Data Science Commons^™

Linking Cancer Clinical Trials To Their Result Publications, Evan Pan, Kirk Roberts

Faculty, Staff and Student Publications

The results of clinical trials are a valuable source of evidence for researchers, policy makers, and healthcare professionals. However, online trial registries do not always contain links to the publications that report on their results, instead requiring a time-consuming manual search. Here, we explored the application of pre-trained transformer-based language models to automatically identify result-reporting publications of cancer clinical trials by computing dense vectors and performing semantic search. Models were fine-tuned on text data from trial registry fields and article metadata using a contrastive learning approach. The best performing model was PubMedBERT, which achieved a mean average precision of 0.592 …

Community Scientist Program Provides Bi-Directional Communication And Co-Learning Between Researchers And Community Members, Jessica Alvarado, Larkin L Strong, Birnur Buzcu-Guven, Leonetta B Thompson, Erica Cantu, Chelsea C Carrier, Chiamaka D Chukwu, Cassandra L Harris, Luz K Melendez, Crystal L Roberson, Angela M Ross, Sophia C Russell, Pablo Sanchez, Amirali Tahanan, Blair C Zdenek, Belinda M Reininger, Lorna H Mcneill

Faculty, Staff and Student Publications

Community involvement in research is key to translating science into practice, and new approaches to engaging community members in research design and implementation are needed. The Community Scientist Program, established at the MD Anderson Cancer Center in Houston in 2018 and expanded to two other Texas institutions in 2021, provides researchers with rapid feedback from community members on study feasibility and design, cultural appropriateness, participant recruitment, and research implementation. This paper aims to describe the Community Scientist Program and assess Community Scientists' and researchers' satisfaction with the program. We present the analysis of the data collected from 116 Community Scientists …

Human Equilibrative Nucleoside Transporter 1: Novel Biomarker And Prognostic Indicator For Patients With Gemcitabine-Treated Pancreatic Cancer, Jianchun Xiao, Fangyu Zhao, Wenhao Luo, Gang Yang, Yicheng Wang, Jiangdong Qiu, Yueze Liu, Lei You, Lianfang Zheng, Taiping Zhang

Faculty, Staff and Student Publications

AIM: This article aimed to find appropriate pancreatic cancer (PC) patients to treat with Gemcitabine with better survival outcomes by detecting hENT1 levels.

METHODS: We collected surgical pathological tissues from PC patients who received radical surgery in our hospital from September 2004 to December 2014. A total of 375 PC tissues and paired adjacent nontumor tissues were employed for the construction of 4 tissue microarrays (TMAs). The quality of the 4 TMAs was examined by HE staining. We performed immunohistochemistry analysis to evaluate hENT1 expression in the TMAs. Moreover, we detected hENT1 expression level and proved the role of hENT1 …

Visualsphere: A Web-Based Interactive Visualization System For Clinical Research Data, Shiwei Lin, Shiqiang Tao, Wei-Chun Chou, Guo-Qiang Zhang, Xiaojin Li

Faculty, Staff and Student Publications

Clinical research data visualization is integral to making sense of biomedical research and healthcare data. The complexity and diversity of data, along with the need for solid programming skills, can hinder advances in clinical research data visualization. To overcome these challenges, we introduce VisualSphere, a web-based interactive visualization system that directly interfaces with clinical research data repositories, streamlining and simplifying the visualization workflow. VisualSphere is founded on three primary component modules: Connection, Configuration, and Visualization. An end-user can set up connections to the data repositories, create charts by selecting the desired tables and variables, and render visualization dashboards generated by …

A Real-World Disproportionality Analysis Of Everolimus: Data Mining Of The Public Version Of Fda Adverse Event Reporting System, Bin Zhao, Yumei Fu, Shichao Cui, Xiangning Chen, Shu Liu, Lan Luo

Faculty, Staff and Student Publications

Background: Everolimus is an inhibitor of the mammalian target of rapamycin and is used to treat various tumors. The presented study aimed to evaluate the Everolimus-associated adverse events (AEs) through data mining of the US Food and Drug Administration Adverse Event Reporting System (FAERS).

