Data Science Commons^™

Fusiongdb 20: Fusion Gene Annotation Updates Aided By Deep Learning, Pora Kim, Hua Tan, Jiajia Liu, Haeseung Lee, Hyesoo Jung, Himanshu Kumar, Xiaobo Zhou

Faculty, Staff and Student Publications

A knowledgebase of the systematic functional annotation of fusion genes is critical for understanding genomic breakage context and developing therapeutic strategies. FusionGDB is a unique functional annotation database of human fusion genes and has been widely used for studies with diverse aims. In this study, we report fusion gene annotation updates aided by deep learning (FusionGDB 2.0) available at https://compbio.uth.edu/FusionGDB2/. FusionGDB 2.0 has substantial updates of contents such as up-to-date human fusion genes, fusion gene breakage tendency score with FusionAI deep learning model based on 20 kb DNA sequence around BP, investigation of overlapping between fusion breakpoints with 44 human …

Explainabilityaudit: An Automated Evaluation Of Local Explainability In Rooftop Image Classification, Duleep Rathgamage Don, Jonathan Boardman, Sudhashree Sayenju, Ramazan Aygun, Yifan Zhang, Bill Franks, Sereres Johnston, George Lee, Dan Sullivan, Girish Modgil

Published and Grey Literature from PhD Candidates

Explainable Artificial Intelligence (XAI) is a key concept in building trustworthy machine learning models. Local explainability methods seek to provide explanations for individual predictions. Usually, humans must check these explanations manually. When large numbers of predictions are being made, this approach does not scale. We address this deficiency for a rooftop classification problem specifically with ExplainabilityAudit, a method that automatically evaluates explanations generated by a local explainability toolkit and identifies rooftop images that require further auditing by a human expert. The proposed method utilizes explanations generated by the Local Interpretable Model-Agnostic Explanations (LIME) framework as the most important superpixels of …

Humanizing Computational Literature Analysis Through Art-Based Visualizations, Alexandria Leto

Electronic Theses and Dissertations

Inequalities in gender representation and characterization in fictional works are issues that have long been discussed by social scientists. This work addresses these inequalities with two interrelated components. First, it contributes a sentiment and word frequency analysis task focused on gender-specific nouns and pronouns in 15,000 fictional works taken from the online library, Project Gutenberg. This analysis allows for both quantifying and offering further insight on the nature of this disparity in gender representation. Then, the outcomes of the analysis are harnessed to explore novel data visualization formats using computational and studio art techniques. Our results call attention to the …

Cardiovascular Applications Of Artificial Intelligence In Research, Diagnosis, And Disease Management, Viswanathan Rajagopalan, Houwei Cao

Center for No Boundary Thinking

Despite significant advancements in diagnosis and disease management, cardiovascular (CV) disorders remain the No. 1 killer both in the United States and across the world, and innovative and transformative technologies such as artificial intelligence (AI) are increasingly employed in CV medicine. In this chapter, the authors introduce different AI and machine learning (ML) tools including support vector machine (SVM), gradient boosting machine (GBM), and deep learning models (DL), and their applicability to advance CV diagnosis and disease classification, and risk prediction and patient management. The applications include, but are not limited to, electrocardiogram, imaging, genomics, and drug research in different …

A Predictive Model To Predict Cyberattack Using Self-Normalizing Neural Networks, Oluwapelumi Eniodunmo

Theses, Dissertations and Capstones

Cyberattack is a never-ending war that has greatly threatened secured information systems. The development of automated and intelligent systems provides more computing power to hackers to steal information, destroy data or system resources, and has raised global security issues. Statistical and Data mining tools have received continuous research and improvements. These tools have been adopted to create sophisticated intrusion detection systems that help information systems mitigate and defend against cyberattacks. However, the advancement in technology and accessibility of information makes more identifiable elements that can be used to gain unauthorized access to systems and resources. Data mining and classification tools …

An Exploration In Health Analytics: Pediatric Burns, Care Policy Assessment And Interrupted Time Series, Chao Wang

2022

Healthcare systems globally face multiple challenges in the face of population growth and changes in disease pathology. With regard to the rising demand of the healthcare and the global threats of the pandemic, the medical datasets can be trained further to develop preventive methods. Meanwhile, policy reforms of health systems could be a critical aspect to deal with the public crisis and concerns. However, two basic problems must be addressed first: identification of key factors on a priority basis and evaluation of changes.

