data in diverse formats, explore relationships between variables, preprocess data using various techniques, and assess the performance of the ML model using customizable metrics. With its user-friendly interface, this framework offers invaluable insights for forecasting tasks in various domains, catering to the evolving needs of predictive analytics. EDUMX …

Bayesian Neural Netwok Variational Autoencoder Inverse Mapper (Bnn-Vaim) And Its Application In Compton Form Factors Extraction, Md Fayaz Bin Hossen, Tareq Alghamdi, Manal Almaeen, Yaohang Li

Computer Science Faculty Publications

We extend the Variational Autoencoder Inverse Mapper (VAIM) framework for the inverse problem of extracting Compton Form Factors (CFFs) from deeply virtual exclusive reactions, such as the unpolarized Deeply virtual exclusive scattering (DVCS) cross section. VAIM is an end-to-end deep learning framework to address the solution ambiguity issue in ill-posed inverse problems, which comprises of a forward mapper and a backward mapper to simulate the forward and inverse processes, respectively. In particular, we incorporate Bayesian Neural Network (BNN) into the VAIM architecture (BNN-VAIM) for uncertainty quantification. By sampling the weights and biases distributions of the BNN in the backward mapper …

Improving The Quality Of Micronutrient Food Composition Data In Sub-Saharan Africa Using Predictive Analytics, Junior Mbuyamba Muka

Theses and Dissertations

High-quality food composition data are indispensable for decision making in several health, agricultural, and nutrition-related activities. Analytical data are the most accurate type of food composition data (FCD). Yet, most food composition databases (FCDBs) compiled in Sub-Saharan Africa only contain a small amount of analytical data collected from foods consumed in this region. Most of the data are either borrowed / copied from FCDBs collected in other parts of the world, calculated, imputed, or presumed data. Even with these alternative types, FCDBs in Sub-Saharan Africa have not reached a satisfactory level of completeness, as they still have missing data for …

Deep Learning Image Analysis To Isolate And Characterize Different Stages Of S-Phase In Human Cells, Kevin A. Boyd, Rudranil Mitra, John Santerre, Christopher L. Sansam

SMU Data Science Review

Abstract. This research used deep learning for image analysis by isolating and characterizing distinct DNA replication patterns in human cells. By leveraging high-resolution microscopy images of multiple cells stained with 5-Ethynyl-2′-deoxyuridine (EdU), a replication marker, this analysis utilized Convolutional Neural Networks (CNNs) to perform image segmentation and to provide robust and reliable classification results. First multiple cells in a field of focus were identified using a pretrained CNN called Cellpose. After identifying the location of each cell in the image a python script was created to crop out each cell into individual .tif files. After careful annotation, a CNN was …

Differentiation Of Human, Dog, And Cat Hair Fibers Using Dart Tofms And Machine Learning, Laura Ahumada, Erin R. Mcclure-Price, Chad Kwong, Edgard O. Espinoza, John Santerre

SMU Data Science Review

Hair is found in over 90% of crime scenes and has long been analyzed as trace evidence. However, recent reviews of traditional hair fiber analysis techniques, primarily morphological examination, have cast doubt on its reliability. To address these concerns, this study employed machine learning algorithms, specifically Linear Discriminant Analysis (LDA) and Random Forest, on Direct Analysis in Real Time time-of-flight mass spectra collected from human, cat, and dog hair samples. The objective was to develop a chemistry- and statistics-based classification method for unbiased taxonomic identification of hair. The results of the study showed that LDA and Random Forest were highly …

Cm-Ii Meditation As An Intervention To Reduce Stress And Improve Attention: A Study Of Ml Detection, Spectral Analysis, And Hrv Metrics, Sreekanth Gopi

Master of Science in Computer Science Theses

Students frequently face heightened stress due to academic and social pressures, particularly in de- manding fields like computer science and engineering. These challenges are often associated with serious mental health issues, including ADHD (Attention Deficit Hyperactivity Disorder), depression, and an increased risk of suicide. The average student attention span has notably decreased from 21⁄2 minutes to just 47 seconds, and now it typically takes about 25 minutes to switch attention to a new task (Mark, 2023). Research findings suggest that over 95% of individuals who die by suicide have been diagnosed with depression (Shahtahmasebi, 2013), and almost 20% of students …

Addressing The Analytical And Computational Challenges Using Machine Learning In Biomedical Research, Yizhuo Wang

Dissertations and Theses (Open Access)

In the contemporary healthcare field, professionals are confronted with an ever-growing volume of clinical data stored in electronic health records, alongside the genomic data stemming from laboratory experiments. As a response to this deluge of data, the application of machine learning (ML) techniques is gaining popularity since ML techniques have demonstrated an exceptional proficiency in processing big data and deciphering complex nonlinear patterns that are intrinsic to biomedical research.