Methods: The AE records were selected by searching the FDA Adverse Event Reporting System database from the first quarter of 2009 to the first quarter of 2022. Potential adverse event signals were mined using the disproportionality analysis, including reporting odds ratio the proportional reporting ratio the Bayesian confidence propagation neural network and the empirical Bayes geometric …

Linking Artificial Sweetener Intake With Kidney Function: Insights From Nhanes 2003-2006 And Findings From Mendelian Randomization Research, Zhuoling Ran, Yuxuan Zheng, Lin Yu, Yuxian Zhang, Zhenjiang Zhang, Huijie Li, Xuhan Li, Jing Song, Li Zhang, Ran Zhang, Chang Lu, Yang Gong, Jian Gong

Faculty, Staff and Student Publications

BACKGROUND: The current investigation examines the association between artificial sweetener (AS) consumption and the likelihood of developing chronic kidney disease (CKD), along with its impact on kidney function.

METHODS: We utilized data from the National Health and Nutrition Examination Survey from 2003-2006 to conduct covariance analysis and weighted adjusted logistic regression, aiming to assess the association between artificial sweetener intake and CKD risk, as well as kidney function indicators. Subsequently, we employed Mendelian randomization methods to validate the causal relationship between the intake of artificial sweeteners, CKD risk, and kidney function indicators. Instrumental variable analysis using inverse-variance weighting and Robust …

Siglec15, Negatively Correlated With Pd-L1 In Hcc, Could Induce Cd8+ T Cell Apoptosis To Promote Immune Evasion, Zheng Chen, Mincheng Yu, Bo Zhang, Lei Jin, Qiang Yu, Shuang Liu, Binghai Zhou, Jiuliang Yan, Wentao Zhang, Xiaoqiang Li, Yongfeng Xu, Yongsheng Xiao, Jian Zhou, Jia Fan, Mien-Chie Hung, Qinghai Ye, Hui Li, Lei Guo

Faculty, Staff and Student Publications

Functional roles of SIGLEC15 in hepatocellular carcinoma (HCC) were not clear, which was recently found to be an immune inhibitor with similar structure of inhibitory B7 family members. SIGLEC15 expression in HCC was explored in public databases and further examined by PCR analysis. SIGLEC15 and PD-L1 expression patterns were examined in HCC samples through immunohistochemistry. SIGLEC15 expression was knocked-down or over-expressed in HCC cell lines, and CCK8 tests were used to examine cell proliferative ability in vitro. Influences of SIGLEC15 expression on tumor growth were examined in immune deficient and immunocompetent mice respectively. Co-culture system of HCC cell lines and …

Modernizing And Harmonizing Regulatory Data Requirements For Genetically Modified Crops-Perspectives From A Workshop, Nicholas P Storer, Abigail R Simmons, Jordan Sottosanto, Jennifer A Anderson, Ming Hua Huang, Debbie Mahadeo, Carey A Mathesius, Mitscheli Sanches Da Rocha, Shuang Song, Ewa Urbanczyk-Wochniak

Faculty, Staff and Student Publications

Genetically modified (GM) crops that have been engineered to express transgenes have been in commercial use since 1995 and are annually grown on 200 million hectares globally. These crops have provided documented benefits to food security, rural economies, and the environment, with no substantiated case of food, feed, or environmental harm attributable to cultivation or consumption. Despite this extensive history of advantages and safety, the level of regulatory scrutiny has continually increased, placing undue burdens on regulators, developers, and society, while reinforcing consumer distrust of the technology. CropLife International held a workshop at the 16th International Society of Biosafety Research …

Vagus Nerve Stimulation For The Therapy Of Dravet Syndrome: A Systematic Review And Meta-Analysis, Shuang Chen, Man Li, Ming Huang

Faculty, Staff and Student Publications

OBJECTIVE: Dravet syndrome (DS) is a refractory developmental and epileptic encephalopathy characterized by seizures, developmental delay and cognitive impairment with a variety of comorbidities, including autism-like behavior, speech dysfunction, and ataxia. Vagus nerve stimulation (VNS) is one of the common therapies for DS. Here, we aim to perform a meta-analysis and systematic review of the efficacy of VNS in DS patients.