Thus, the paper presents a series of trials on the application of data analytics to health-related problems, …

Check Yourself Before You Wrek Yourself: Unpacking And Generalizing Randomized Extended Kaczmarz, William Gilroy

HMC Senior Theses

Linear systems are fundamental in many areas of science and engineering. With the advent of computers there now exist extremely large linear systems that we are interested in. Such linear systems lend themselves to iterative methods. One such method is the family of algorithms called Randomized Kaczmarz methods.
Among this family, there exists a Randomized Kaczmarz variant called Randomized
Extended Kaczmarz which solves for least squares solutions in inconsistent linear systems.
Among Kaczmarz variants, Randomized Extended Kaczmarz is unique in that it modifies input system in a special way to solve for the least squares solution. In this work we …

The Pandemic’S Effects On The Use Of Personal Listening Devices And Prevalence Of Hearing Damage In College Students, Morgan Fink

Senior Honors Projects

Personal listening devices (PLDs), such as earbuds and headphones, are prevalent in today’s society, and overuse of these devices can cause hearing damage. Since the pandemic caused lockdowns and online classes, college students have presumably had more time to be indoors and to use PLDs, leading to a higher risk or developing hearing damage. Previous studies have explored the PLD use and the prevalence of hearing damage in college students, but this study investigates whether the coronavirus pandemic has affected college students’ PLD listening habits and whether these changes are related to the students’ disclosure of suspected symptoms of hearing …

Understanding The Enumerated World: Making Sense Of Data As An Information Source, Kristi Thompson, Elizabeth Hill, Alexandra Cooper

Western Libraries Publications

Chapter in ACRL publication The Data Literacy Cookbook.

This recipe is a guide to preparing an instructional session aimed at postsecondary students in the social or health sciences or related disciplines on locating, evaluating, and using secondary data sources as information resources. Who collects data? Where can you access them? Why are data available on some topics and not others? Why are some statistics available at a detailed level of geography and others only nationally? What are some key limitations of official statistics, and where can information be found to fill in the gaps? This recipe uses these questions to …

Estimating Efforts For Various Activities In Agile Software Development: An Empirical Study, Lan Cao

Information Technology & Decision Sciences Faculty Publications

Effort estimation is an important practice in agile software development. The agile community believes that developers’ estimates get more accurate over time due to the cumulative effect of learning from short and frequent feedback. However, there is no empirical evidence of an improvement in estimation accuracy over time, nor have prior studies examined effort estimation in different development activities, which are associated with substantial costs. This study fills the knowledge gap in the field of software estimation in agile software development by investigating estimations across time and different development activities based on data collected from a large agile project. This …

Integrated Gradients Is A Nonlinear Generalization Of The Industry Standard Approach To Variable Attribution For Credit Risk Models, Jonathan Boardman, Md Shafiul Alam, Xiao Huang, Ying Xie

Published and Grey Literature from PhD Candidates

In modern society, epistemic uncertainty limits trust in financial relationships, necessitating transparency and accountability mechanisms for both consumers and lenders. One upshot is that credit risk assessments must be explainable to the consumer. In the United States regulatory milieu, this entails both the identification of key factors in a decision and the provision of consistent actions that would improve standing. The traditionally accepted approach to explainable credit risk modeling involves generating scores with Generalized Linear Models (GLMs) - usually logistic regression, calculating the contribution of each predictor to the total points lost from the theoretical maximum, and generating reason codes …

Using Neural Networks To Model Guitar Distortion, Caleb Koch, Scott Hawley, Andrew Fyfe

Science University Research Symposium (SURS)

Guitar players have been modifying their guitar tone with audio effects ever since the mid-20th century. Traditionally, these effects have been achieved by passing a guitar signal through a series of electronic circuits which modify the signal to produce the desired audio effect. With advances in computer technology, audio “plugins” have been created to produce audio effects digitally through programming algorithms. More recently, machine learning researchers have been exploring the use of neural networks to produce audio effects that yield strikingly similar results to their analog counterparts. Recurrent Neural Networks and Temporal Convolutional Networks have proven to be exceptional at …

Towards A Burden-Free Implicit Authentication For Wearable Device Users, Bryan Lee, Sudip Vhaduri