My research leverages ML's capabilities to address the computational challenges spanning diverse areas, including adaptive clinical trial designs, survival analysis, and high-dimensional genetic data analysis. Specifically, Chapter 2 focused on the …

Dei: Exploring Academic Reflections Using Natural Language Processing To Create A Roadmap Of Student Success And Foster Inclusive Engineering Education, Rajvir H. Vyas, Nidhi Raviprasad

College of Engineering Summer Undergraduate Research Program

Every year, the College of Engineering (CENG) students and faculty reach out to admitted students through “Text-a-Thon” programs to answer their questions about being a student at Cal Poly. In order to improve CENG outreach efforts, we analyzed these text conversations to predict the likelihood of an admitted student accepting an offer of admission from Cal Poly. Through our research, we discovered key factors that play a role in a student committing to Cal Poly through data-based insights. Additionally, we successfully used a human-on-the-loop system to help create Machine Learning (ML) models that predict satisfaction of response by way of …

Spoken Language Processing And Modeling For Aviation Communications, Aaron Van De Brook

Doctoral Dissertations and Master's Theses

With recent advances in machine learning and deep learning technologies and the creation of larger aviation-specific corpora, applying natural language processing technologies, especially those based on transformer neural networks, to aviation communications is becoming increasingly feasible. Previous work has focused on machine learning applications to natural language processing, such as N-grams and word lattices. This thesis experiments with a process for pretraining transformer-based language models on aviation English corpora and compare the effectiveness and performance of language models transfer learned from pretrained checkpoints and those trained from their base weight initializations (trained from scratch). The results suggest that transformer language …

Verifying Empirical Predictive Modeling Of Societal Vulnerability To Hazardous Events: A Monte Carlo Experimental Approach, Yi Victor Wang, Seung Hee Kim, Menas C. Kafatos

Institute for ECHO Articles and Research

With the emergence of large amounts of historical records on adverse impacts of hazardous events, empirical predictive modeling has been revived as a foundational paradigm for quantifying disaster vulnerability of societal systems. This paradigm models societal vulnerability to hazardous events as a vulnerability curve indicating an expected loss rate of a societal system with respect to a possible spectrum of intensity measure (IM) of an event. Although the empirical predictive models (EPMs) of societal vulnerability are calibrated on historical data, they should not be experimentally tested with data derived from field experiments on any societal system. Alternatively, in this paper, …

The Influence Of Allostery Governing The Changes In Protein Dynamics Upon Substitution, Joseph Hess

All Dissertations

The focus of this research is to investigate the effects of allostery on the function/activity of an enzyme, human immunodeficiency virus type 1 (HIV-1) protease, using well-defined statistical analyses of the dynamic changes of the protein and variants with unique single point substitutions ¹. The experimental data¹ evaluated here only characterized HIV-1 protease with one of its potential target substrates. Probing the dynamic interactions of the residues of an enzyme and its variants can offer insight of the developmental importance for allosteric signaling and their connection to a protein’s function. The realignment of the secondary structure elements can …

Characterization And Estimation Of Musculoskeletal Pain Using Machine Learning, Boluwatife Faremi

Master's Theses

Traditional scales utilized for recording pain are known to be highly subjective and biased due to inaccuracies in recollecting actual pain intensities. As a result, machine learning (ML) models that are trained using these scores as ground truth are reported to have low performance for objective pain classification because of the huge disparity between what was felt in moments of pain and the scores recorded afterward.

In the present study, two devices were designed for gathering real-time, continuous in-session subjective pain scores and the recording of the autonomic nervous system (ANS) altered endodermal (EDA) activity. 24 participants were recruited to …

Towards An Experimental Bibliography Of Hemispheric Reconstruction Newspapers, Joshua Ortiz Baco, Benjamin Charles Germain Lee, Jim Casey, Sarah H. Salter

Criticism

Digital collections of newspapers have drawn broader attention to the fragmented and scattered print histories of minoritized communities. Attempts to survey these histories through bibliography, however, quickly meet with a fundamental problem: the practice of bibliographic description calls for creating a static record of social affiliations. Given the overwhelming scholarly consensus that categories such as race, ethnicity, and language are socially constructed, this article introduces an experimental bibliographic method for mapping the vast landscape of historical newspapers. This method extends the machine learning affordances of a recent project called Newspaper Navigator to enumerate the newspapers in Chronicling America according to …

Statistical And Biological Analyses Of Acoustic Signals In Estrildid Finches, Moises Rivera