METHODS: We systematically searched four databases (PubMed, Embase, Cochrane and CNKI) to identify potentially eligible studies from their inception to January 2024. These studies provided the effective rate of VNS in treating patients with DS. The proportions of DS …

Statistical Modeling Of Bankruptcy Data, Andrew Elsfelder

Williams Honors College, Honors Research Projects

My project uses a dataset of bankrupt and non-bankrupt companies in Taiwan from 1999 to 2009. This data was collected from the Taiwan Economic Journal. The statistical methods I used to model the data are CHAID, CART, and logistic regression. The models created are tools that can predict if a company is bankrupt, or not-bankrupt based on other data about the company. I created multiple models for each of the methods to find the best model for each method. I then analyzed the output from each method. Lastly, I determined which model was the best for this data based on …

Classification Models Using Python In Industrial/Organizational Psychology, Beyza Ceylan

Williams Honors College, Honors Research Projects

Companies, industries, and places of business use artificial intelligence and statistics to predict the characteristics of their employees and staff. Data collected from these individuals is also used to make decisions about them regarding their work life, such as promotions, salaries, or within the hiring process. Two models that are commonly used throughout the field of psychology and specifically in industrial/organizational psychology are the linear regression and the logistic regression. Examining different classification models using Python shows the potential that there may be different models that are more accurate in their predictions of employee success, including a Random Forest model …

A Hybrid Bi-Lstm And Rbm Approach For Advanced Underwater Object Detection, Manimurugan S, Karthikeyan P, Narmatha C, Majed M. Aborokbah, Anand Paul, Subramaniam Ganesan, Rajendran T, Mohammad Ammad-Uddin

School of Public Health Faculty Publications

This research addresses the imperative need for efficient underwater exploration in the domain of deep-sea resource development, highlighting the importance of autonomous operations to mitigate the challenges posed by high-stress underwater environments. The proposed approach introduces a hybrid model for Underwater Object Detection (UOD), combining Bi-directional Long Short-Term Memory (Bi-LSTM) with a Restricted Boltzmann Machine (RBM). Bi-LSTM excels at capturing long-term dependencies and processing sequences bidirectionally to enhance comprehension of both past and future contexts. The model benefits from effective feature learning, aided by RBMs that enable the extraction of hierarchical and abstract representations. Additionally, this architecture handles variable-length sequences, …

Pneumothorax Detection And Segmentation From Chest X-Ray Radiographs Using A Patch-Based Fully Convolutional Encoder-Decoder Network, Jakov Ivan S. Dumbrique, Reynan Hernandez, Juan Miguel L. Cruz, Ryan M. Pagdanganan, Prospero C. Naval

Mathematics Faculty Publications

Pneumothorax, a life-threatening condition characterized by air accumulation in the pleural cavity, requires early and accurate detection for optimal patient outcomes. Chest X-ray radiographs are a common diagnostic tool due to their speed and affordability. However, detecting pneumothorax can be challenging for radiologists because the sole visual indicator is often a thin displaced pleural line. This research explores deep learning techniques to automate and improve the detection and segmentation of pneumothorax from chest X-ray radiographs. We propose a novel architecture that combines the advantages of fully convolutional neural networks (FCNNs) and Vision Transformers (ViTs) while using only convolutional modules to …

Data Driven And Machine Learning Based Modeling And Predictive Control Of Combustion At Reactivity Controlled Compression Ignition Engines, Behrouz Khoshbakht Irdmousa

Dissertations, Master's Theses and Master's Reports

Reactivity Controlled Compression Ignition (RCCI) engines operates has capacity to provide higher thermal efficiency, lower particular matter (PM), and lower oxides of nitrogen (NOx) emissions compared to conventional diesel combustion (CDC) operation. Achieving these benefits is difficult since real-time optimal control of RCCI engines is challenging during transient operation. To overcome these challenges, data-driven machine learning based control-oriented models are developed in this study. These models are developed based on Linear Parameter-Varying (LPV) modeling approach and input-output based Kernelized Canonical Correlation Analysis (KCCA) approach. The developed dynamic models are used to predict combustion timing (CA50), indicated mean effective pressure (IMEP), …

