Computer Sciences Commons^™

Gender-Specific Mental Health Outcomes In Central America: A Natural Experiment, Thea Nagasuru

Computer Science Summer Fellows

While COVID lockdown measures have had varying effects on the mental health of different demographics, several bodies of research have noted their disparate effect on women. Why is women's mental health more negatively impacted by lockdown measures, and how much more are they impacted than men? How can we predict and mitigate these negative effects on women? This paper aims to contribute to answering those questions by comparing COVID stringency measures and their effect on the gap in depression rates between men and women in two neighboring countries: Nicaragua and Honduras.

Editorial: Ethical Considerations In Electronic Data In Healthcare, Dheya Mustafa, Mousa Al-Kfairy

All Works

No abstract provided.

Vysion Software, Isaias Hernandez-Dominguez Jr, Chander Luderman Miller

2024 Symposium

Vision loss presents significant challenges in daily life. Existing solutions for blind and visually impaired individuals are often limited in functionality, expensive, or complex to use. Vysion Software addresses this gap by developing a user-friendly, all-in-one AI companion app that provides features including text summarization, real-time audio descriptions, and AI-enhanced navigation. This project details the development plan, initial functionalities, and future vision for Vysion Software.

Enhancing Tumor Classification Through Machine Learning Algorithms For Breast Cancer Diagnosis, Lawrence Agbota, Edmund F. Agyemang, Priscilla Kissi-Appiah, Lateef Moshood, Akua Osei- Nkwantabisa, Vincent Agbenyeavu, Abraham Nsiah, Augustina Adjei

School of Mathematical & Statistical Sciences Faculty Publications

In cancer diagnosis, machine learning helps improve cancer detection by providing doctors with a second perspective and allowing for faster and more accurate determination and decisions. Numerous studies have used both classic machine learning approaches and deep learning to address cancer classification. In this study, we examine the efficacy of five commonly used machine learning algorithms; both traditional and deep learning models namely, Logistic Regression, Support Vector Machines (SVM), Random Forest (RF), Decision Tree and Deep Neural Networks (DNN). We analyze their ability to properly classify tumors as Benign or Malignant using the Wisconsin breast cancer dataset (WBCD). Random Forest …

3d Organ-Scale Models Of Tumor Growth And Treatment, Rafael Ramon Bravo

USF Tampa Graduate Theses and Dissertations

To understand the dynamics of cancer, mathematical oncologists have developed models of tumor growth and treatment response. Some models are mechanistic and approach tumor growth at the cell-scale, focusing on the evolution of cancerous cells within the ecology of normal tissue, and are often simulated with agent-based modeling. Other models are more clinically motivated and model tumor growth operating at the organ-scale, using patient data to predict treatment response, and are often simulated with partial differential equations. We developed the Hybrid Automata Library which includes both agent-based modeling and partial differential equations for modeling at either of these scales. We …

The Confluence, Volume3, Issue 2, Full Issue

The Confluence

No abstract provided.

From Graph Theory For Robust Deep Networks To Graph Learning For Multimodal Cancer Analysis, Asim Waqas

USF Tampa Graduate Theses and Dissertations

This dissertation explores the intersection of graph theory and deep learning, focusing on enhancing the robustness of deep neural networks (DNNs) and applying these advancements to complex problems like cancer diagnosis and treatment. We investigate the structural properties of graphs and their influence on neural network performance, particularly in multimodal learning. The work delves into the design space of DNN architectures using graph-theoretic measures, transforming graphs into DNN architectures for various tasks, and examining their robustness against noise and adversarial attacks. The study extends to medical imaging, highlighting advanced DNN architectures like U-Net for brain tumor segmentation. It addresses the …

Mixed Uncertainty Analysis On Pumping By Peristaltic Hearts Using Dempster-Shafer Theory, Yanyan He, Nicholas A. Battista, Lindsay D. Waldrop

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this paper, we introduce the numerical strategy for mixed uncertainty propagation based on probability and Dempster–Shafer theories, and apply it to the computational model of peristalsis in a heart-pumping system. Specifically, the stochastic uncertainty in the system is represented with random variables while epistemic uncertainty is represented using non-probabilistic uncertain variables with belief functions. The mixed uncertainty is propagated through the system, resulting in the uncertainty in the chosen quantities of interest (QoI, such as flow volume, cost of transport and work). With the introduced numerical method, the uncertainty in the statistics of QoIs will be represented using belief …