Discovery Undergraduate Interdisciplinary Research Internship

The state of current knowledge-based wearable authentication systems requires users to physically interact with a device to initiate and validate their presence, thereby imposing a burden on the user. However, with the recent advancements of sensor technologies in consumer smart wearables (e.g., Fitbit and Apple watches), we were able to utilize vectors of statistical features extracted from the continuous stream of data from these IoT devices to implicitly validate a user's activities and its spatiotemporal context via the use of machine learning techniques. To improve the performance of our models, additional soft biometric data (i.e., respiratory sounds) was collected, and …

Non-Inferiority Testing: Kernel Estimation And Overlap Measure, Larie C. Ward

College of Graduate Studies: Theses & Dissertations

In non-inferiority testing, the decision of whether a proposed treatment is non-inferior to a reference treatment depends on model assumptions and choices of acceptable tolerance limits. Here, we consider a method that employs kernels to estimate the probability density functions of both the experimental and reference populations from two independent samples. Based on these densities, we introduce a quantity called the overlap coefficient or overlap measure. A bootstrap technique is helpful in exploring the distribution and variance empirically. We derive the distribution of this measure and define a hypothesis test that can be applied to the non-inferiority setting under some …

Eeg Signals Classification Using Lstm-Based Models And Majority Logic, James A. Orgeron

College of Graduate Studies: Theses & Dissertations

The study of elecroencephalograms (EEGs) has gained enormous interest in the last decade with the increase of computational power and availability of EEG signals collected from various human activities or produced during medical tests. The applicability of analyzing EEG signals ranges from helping impaired people communicate or move (using appropriate medical equipment) to understanding people's feelings and detecting diseases.

We proposed new methodology and models for analyzing and classifying EEG signals collected from individuals observing visual stimuli. Our models rely on powerful Long-Short Term Memory (LSTM) Neural Network models, which are currently the state of the art models for performing …

Ooi Biogeochemical Sensor Data: Best Practices And User Guide. Version 1.0.0., Hilary I. Palevsky, Sophie Clayton, Dariia Atamanchuk, Roman Battisti, Jennifer Batryn, Annie Bourbonnais, Ellen M. Briggs, Filipa Carvalho, Alison P. Chase, Rachel Eveleth, Rob Fatland, Kristen E. Fogaren, Jonathan Peter Fram, Susan E. Hartman, Isabela Le Bras, Cara C.M. Manning, Joseph A. Needoba, Merrie Beth Neely, Hilde Oliver, Andrew C. Reed, Jennie E. Rheuban, Christina Schallenberg, Michael F. Vardaro, Ian Walsh, Christopher Wingard

OES Faculty Publications

The OOI Biogeochemical Sensor Data Best Practices and User Guide is intended to provide current and prospective users of data generated by biogeochemical sensors deployed on the Ocean Observatories Initiative (OOI) arrays with the information and guidance needed for them to ensure that the data is science-ready. This guide is aimed at researchers with an interest or some experience in ocean biogeochemical processes. We expect that users of this guide will have some background in oceanography, however we do not assume any prior experience working with biogeochemical sensors or their data. While initially envisioned as a “cookbook” for end users …

Tropical Cyclone Frequency: Turning Paleoclimate Into Projections, E. J. Wallace, S. G. Dee

OES Faculty Publications

Future changes to tropical cyclone (TC) climate have the potential to dramatically impact the social and economic landscape of coastal communities. Paleoclimate modeling and paleohurricane proxy development offer exciting opportunities to understand how TC properties (like frequency) change in response to climate variability on long time scales. However, sampling biases in proxies make it difficult to ascertain whether signals in paleohurricane records are related to climate variability or just stochasticity. Short observations and simulation biases prevent TC models from capturing the full range of climate variability and TC characteristics. Integration of these two data types can help address these uncertainties. …

Vertical Artifacts In High-Resolution Worldview-2 And Worldview-3 Satellite Imagery Of Aquatic Systems, Megan M. Coffer, Peter J. Whitman, Blake A. Schaeffer, Victoria Hill, Richard C. Zimmerman, Wilson B. Salls, Marie C. Lebrasse, David D. Graybill