Dissertations, Theses, and Capstone Projects

Acoustic communication is a process that involves auditory perception and signal processing. Discrimination and recognition further require cognitive processes and supporting mechanisms in order to successfully identify and appropriately respond to signal senders. Although acoustic communication is common across birds, classical research has largely disregarded the perceptual abilities of perinatal altricial taxa. Chapter 1 reviews the literature of perinatal acoustic stimulation in birds, highlighting the disproportionate focus on precocial birds (e.g., chickens, ducks, quails). The long-held belief that altricial birds were incapable of acoustic perception in ovo was only recently overturned, as researchers began to find behavioral and physiological evidence …

Data-Optimized Spatial Field Predictions For Robotic Adaptive Sampling: A Gaussian Process Approach, Zachary Nathan

Computer Science Senior Theses

We introduce a framework that combines Gaussian Process models, robotic sensor measurements, and sampling data to predict spatial fields. In this context, a spatial field refers to the distribution of a variable throughout a specific area, such as temperature or pH variations over the surface of a lake. Whereas existing methods tend to analyze only the particular field(s) of interest, our approach optimizes predictions through the effective use of all available data. We validated our framework on several datasets, showing that errors can decline by up to two-thirds through the inclusion of additional colocated measurements. In support of adaptive sampling, …

Towards Generalizable Machine Learning Models For Computer-Aided Diagnosis In Medicine, Yiyang Wang

College of Computing and Digital Media Dissertations

Hidden stratification represents a phenomenon in which a training dataset contains unlabeled (hidden) subsets of cases that may affect machine learning model performance. Machine learning models that ignore the hidden stratification phenomenon--despite promising overall performance measured as accuracy and sensitivity--often fail at predicting the low prevalence cases, but those cases remain important. In the medical domain, patients with diseases are often less common than healthy patients, and a misdiagnosis of a patient with a disease can have significant clinical impacts. Therefore, to build a robust and trustworthy CAD system and a reliable treatment effect prediction model, we cannot only pursue …

Automated Delineation Of Visual Area Boundaries And Eccentricities By A Cnn Using Functional, Anatomical, And Diffusion-Weighted Mri Data, Noah C. Benson, Bogeng Song, Toshikazu Miyata, Hiromasa Takemura, Jonathan Winawer

MODVIS Workshop

Delineating visual field maps and iso-eccentricities from fMRI data is an important but time-consuming task for many neuroimaging studies on the human visual cortex because the traditional methods of doing so using retinotopic mapping experiments require substantial expertise as well as scanner, computer, and human time. Automated methods based on gray-matter anatomy or a combination of anatomy and functional mapping can reduce these requirements but are less accurate than experts. Convolutional Neural Networks (CNNs) are powerful tools for automated medical image segmentation. We hypothesize that CNNs can define visual area boundaries with high accuracy. We trained U-Net CNNs with ResNet18 …

Ptmtorrent: A Dataset For Mining Open-Source Pre-Trained Model Packages, Wenxin Jiang, Nicholas Synovic, Purvish Jajal, Taylor R. Schorlemmer, Arav Tewari, Bhavesh Pareek, George K. Thiruvathukal, James C. Davis

Computer Science: Faculty Publications and Other Works

Due to the cost of developing and training deep learning models from scratch, machine learning engineers have begun to reuse pre-trained models (PTMs) and fine-tune them for downstream tasks. PTM registries known as “model hubs” support engineers in distributing and reusing deep learning models. PTM packages include pre-trained weights, documentation, model architectures, datasets, and metadata. Mining the information in PTM packages will enable the discovery of engineering phenomena and tools to support software engineers. However, accessing this information is difficult — there are many PTM registries, and both the registries and the individual packages may have rate limiting for accessing …

An Analysis Of Text-Based Machine Learning Models For Vulnerability Detection, Kollin Ryne Napier

Theses and Dissertations

With an increase in complexity of software, developers rely more on reuse and dependencies in their source code via code snippets. As a result, it is becoming harder to identify and mitigate vulnerabilities. Although traditional analysis tools are still utilized, machine learning models are being adopted to expand efforts and combat such threats. Given the possibilities towards usage of such models, research in this area has introduced various approaches which vary in usability and prediction. In generalizing models to a more natural language approach, researchers have opted to train models on source code to identify existing and potential vulnerabilities. Exploratory …

Dense & Attention Convolutional Neural Networks For Toe Walking Recognition, Junde Chen, Rahul Soangra, Marybeth Grant-Beuttler, Y. A. Nanehkaran, Yuxin Wen

Physical Therapy Faculty Articles and Research

Idiopathic toe walking (ITW) is a gait disorder where children’s initial contacts show limited or no heel touch during the gait cycle. Toe walking can lead to poor balance, increased risk of falling or tripping, leg pain, and stunted growth in children. Early detection and identification can facilitate targeted interventions for children diagnosed with ITW. This study proposes a new one-dimensional (1D) Dense & Attention convolutional network architecture, which is termed as the DANet, to detect idiopathic toe walking. The dense block is integrated into the network to maximize information transfer and avoid missed features. Further, the attention modules are …