Methionine Sulfoxide Speciation In Mouse Hippocampus Revealed By Global Proteomics Exhibits Age- And Alzheimer’S Disease-Dependent Changes Targeted To Mitochondrial And Glycolytic Pathways, Filipa Blasco Tavares Pereira Lopes, Daniela Schlatzer, Mengzhen Li, Serhan Yılmaz, Rihua Wang, Xin Qi, Marzieh Ayati, Mehmet Koyutürk, Mark R. Chance

Computer Science Faculty Publications

Methionine oxidation to the sulfoxide form (MSox) is a poorly understood post-translational modification of proteins associated with non-specific chemical oxidation from reactive oxygen species (ROS), whose chemistries are linked to various disease pathologies, including neurodegeneration. Emerging evidence shows MSox site occupancy is, in some cases, under enzymatic regulatory control, mediating cellular signaling, including phosphorylation and/or calcium signaling, and raising questions as to the speciation and functional nature of MSox across the proteome. The 5XFAD lineage of the C57BL/6 mouse has well-defined Alzheimer’s and aging states. Using this model, we analyzed age-, sex-, and disease-dependent MSox speciation in the mouse hippocampus. …

Design And Implementation Of A Vision-Based Deep-Learning Protocol For Kinematic Feature Extraction With Application To Stroke Rehabilitation, Juan Diego Luna Inga

Master's Theses

Stroke is a leading cause of long-term disability, affecting thousands of individuals annually and significantly impairing their mobility, independence, and quality of life. Traditional methods for assessing motor impairments are often costly and invasive, creating substantial barriers to effective rehabilitation. This thesis explores the use of DeepLabCut (DLC), a deep-learning-based pose estimation tool, to extract clinically meaningful kinematic features from video data of stroke survivors with upper-extremity (UE) impairments.

To conduct this investigation, a specialized protocol was developed to tailor DLC for analyzing movements characteristic of UE impairments in stroke survivors. This protocol was validated through comparative analysis using peak …

Accessible Real-Time Eye-Gaze Tracking For Neurocognitive Health Assessments, A Multimodal Web-Based Approach, Daniel C. Tisdale

Master's Theses

We introduce a novel integration of real-time, predictive eye-gaze tracking models into a multimodal dialogue system tailored for remote health assessments. This system is designed to be highly accessible requiring only a conventional webcam for video input along with minimal cursor interaction and utilizes engaging gaze-based tasks that can be performed directly in a web browser. We have crafted dynamic subsystems that capture high-quality data efficiently and maintain quality through instances of user attrition and incomplete calls. Additionally, these subsystems are designed with the foresight to allow for future re-analysis using improved predictive models, as well as enable the creation …

Physician-Patient Interactions In Online Healthcare Communities: The Effects Of Preconsultation On Service Delivery And Patient Satisfaction, Qian Tang, Anqi Zhao

Research Collection School Of Computing and Information Systems

Preconsultation by medical professionals is a common practice in offline healthcare services to improve consultation efficiency but is rarely adopted for online healthcare services. In a noteworthy departure from this trend, a Chinese online healthcare community (OHC) has instituted preconsultation by assistant physicians prior to online consultations. Using comprehensive service data from this OHC, this study scrutinizes the effects of preconsultation on online healthcare services from both the physician and patient perspectives. The findings reveal that preconsultation by the assistant physician can significantly increase the attending physician’s response speed, length, and provision of informational support, while maintaining a consistent level …

Predicting Mild Cognitive Impairment Through Ambient Sensing And Artificial Intelligence, Ah-Hwee Tan, Weng Yan Ying, Budhitama Subagdja, Anni Huang, Shanthoshigaa D, Tony Chin-Ian Tay, Iris Rawtaer

Research Collection School Of Computing and Information Systems

This paper reports an emerging application leveraging ambient and artificial intelligence techniques for in-home sensing and cognitive health assessment. The application involves a prospective longitudinal study, wherein non-pervasive sensing devices are installed in homes of over 63 real users undergoing clinical cognitive assessment, and digital signals of the users’ activities and behaviour are transmitted to a central cloud-based data server for further processing and analysis. Based on the sensor readings, we identify a set of digital biomarkers covering four key aspects of daily living, namely physical, activity, cognitive, and sleep, and develop a suite of customized feature extraction methods for …