OES Faculty Publications

Satellite image artefacts are features that appear in an image but not in the original imaged object and can negatively impact the interpretation of satellite data. Vertical artefacts are linear features oriented in the along-track direction of an image system and can present as either banding or striping; banding are features with a consistent width, and striping are features with inconsistent widths. This study used high-resolution data from DigitalGlobeʻs (now Maxar) WorldView-3 satellite collected at Lake Okeechobee, Florida (FL), on 30 August 2017. This study investigated the impact of vertical artefacts on both at-sensor radiance and a spectral index for …

A Study On Developing Novel Methods For Relation Extraction, Darshini Mahendran

Theses and Dissertations

Relation Extraction (RE) is a task of Natural Language Processing (NLP) to detect and classify the relations between two entities. Relation extraction in the biomedical and scientific literature domain is challenging as text can contain multiple pairs of entities in the same instance. During the course of this research, we developed an RE framework (RelEx), which consists of five main RE paradigms: rule-based, machine learning-based, Convolutional Neural Network (CNN)-based, Bidirectional Encoder Representations from Transformers (BERT)-based, and Graph Convolutional Networks (GCNs)-based approaches. RelEx's rule-based approach uses co-location information of the entities to determine whether a relation exists between a selected entity …

Universal Design In Bci: Deep Learning Approaches For Adaptive Speech Brain-Computer Interfaces, Srdjan Lesaja

Theses and Dissertations

In the last two decades, there have been many breakthrough advancements in non-invasive and invasive brain-computer interface (BCI) systems. However, the majority of BCI model designs still follow a paradigm whereby neural signals are preprocessed and task-related features extracted using static, and generally customized, data-independent designs. Such BCI designs commonly optimize narrow task performance over generalizability, adaptability, and robustness, which is not well suited to meeting individual user needs. If one day BCIs are to be capable of decoding our higher-order cognitive commands and conceptual maps, their designs will need to be adaptive architectures that will evolve and grow in …

A Unified Health Information System Framework For Connecting Data, People, Devices, And Systems, Wu He, Justin Zuopeng Zhang, Huanmei Wu, Wenzhuo Li, Sachin Shetty

Information Technology & Decision Sciences Faculty Publications

The COVID-19 pandemic has heightened the necessity for pervasive data and system interoperability to manage healthcare information and knowledge. There is an urgent need to better understand the role of interoperability in improving the societal responses to the pandemic. This paper explores data and system interoperability, a very specific area that could contribute to fighting COVID-19. Specifically, the authors propose a unified health information system framework to connect data, systems, and devices to increase interoperability and manage healthcare information and knowledge. A blockchain-based solution is also provided as a recommendation for improving the data and system interoperability in healthcare.

Finding The Best Predictors For Foot Traffic In Us Seafood Restaurants, Isabel Paige Beaulieu

Honors Theses and Capstones

COVID-19 caused state and nation-wide lockdowns, which altered human foot traffic, especially in restaurants. The seafood sector in particular suffered greatly as there was an increase in illegal fishing, it is made up of perishable goods, it is seasonal in some places, and imports and exports were slowed. Foot traffic data is useful for business owners to have to know how much to order, how many employees to schedule, etc. One issue is that the data is very expensive, hard to get, and not available until months after it is recorded. Our goal is to not only find covariates that …

Towards Exchanging Wearable-Pghd With Ehrs: Developing A Standardized Information Model For Wearable-Based Patient Generated Health Data, Abdullahi Abubakar Kawu, Dympna O'Sullivan, Lucy Hederman

Articles

Wearables have become commonplace for tracking and making sense of patient lifestyle, wellbeing and health data. Most of this tracking is done by individuals outside of clinical settings, however some data from wearables may be useful in a clinical context. As such, wearables may be considered a prominent source of Patient Generated Health Data (PGHD). Studies have attempted to maximize the use of the data from wearables including integrating with Electronic Health Records (EHRs). However, usually a limited number of wearables are considered for integration and, in many cases, only one brand is investigated. In addition, we find limited studies …

Image-Data-Driven Deep Learning For Slope Stability Analysis, Behnam Azmoon

Dissertations, Master's Theses and Master's Reports

Landslides cause major infrastructural issues, damage the environment, and cause socio-economic disruptions. Therefore, various slope stability analysis methods have been developed to evaluate the stability of slopes and the probability of their failure. This dissertation attempts to take advantage of the recent advancements in remote sensing and computer technology to implement a deep-learning-based landslide prediction method.