Modeling Antihypertensive Therapeutic Inertia And Intensification To Support Clinical Action Toward Hypertension Control, Benjamin Martin

All Dissertations

Background

Hypertension is the leading modifiable risk factor for cardiovascular disease and consequent mortality worldwide. In the U.S., more than half of hypertension cases remain uncontrolled, despite availability of effective pharmaceutical treatment options. Evidence suggests that therapeutic inertia, defined as clinician failure to initiate or increase therapy when treatment goals are unmet, is the most influential barrier to improving hypertension control. Substantial rates of therapeutic inertia have been reported in ambulatory primary care settings where hypertension is typically treated and managed. Understanding and overcoming the forces driving therapeutic inertia in hypertension management is a critical strategy to reach population health …

Comparing Igneous Geochemical Data From Hawaii And Southern California Via Machine Learning, Miro Manestar

MS in Computer Science Project Reports

Bi-plots are commonly used in geochemical analyses. However, their use can become cumbersome in the case of multi-variate analyses. Therefore, this thesis explores the application of unsupervised machine learning techniques, specifically PCA and K-Means, to analyze large geochemical data sets from two distinct regions, Hawaii and the \acrfull{prb} in Southern California. The IBM Foundational Methodology for Data Science was utilized to ensure proper data preparation and analysis. PCA provided dimensionality reduction, revealing which features correlated most strongly with variances within the data. K-Means clustering allowed for deeper interpretation of the data. The analysis yielded valuable insights into the composition and …

Reducing Restaurant Inventory Costs Through Sales Forecasting, Tyler Mason, Chris Schoen, Trevor Gilbert, Jonathan Enriquez

Senior Design Project For Engineers

Family Restaurant is a local restaurant in the greater Atlanta area that serves a variety of dishes that include an assortment of 19 different proteins. Currently, Family Restaurant places protein orders based on business intuition, and tends to over-stock and sometimes under-stock. To minimize inventory costs by reducing over-stocking and preventing under-stocking of proteins, we applied Facebook Prophet (FB Prophet), ARIMA, and XG Boost machine learning models to predict protein demand and then fed these results into a Fixed Time Period inventory model to make an overall order suggestion based on the specified time period. We trained our models on …

Gpu Utilization: Predictive Sarimax Time Series Analysis, Dorothy Dorie Parry

Modeling, Simulation and Visualization Student Capstone Conference

This work explores collecting performance metrics and leveraging the output for prediction on a memory-intensive parallel image classification algorithm - Inception v3 (or "Inception3"). Experimental results were collected by nvidia-smi on a computational node DGX-1, equipped with eight Tesla V100 Graphic Processing Units (GPUs). Time series analysis was performed on the GPU utilization data taken, for multiple runs, of Inception3’s image classification algorithm (see Figure 1). The time series model applied was Seasonal Autoregressive Integrated Moving Average Exogenous (SARIMAX).

Comparison Of Sampling Methods For Predicting Wine Quality Based On Physicochemical Properties, Robert Burigo, Scott Frazier, Eli Kravez, Nibhrat Lohia

SMU Data Science Review

Using the physicochemical properties of wine to predict quality has been done in numerous studies. Given the nature of these properties, the data is inherently skewed. Previous works have focused on handful of sampling techniques to balance the data. This research compares multiple sampling techniques in predicting the target with limited data. For this purpose, an ensemble model is used to evaluate the different techniques. There was no evidence found in this research to conclude that there are specific oversampling methods that improve random forest classifier for a multi-class problem.

Professor Text: University Fundraising Optimization, Braden Anderson, Connor Dobbs, Hien Lam, John Santerre

SMU Data Science Review

University fundraising campaigns are a unique type of cause-related marketing with its own challenges and opportunities. Campaigns like this typically last an extended period, such as five or more years, and goals exist beyond the dollar amount raised. These supplemental goals, such as awareness among potential future donators or brand reputation within the local community, are important to consider and strategize. There can also be unique limitations, such as requiring advertising specifically on recent large gifts or endowment programs. This research explores how machine learning techniques such as natural language processing can be used to optimize a fundraising campaign strategy, …

Nviz: Unraveling Neural Networks Through Visualization, Kevin Hoffman

Mathematics, Computer Science & Statistics Presentations

The growing utility of artificial intelligence (AI) is attributed to the development of neural networks. These networks are a class of models that make predictions based on previously observed data. While the inferential power of neural networks is great, the ability to explain their results is difficult because the underlying model is automatically generated. The AI community commonly refers to neural networks as black boxes because the patterns they learn from the data are not easily understood. This project aims to improve the visibility of patterns that neural networks identify in data. Through an interactive web application, NVIZ affords the …