Investigating Uncertainty In Gaussian Process Models, Wilson Strasilla

Master's Projects

N. A.

Federated Learning: Overview, Strategies, Applications, Tools And Future Directions, Betul Yurdem, Murat Kuzlu, Mehmet Kemal Gullu, Maliha Tabassum

Engineering Technology Faculty Publications

Federated learning (FL) is a distributed machine learning process, which allows multiple nodes to work together to train a shared model without exchanging raw data. It offers several key advantages, such as data privacy, security, efficiency, and scalability, by keeping data local and only exchanging model updates through the communication network. This review paper provides a comprehensive overview of federated learning, including its principles, strategies, applications, and tools along with opportunities, challenges, and future research directions. The findings of this paper emphasize that federated learning strategies can significantly help overcome privacy and confidentiality concerns, particularly for high-risk applications.

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 …

Reducing Generalization Error In Multiclass Classification Through Factorized Cross Entropy Loss, Oleksandr Horban

CMC Senior Theses

This paper introduces Factorized Cross Entropy Loss, a novel approach to multiclass classification which modifies the standard cross entropy loss by decomposing its weight matrix W into two smaller matrices, U and V, where UV is a low rank approximation of W. Factorized Cross Entropy Loss reduces generalization error from the conventional O( sqrt(k / n) ) to O( sqrt(r / n) ), where k is the number of classes, n is the sample size, and r is the reduced inner dimension of U and V.

Exploring U.S. Natural Disasters And Psychological Distress: From Time Series Trends To Machine Learning Insights On Hurricane Helene, Sarah Jane Fullerton

CMC Senior Theses

This research investigates the historical trends of psychological distress in the U.S. in relation to natural disaster occurrences. By analyzing long-term data, we examine how significant natural disasters relate to levels of psychological distress over time. The research employs Exploratory Data Analysis (EDA) and Time Series Analysis to identify patterns and trends between the frequency and intensity of natural disasters and the rise of psychological distress across various periods in U.S. history. Additionally, real-time data from Reddit was collected through a custom-built Reddit web scraper specialized for Hurricane Helene. This dataset was labeled for sentiment and used to train machine …

Towards Algorithmic Justice: Human Centered Approaches To Artificial Intelligence Design To Support Fairness And Mitigate Bias In The Financial Services Sector, Jihyun Kim

CMC Senior Theses

Artificial Intelligence (AI) has positively transformed the Financial services sector but also introduced AI biases against protected groups, amplifying existing prejudices against marginalized communities. The financial decisions made by biased algorithms could cause life-changing ramifications in applications such as lending and credit scoring. Human Centered AI (HCAI) is an emerging concept where AI systems seek to augment, not replace human abilities while preserving human control to ensure transparency, equity and privacy. The evolving field of HCAI shares a common ground with and can be enhanced by the Human Centered Design principles in that they both put humans, the user, at …

Sparse Representation Learning For Temporal Networks, Maxwell Mcneil

Electronic Theses & Dissertations (2024 - present)

Temporal networks arise in many domains including activity of social network users, sensor network readings over time, and time course gene expression within the interaction network of a model organism. Data of this type contains a wealth of prior information such as the connectivity among nodes (e.g., a friendship graph), and prior knowledge of expected temporal patterns (e.g., periodicity). Modeling these temporal and network patterns jointly is essential for state-of-the-art performance in temporal network data analysis and mining. Sparse dictionary encoding is one modeling approach for such underlying patterns. However, most classical approaches consider only one dimension of the data …

Leveraging Redundancy As A Link Between Spreading Dynamics On And Of Networks, Felipe Xavier Costa

Electronic Theses & Dissertations (2024 - present)

