Data Science Commons^™

Ageannomo: A Knowledgebase Of Multi-Omics Annotation For Animal Aging, Haixia Xu, Qingxuan Li, Yuhao Jia, Liyu Huang, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

Aging entails gradual functional decline influenced by interconnected factors. Multiple hallmarks proposed as common and conserved underlying denominators of aging on the molecular, cellular and systemic levels across multiple species. Thus, understanding the function of aging hallmarks and their relationships across species can facilitate the translation of anti-aging drug development from model organisms to humans. Here, we built AgeAnnoMO (https://relab.xidian.edu.cn/AgeAnnoMO/#/), a knowledgebase of multi-omics annotation for animal aging. AgeAnnoMO encompasses an extensive collection of 136 datasets from eight modalities, encompassing 8596 samples from 50 representative species, making it a comprehensive resource for aging and longevity research. AgeAnnoMO characterizes …

Fusionneoantigen: : A Resource Of Fusion Gene-Specific Neoantigens, Xiaobo Zhou, Pora Kim

Faculty, Staff and Student Publications

Among the diverse sources of neoantigens (i.e. single-nucleotide variants (SNVs), insertions or deletions (Indels) and fusion genes), fusion gene-derived neoantigens are generally more immunogenic, have multiple targets per mutation and are more widely distributed across various cancer types. Therefore, fusion gene-derived neoantigens are a potential source of highly immunogenic neoantigens and hold great promise for cancer immunotherapy. However, the lack of fusion protein sequence resources and knowledge prevents this application. We introduce 'FusionNeoAntigen', a dedicated resource for fusion-specific neoantigens, accessible at https://compbio.uth.edu/FusionNeoAntigen. In this resource, we provide fusion gene breakpoint crossing neoantigens focused on ∼43K fusion proteins of ∼16K in-frame …

Cov2var, A Function Annotation Database Of Sars-Cov-2 Genetic Variation, Jianguo Wen, Weiling Zhao, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has resulted in the loss of millions of lives and severe global economic consequences. Every time SARS-CoV-2 replicates, the viruses acquire new mutations in their genomes. Mutations in SARS-CoV-2 genomes led to increased transmissibility, severe disease outcomes, evasion of the immune response, changes in clinical manifestations and reducing the efficacy of vaccines or treatments. To date, the multiple resources provide lists of detected mutations without key functional annotations. There is a lack of research examining the relationship between mutations and various factors such as disease severity, pathogenicity, patient age, patient gender, cross-species …

Drmref: Comprehensive Reference Map Of Drug Resistance Mechanisms In Human Cancer, Kexin Huang, Jiajia Liu, Grant Wang, Pora Kim, Qianqian Song, Xiaobo Zhou

Faculty, Staff and Student Publications

Drug resistance poses a significant challenge in cancer treatment. Despite the initial effectiveness of therapies such as chemotherapy, targeted therapy and immunotherapy, many patients eventually develop resistance. To gain deep insights into the underlying mechanisms, single-cell profiling has been performed to interrogate drug resistance at cell level. Herein, we have built the DRMref database (https://ccsm.uth.edu/DRMref/) to provide comprehensive characterization of drug resistance using single-cell data from drug treatment settings. The current version of DRMref includes 42 single-cell datasets from 30 studies, covering 382 samples, 13 major cancer types, 26 cancer subtypes, 35 treatment regimens and 42 drugs. All datasets in …

Inpatient Costs Of Treating Patients With Covid-19, Ankita Podichetty, Raymond S Greenberg

Faculty, Staff and Student Publications

IMPORTANCE: With more than 6.2 million hospitalizations due to COVID-19 in the US, recognition of the average hospital costs to provide inpatient care during the pandemic is necessary to understanding the national medical resource use and improving public health readiness and related policies.

OBJECTIVE: To examine the mean cost to provide inpatient care to treat COVID-19 and how it varied through the pandemic waves and by important sociodemographic patient characteristics.

DESIGN, SETTING, AND PARTICIPANTS: This cross-sectional study used inpatient-level data from March 1, 2020, to March 31, 2022, extracted from a repository of clinical, administrative, and financial information covering 97% …

Experimental Data For: "Effects Of Network Connectivity And Functional Diversity Distribution On Human Collective Ideation", Yiding Cao, Yingjun Dong, Minjun Kim, Neil G. Maclaren, Sriniwas Pandey, Shelley D. Dionne, Francis J. Yammarino, Hiroki Sayama

Systems Science and Industrial Engineering Faculty Scholarship

This is the dataset collected from our online human-subject experiments described in the following manuscript:

Yiding Cao, Yingjun Dong, Minjun Kim, Neil G. MacLaren, Sriniwas Pandey, Shelley D. Dionne, Francis J. Yammarino, and Hiroki Sayama:
"Effects of Network Connectivity and Functional Diversity Distribution on Human Collective Ideation"
https://arxiv.org/abs/2307.04284

Uab Data Catalog - Faq, Marla Hertz, Amy Reese

Research Data Catalog

No abstract provided.