Charting A Path To The Quintuple Aim: Harnessing Ai To Address Social Determinants Of Health, Yash Shah, Zachary Goldberg, Erika Harness, David Nash

College of Population Health Faculty Papers

The Quintuple Aim seeks to improve healthcare by addressing social determinants of health (SDOHs), which are responsible for 70-80% of medical outcomes. SDOH-related concerns have traditionally been addressed through referrals to social workers and community-based organizations (CBOs), but these pathways have had limited success in connecting patients with resources. Given that health inequity is expected to cost the United States nearly USD 300 billion by 2050, new artificial intelligence (AI) technology may aid providers in addressing SDOH. In this commentary, we present our experience with using ChatGPT to obtain SDOH management recommendations for archetypal patients in Philadelphia, PA. ChatGPT identified …

Emotional Regulation On Modulating Associations Between Depression And Physical Activity As Characterized Via Deep Learning, Franklin Ye Ruan

Computer Science Senior Theses

Emotional regulation and physical activity are known to be associated with depression; however, a deeper understanding of how emotional regulation may strengthen or weaken the bonds between depressive symptoms and physical activity may aid clinicians and researchers in developing cognitive behavioral therapy (CBT) for those adversely affected by depression. As part of the Tracking Depression Study, this analysis uses data collected from 306 participants diagnosed with Major Depressive Disorder. To study their behavior, we analyze actigraphy data, or longitudinal physical activity intensity data, as it relates to depression severity, quantified by the daily PHQ-9 questionnaires. We study these associations through …

Advancing Objective Mobile Device Use Measurement Inchildren Ages 6–11 Through Built-In Device Sensors: A Proof-Of-Concept Study, Olivia L. Finnegan, Robert Glenn Weaver Med, Phd, Hongpeng Yang, James W. White, Srihari Nelakuditi, Zifei Zhong, Rahul Ghosal Ph.D., Yan Tong, Aliye B. Cepni, Elizabeth L. Adams, Sarah Burkart Mph, Ph.D., Michael W. Beets Med, Mph, Phd, Bridget Armstrong Ph.D.

Faculty Publications

Mobile devices (e.g., tablets and smartphones) have been rapidly integrated into the lives of children and have impacted howchildren engage with digital media. The portability of these devices allows for sporadic, on-demand interaction, reducing theaccuracy of self-report estimates of mobile device use. Passive sensing applications objectively monitor time spent on a givendevice but are unable to identify who is using the device, a significant limitation in child screen time research. Behavioralbiometric authentication, using embedded mobile device sensors to continuously authenticate users, could be applied toaddress this limitation. This study examined the preliminary accuracy of machine learning models trained on iPad …

A Potential Of Watercress Nasturtium Officinale Bioactive Compounds In Inhibiting Infectious Myonecrosis Virus (Imnv) By Targeting Rna-Dependent Rna Polymerase (Rdrp) Virus From Several Countries: In Silico Approach, Qurrota A’Yunin, Fatchiyah Fatchiyah, Maftuch Maftuch, Feri Eko Hermanto, Muhammad Hermawan Widyananda, Narendra Santika Hartana, Muhaimin Rifa’I, Yoga Dwi Jatmiko

Karbala International Journal of Modern Science

Infectious myonecrosis virus (IMNV) disease causes mass mortality and decreased shrimp production. The RdRp region projects to the interior, where it may function in transcription. The focus of this study was to determine the effect of amino acid polymorphisms from several countries on the structure of RdRp and identify the potential of watercress in inhibiting IMNV by targeting the RdRp protein of IMNV through an in silico approach. The results showed that the structure of the IMNV RdRp protein from Indonesia was similar to Mexico, and the protein structure from India_QDN was identical to India_QIL. Ligand binding affinity values showed …

Making The Most Of Artificial Intelligence And Large Language Models: A Novel Approach For Book Recommendation And Discovery In Medical Libraries, Ivan Portillo, David Carson

Library Presentations, Posters, and Audiovisual Materials

This poster presentation evaluates the use of Artificial Intelligence and large language models (LLMs) to assist health science libraries in recommending and discovering book titles as part of their collection development. Using pre-determined prompts, the researchers evaluated ChatGPT 4.0, Bing Chat, and Google Bard as recommender systems for book discovery and ranking existing titles.