Considering the novelty of this approach, this dissertation leads with proof-of-concept studies to evaluate and establish the suitability of deep learning models for slope stability analysis. To achieve this, a simulated 2D dataset of slope images was created with different geometries and soil properties. …

Towards A Better Understanding Of The Development Of Collaborative Consumption Pricing, Funda Sarican

2022

With the rise of social platforms, consumers started creating value by sharing human and physical resources. As a result, there has been an increase in collaborative consumption. My papers focus on the peer-to-peer travel accommodation service Airbnb, a popular online market for short-term housing rentals.

In paper one, an integrated framework for collaborative consumption pricing is developed by adopting the hedonic demand theory and leveraging the multilevel modeling method that accounts for various factors from nested data. This paper contributes to the research literature by extending the usage of multilevel modeling across cities to consider city effects and broadening the …

The Performance Optimization Of Asp Solving Based On Encoding Rewriting And Encoding Selection, Liu Liu

Theses and Dissertations--Computer Science

Answer set programming (ASP) has long been used for modeling and solving hard search problems. These problems are modeled in ASP as encodings, a collection of rules that declaratively describe the logic of the problem without explicitly listing how to solve it. It is common that the same problem has several different but equivalent encodings in ASP. Experience shows that the performance of these ASP encodings may vary greatly from instance to instance when processed by current state-of-the-art ASP grounder/solver systems. In particular, it is rarely the case that one encoding outperforms all others. Moreover, running an ASP system on …

Batch Normalization Preconditioning For Neural Network Training, Susanna Luisa Gertrude Lange

Theses and Dissertations--Mathematics

Batch normalization (BN) is a popular and ubiquitous method in deep learning that has been shown to decrease training time and improve generalization performance of neural networks. Despite its success, BN is not theoretically well understood. It is not suitable for use with very small mini-batch sizes or online learning. In this work, we propose a new method called Batch Normalization Preconditioning (BNP). Instead of applying normalization explicitly through a batch normalization layer as is done in BN, BNP applies normalization by conditioning the parameter gradients directly during training. This is designed to improve the Hessian matrix of the loss …

Statistical Theory For Specialized Linear Regression Adjustment Methods Compared To Multiple Linear Regression In The Presence And Absence Of Interaction Effects, Leon Su

Theses and Dissertations--Statistics

When building models to investigate outcomes and variables of interest, researchers often want to adjust for other variables. There is a variety of ways that these adjustments are performed. In this work, we will consider four approaches to adjustment utilized by researchers in various fields. We will compare the efficacy of these methods to what we call the ”true model method”, fitting a multiple linear regression model in which adjustment variables are model covariates. Our goal is to show that these adjustment methods have inferior performance to the true model method by comparing model parameter estimates, power, type I error, …

Addressing Ascertainment Bias In The Study Of Cardiovascular Disease Burden In Opioid Use Disorders - Application Of Natural Language Processing Of Electronic Health Records, Jade Huang Singleton

Theses and Dissertations--Epidemiology and Biostatistics

In the United States, the prevalence of long-term exposure to opioid drugs, for both medically and nonmedically indicated purposes, has increased considerably since the mid-1990’s. Concerns have emerged about the potential health effects of opioid use. There is also growing interest in other possible connections with opioid use including cardiovascular disease. Electronic health records (EHR) contain information about patient care in the form of structured codes and unstructured notes. Natural language processing (NLP) provides a tool for processing unstructured textual data in EHR clinical notes and extracts useful information for research with structured formats. The purpose of this dissertation was …

Exploration Of Lignin-Based Superabsorbent Polymers (Hydrogels) For Soil Water Management And As A Carrier For Delivering Rhizobium Spp., Toby Adjuik

Theses and Dissertations--Biosystems and Agricultural Engineering

Superabsorbent polymers (hydrogels) as soil amendments may improve soil hydraulic properties and act as carrier materials beneficial to soil microorganisms. Researchers have mostly explored synthetic hydrogels which may not be environmentally sustainable. This dissertation focused on the development and application of lignin-based hydrogels as sustainable soil amendments. This dissertation also explores the development of pedotransfer transfer functions (PTFs) for predicting saturated hydraulic conductivity using statistical and machine learning methods with a publicly available large data set. A lignin-based hydrogel was synthesized, and its impact on soil water retention was determined in silt loam and loamy fine sand soils. Hydrogel treatment …