Deep Transfer Learning For Detection Of Upper And Lower Body Movements: Transformer With Convolutional Neural Network, Kyle Lacroix, Davoud Gholamiangonabadi, Ana Luisa Trejos, Katarina Grolinger

Electrical and Computer Engineering Publications

When humans repeat the same motion, the tendons, muscles, and nerves can be damaged, causing Repetitive Stress Injuries (RSI). If the repetitive motions that lead to RSI are recognized early, actions can be taken to prevent these injuries. As Human Activity Recognition (HAR) aims to identify activities employing wearable or environment sensors, HAR is the first step toward identifying repetitive motions. Deep learning models, such as Convolutional Neural Networks (CNNs), have seen great success in recognizing activities for participants whose data are used in the model training; however, their accuracy drops for new participants as people move in different ways. …

Federated Learning For Sentiment Analysis In Presence Of Non-Iid Data: Sensitivity Of Deep Learning Models, Davoud Gholamiangonabadi, Katarina Grolinger

Electrical and Computer Engineering Publications

In sentiment analysis, data are commonly distributed across many devices, and traditional machine learning requires transferring these data to a central location exposing data to security and privacy risks. Federated Learning (FL) avoids this transfer by training a model without requiring the clients/devices to share their local data; however, FL performance drops when data are not Independent and Identically Distributed (non-IID), such as when label distribution or data size vary across clients. Although techniques for non-IID data have been proposed primarily in the image domain, the sensitivity of various deep learning models to non-IID data needs to be examined. Consequently, …

Diagnostic In Neuroimaging: A Comparative Study Of Deep Learning And Traditional Approaches, Amina Issoufou Anaroua

Data Science and Data Mining

In the realm of medical diagnostics, precise classification of brain tumors is pivotal. This study conducts a comprehensive comparative analysis of a Convolutional Neural Network (CNN) against traditional machine learning models, Logistic Regression (LR) and Support Vector Machines (SVM) on a dataset of MRI scans for multi-class brain tumor classification. The CNN, tailored for image recognition, is evaluated alongside LR and SVM, which have established benchmarks in classification tasks. The investigation reveals that the traditional models hold their ground in terms of precision and interpretability, with the SVM, in particular, achieving remarkable accuracy. However, the CNN distinguishes itself by demonstrating …

Understanding Social Dynamics In Toxic Conversations And Public Health Intervention Acceptance On Social Media, Ana Aleksandric

Computer Science and Engineering Dissertations - Archive

Social media is now central to daily life, offering users a space to share content and opinions. However, these platforms also facilitate the spread of hate speech and misinformation, which can negatively impact public health. This dissertation develops methodologies to analyze social media data for insights that could inform health interventions. The research first examines user responses to toxic content, focusing on behavioral and emotional reactions, as well as group dynamics and bystander effects in toxic interactions. Another key focus is public opinion toward health interventions, particularly COVID-19 vaccination, using geolocated posts and analyzing factors such as race, ethnicity, and …

Advancing Deep Learning With Graph-Based Structural Insights: From Graph Classification To Semantic Segmentation, Xin Ma

Computer Science and Engineering Dissertations - Archive

Deep learning has profoundly transformed machine learning by offering sophisticated data representations, yet effectively incorporating structural information remains a challenge. Structural data, whether explicit or implicit, has the potential to significantly enhance the performance of deep learning tasks. This research investigates the benefits of structural information across three crucial tasks: classification, clustering, and segmentation. For explicit structural data, where inputs are directly represented as graphs, we investigate graph-level classification in brain connectivity networks. We introduce the Multi-resolution Edge Network (MENET), a novel framework designed to identify disease-specific connectomic benchmarks with high discriminatory power across diagnostic categories. MENET leverages graph-level representations …

Orthogonal Single-View And Multi-View Feature Selection Models Via Spectral Theory Based Methods, Zachary Chairez

Mathematics Dissertations - Archive

As the digital world continues to grow in the age of big data, there beckons a need for efficient and robust methods for data exploration. Under the umbrella of machine learning, feature selection positions itself as a fruitful approach that uncovers buried truths and illuminates important features of data, all while minimizing long-term storage requirements. In this work, we introduce a set of novel single-view and multi-view supervised feature selection models which are embedded with orthogonality constraints to maintain data's structural integrity while confining the optimal solution's search space.