Supporting South Korea’S Aging Population: How Ai And Iot Acceptance Connects The Young And Old, Bobby Im

Master's Projects and Capstones

In 2024, South Korea surpassed every other nation by becoming the country with the lowest fertility rate (below 0.7%). Population decline will hinder future ability to care for their aging population and although the government and private corporations are investing millions of dollars on developing Artificial Intelligence-Internet of Things (AI-IoT) devices to support the aging, the acceptance levels and the amount of family support required is undervalued. By examining AI-IoT’s current use and role in South Korea’s public health system this paper shows how intergenerational support helps optimize existing procedures and equipment, increases the level of acceptance and use, and …

Missing Wedge Completion Via Unsupervised Learning With Coordinate Networks, Dave Van Veen, Jesús G Galaz-Montoya, Liyue Shen, Philip Baldwin, Akshay S Chaudhari, Dmitry Lyumkis, Michael F Schmid, Wah Chiu, John Pauly

Faculty, Staff and Students Publications

Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input …

A Comparative Analysis Of Source Identification Algorithms, Pablo A. Curiel

Biology and Medicine Through Mathematics Conference

No abstract provided.

Inchi Isotopologue And Isotopomer Specifications, Hunter N. B. Moseley, Philippe Rocca-Serra, Reza M. Salek, Masanori Arita, Emma L. Schymanski

Markey Cancer Center Faculty Publications

This work presents a proposed extension to the International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) standard that allows the representation of isotopically‑resolved chemi‑ cal entities at varying levels of ambiguity in isotope location. This extension includes an improved interpretation of the current isotopic layer within the InChI standard and a new isotopologue layer specification for representing chemical intensities with ambiguous isotope localization. Both improvements support the unique isotopically‑ resolved chemical identification of features detected and measured in analytical instrumentation, specifically nuclear magnetic resonance and mass spectrometry.

Scientific contribution

This new extension to the InChI standard …

Accuracy Of Machine Learning To Predict The Outcomes Of Shoulder Arthroplasty: A Systematic Review, Amir H. Karimi, Joshua Langberg, Ajith Malige, Omar Rahman, Joseph A. Abboud, Michael A. Stone

Department of Orthopaedic Surgery Faculty Papers

BACKGROUND: Artificial intelligence (AI) uses computer systems to simulate cognitive capacities to accomplish goals like problem-solving and decision-making. Machine learning (ML), a branch of AI, makes algorithms find connections between preset variables, thereby producing prediction models. ML can aid shoulder surgeons in determining which patients may be susceptible to worse outcomes and complications following shoulder arthroplasty (SA) and align patient expectations following SA. However, limited literature is available on ML utilization in total shoulder arthroplasty (TSA) and reverse TSA.

METHODS: A systematic literature review in accordance with PRISMA guidelines was performed to identify primary research articles evaluating ML's ability to …

Proof-Of-Concept For Converging Beam Small Animal Irradiator, Benjamin Insley

Dissertations and Theses (Open Access)

The Monte Carlo particle simulator TOPAS, the multiphysics solver COMSOL., and

several analytical radiation transport methods were employed to perform an in-depth proof-ofconcept

for a high dose rate, high precision converging beam small animal irradiation platform.

In the first aim of this work, a novel carbon nanotube-based compact X-ray tube optimized for

high output and high directionality was designed and characterized. In the second aim, an

optimization algorithm was developed to customize a collimator geometry for this unique Xray

source to simultaneously maximize the irradiator’s intensity and precision. Then, a full

converging beam irradiator apparatus was fit with a multitude …

An Evaluation Of Heart Rate Monitoring With In-Ear Microphones Under Motion, Kayla-Jade Butkow, Ting Dang, Andrea Ferlini, Dong Ma, Yang Liu, Cecilia Mascolo

Research Collection School Of Computing and Information Systems

With the soaring adoption of in-ear wearables, the research community has started investigating suitable in-ear heart rate detection systems. Heart rate is a key physiological marker of cardiovascular health and physical fitness. Continuous and reliable heart rate monitoring with wearable devices has therefore gained increasing attention in recent years. Existing heart rate detection systems in wearables mainly rely on photoplethysmography (PPG) sensors, however, these are notorious for poor performance in the presence of human motion. In this work, leveraging the occlusion effect that enhances low-frequency bone-conducted sounds in the ear canal, we investigate for the first time in-ear audio-based motion-resilient …