A constant quest in network science has been in the development of methods to identify the most relevant components in a dynamical system solely via the interaction structure amongst its subsystems. This information allows the development of control and intervention strategies in biochemical signaling and epidemic spreading. We highlight the relevant components in heterogeneous dynamical system by their patterns of redundancy, which can connect how dynamics affect network topology and which pathways are necessary to spreading phenomena on networks. In order to measure the redundancies in a large class of empirical systems, we develop the backbone of directed networks methodology, …

A Comparative Analysis Of A Family Of Advanced Iterative Optimization Methods In Nonlinear Regression, Tanmoy Kumar Debnath

College of Graduate Studies: Theses & Dissertations

Classical statistical supervised learning optimization techniques like the Gauss-Newton Iterative Method (GNIM), Weighted Gauss-Newton Iterative Method (WGNIM), Reweighted Gauss-Newton Iterative Method (RGNIM), and Levenberg-Marquart (LM) algorithm extend the nonlinear least squares method. The WGNIM improves model fitting by controlling heteroscedasticity in the linear and nonlinear models. A comparative analysis of the GNIM, WGNIM, RGNIM, and LM methods for fitting nonlinear models is presented. A step-wise diagnosis for structural multicollinearity in the reweighted linearized model is investigated via the Variance Inflation Factor (VIF) to determine variance inflation in the sequence of estimators for the model parameters. Under restricted multicollinearity levels in …

Classification In Supervised Statistical Learning With The New Weighted Newton-Raphson Method, Toma Debnath

College of Graduate Studies: Theses & Dissertations

In this thesis, the Weighted Newton-Raphson Method (WNRM), an innovative optimization technique, is introduced in statistical supervised learning for categorization and applied to a diabetes predictive model, to find maximum likelihood estimates. The iterative optimization method solves nonlinear systems of equations with singular Jacobian matrices and is a modification of the ordinary Newton-Raphson algorithm. The quadratic convergence of the WNRM, and high efficiency for optimizing nonlinear likelihood functions, whenever singularity in the Jacobians occur allow for an easy inclusion to classical categorization and generalized linear models such as the Logistic Regression model in supervised learning. The WNRM is thoroughly investigated …

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 …

A Copula Discretization Of Time Series-Type Model For Examining Climate Data, Dimuthu Fernando, Olivia Atutey, Norou Diawara

Mathematics & Statistics Faculty Publications

The study presents a comparative analysis of climate data under two scenarios: a Gaussian copula marginal regression model for count time series data and a copula-based bivariate count time series model. These models, built after comprehensive simulations, offer adaptable autocorrelation structures considering the daily average temperature and humidity data observed at a regional airport in Mobile, AL.

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: …

Road Extraction On Remote Sensing Imagery: Historical Mapping Of The Brazilian Amazon, Jonas Paiva Botelho Jr

Graduate Theses/Dissertations

This work proposes an artificial intelligence model based on U-Net architecture to map road networks in the Brazilian Amazon. Over the years, the Amazon region has been heavily exploited, leading to increased deforestation rates, contributing to CO2 emissions, amplifying global warming, and causing a disturbance in local fauna and flora. The expansion into the forest by illegal miners, loggers, and land grabbers can be tracked down by the construction of roads, which we can refer to as the arteries of deforestation. Previous works on the matter proposed algorithms that use high-resolution imagery to map roads precisely. However, this work approach …

Optimizing Sports Outcome Prediction Through Feature Engineering And Machine Learning, Vitor S. Freitas

Graduate Theses/Dissertations

The challenge of predicting the outcome of a team game lies in the high complexity and dynamics of the sports data. This thesis focuses on the aspect of using feature engineering and the genetic algorithm to predict the winner and the score of various sports events. Generally, it deals with how machine learning algorithms are combined with state-of-the-art feature engineering techniques in sports datasets derived from various sports disciplines. In this thesis, five different machine learning models have been applied, classification and regression trees (CART), random forest (RF), stochastic gradient boosting (SGB), eXtreme gradient boosting (XGBoost), and extreme learning machine …

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 …