Taking advantage of the underlying framework of these types of models, …

Testing Informativeness Of Covariate-Induced Group Sizes In Clustered Data, Hasika K. Wickrama Senevirathne, Sandipan Duttta

Mathematics & Statistics Faculty Publications

Clustered data are a special type of correlated data where units within a cluster are correlated while units between different clusters are independent. The number of units in a cluster can be associated with that cluster’s outcome. This is called the informative cluster size (ICS), which is known to impact clustered data inference. However, when comparing the outcomes from multiple groups of units in clustered data, investigating ICS may not be enough. This is because the number of units belonging to a particular group in a cluster can be associated with the outcome from that group in that cluster, leading …

Scalar-On-Function Regression: Estimation And Inference Under Complex Survey Designs, Ekaterina Smirnova, Erjia Cui, Lucia Tabacu, Andrew Leroux

Mathematics & Statistics Faculty Publications

Increasingly, large, nationally representative health and behavioral surveys conducted under a multistage stratified sampling scheme collect high dimensional data with correlation structured along some domain (eg, wearable sensor data measured continuously and correlated over time, imaging data with spatiotemporal correlation) with the goal of associating these data with health outcomes. Analysis of this sort requires novel methodologic work at the intersection of survey statistics and functional data analysis. Here, we address this crucial gap in the literature by proposing an estimation and inferential framework for generalizable scalar-on-function regression models for data collected under a complex survey design. We propose to: …

Adaptive Multi-Label Classification On Drifting Data Streams, Martha Roseberry

Theses and Dissertations

Drifting data streams and multi-label data are both challenging problems. When multi-label data arrives as a stream, the challenges of both problems must be addressed along with additional challenges unique to the combined problem. Algorithms must be fast and flexible, able to match both the speed and evolving nature of the stream. We propose four methods for learning from multi-label drifting data streams. First, a multi-label k Nearest Neighbors with Self Adjusting Memory (ML-SAM-kNN) exploits short- and long-term memories to predict the current and evolving states of the data stream. Second, a punitive k nearest neighbors algorithm with a self-adjusting …

Modeling Health Insurance Premium Using Bayesian Hierarchical Models, Bennedict Kongyir, Emil Agbemade

Data Science and Data Mining

Insurance pricing requires pragmatism and creativity due to the unpredictable nature of risk [3]. This paper explores Bayesian hierarchical models to model health insurance premiums using individual and group predictors like demographics, health status, and geography. Data from Kaggle on health insurance policyholders was utilized, with prior distributions enhanc­ing model interpretability and credibility. Bayesian models improve predictive accuracy and provide valuable insights for actuaries and policymakers, highlighting the signifcant impact of factors such as age and BMI on premium pricing.

A 3-Step, Open-Data, Ride-Hailing Ridership Model With Pricing Applications, Richard A. Mucci

Theses and Dissertations--Civil Engineering

Researchers and practitioners studied the effects ride-hailing had in cities before the covid-19 pandemic. Previous research found ride-hailing to produce negative externalities, such as reducing transit ridership and increasing congestion in various cities. Since the pandemic, ride-hailing ridership has nearly recovered to pre-pandemic levels in Chicago. Ride-hailing ridership has grown steadily since the pandemic while a rider’s willingness to share their trip stagnated. Ride-hailing ridership nearly recovering to pre-covid levels in Chicago suggests that transportation planners, and policy makers, will need to continue assessing the impacts ride-hailing trips have in their cities.

Pickup and drop off locations in the Chicago …

Manifold Learning In Robotics: A Tutorial And Survey, Marcus Hawkins

Computer Science and Engineering Theses - Archive

In this article, we hope to represent the current state of the art of manifold learning in an understandable and approachable way. The authors will present a general overview core algorithms associated with linear and nonlinear dimensionality reduction techniques, give rudimentary definitions from differential geometry, and tenets of robotic perception, manipulation and path planning. Some of the historical applications of these algorithms will be presented, as well as conjectures about future uses, through examples from peer-reviewed journals.

When Brain Meets Artificial Intelligence, Lu Zhang

Computer Science and Engineering Dissertations - Archive

When we review the history of development of artificial intelligence (AI), we will find that brain science plays a pivotal role in fostering breakthroughs in AI, such as artificial neural networks (ANNs). Today, AI has made remarkable strides, particularly with the emergence of large language models (LLMs), surpassing expectations and achieving human-level performance in certain tasks. Nonetheless, an insurmountable gap remains between AI and human intelligence. It is urgent to establish a bridge between brain science and AI, promoting their mutual enhancement and collaborations. This involve establishing connections from brain science to AI (brain-inspired AI), and reversely, from AI to …