Identifying Temporomandibular Disorder Morphological Risk Factors Via Explainable Deep Learning And Multiscale Biomechanical Modeling, Shuchun Sun

All Dissertations

Clarifying multifactorial musculoskeletal disorder etiologies supports risk analysis and development of targeted prevention and treatment modalities. Deep learning enables comprehensive risk factor identification through systematic analysis of disease datasets but does not provide sufficient context for mechanistic understanding, limiting clinical applicability for etiological investigations. Conversely, multiscale biomechanical modeling can evaluate mechanistic etiology within the relevant biomechanical and physiological context. We propose a hybrid approach combining 3D explainable deep learning and multiscale biomechanical modeling; we applied this approach to investigate temporomandibular joint (TMJ) disorder etiology by systematically identifying risk factors and elucidating mechanistic relationships between risk factors and TMJ biomechanics and …

Representation Learning For Generative Models With Applications To Healthcare, Astronautics, And Aviation, Van Minh Nguyen

Theses and Dissertations

This dissertation explores applications of representation learning and generative models to challenges in healthcare, astronautics, and aviation.

The first part investigates the use of Generative Adversarial Networks (GANs) to synthesize realistic electronic health record (EHR) data. An initial attempt at training a GAN on the MIMIC-IV dataset encountered stability and convergence issues, motivating a deeper study of 1-Lipschitz regularization techniques for Auxiliary Classifier GANs (AC-GANs). An extensive ablation study on the CIFAR-10 dataset found that Spectral Normalization is key for AC-GAN stability and performance, while Weight Clipping fails to converge without Spectral Normalization. Analysis of the training dynamics provided further …

Evaluation Of An End-To-End Radiotherapy Treatment Planning Pipeline For Prostate Cancer, Mohammad Daniel El Basha, Court Laurence, Carlos Eduardo Cardenas, Julianne Pollard-Larkin, Steven Frank, David T. Fuentes, Falk Poenisch, Zhiqian H. Yu

Dissertations and Theses (Open Access)

Radiation treatment planning is a crucial and time-intensive process in radiation therapy. This planning involves carefully designing a treatment regimen tailored to a patient’s specific condition, including the type, location, and size of the tumor with reference to surrounding healthy tissues. For prostate cancer, this tumor may be either local, locally advanced with extracapsular involvement, or extend into the pelvic lymph node chain. Automating essential parts of this process would allow for the rapid development of effective treatment plans and better plan optimization to enhance tumor control for better outcomes.

The first objective of this work, to automate the treatment …

Exploring Binding Pockets In The Conformational States Of The Sars-Cov-2 Spike Trimers For The Screening Of Allosteric Inhibitors Using Molecular Simulations And Ensemble-Based Ligand Docking, Grace Gupta, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Understanding mechanisms of allosteric regulation remains elusive for the SARS-CoV-2 spike protein, despite the increasing interest and effort in discovering allosteric inhibitors of the viral activity and interactions with the host receptor ACE2. The challenges of discovering allosteric modulators of the SARS-CoV-2 spike proteins are associated with the diversity of cryptic allosteric sites and complex molecular mechanisms that can be employed by allosteric ligands, including the alteration of the conformational equilibrium of spike protein and preferential stabilization of specific functional states. In the current study, we combine conformational dynamics analysis of distinct forms of the full-length spike protein trimers and …

Sports Science: An Entrepreneurial Venture, Nicole J. Jones

Senior Honors Projects

In sports science, ensuring maximum athlete safety and optimizing data utilization are pivotal yet leave room for further work. My project, Unbeaten SafeWare, addresses these critical issues by focusing on two primary concerns: preventing heat-related and cardiac illnesses, which are significant causes of athlete fatalities, and enhancing the transparency and utility of sports data. This initiative involves developing a shirt integrated with sensors to monitor vital signs and an athlete management system to handle data input, storage, analysis, and accessibility for athletes.

The project has advanced through the efforts of a multidisciplinary team, which includes biomedical engineering undergraduates, two faculty …