Data Science Commons^™

Scproatlas: An Atlas Of Multiplexed Single-Cell Spatial Proteomics Imaging In Human Tissues, Tiangang Wang, Xuanmin Chen, Yujuan Han, Jiahao Yi, Xi Liu, Pora Kim, Liyu Huang, Kexin Huang, Xiaobo Zhou

Faculty, Staff and Student Publications

Spatial proteomics can visualize and quantify protein expression profiles within tissues at single-cell resolution. Although spatial proteomics can only detect a limited number of proteins compared to spatial transcriptomics, it provides comprehensive spatial information with single-cell resolution. By studying the spatial distribution of cells, we can clearly obtain the spatial context within tissues at multiple scales. Spatial context includes the spatial composition of cell types, the distribution of functional structures, and the spatial communication between functional regions, all of which are crucial for the patterns of cellular distribution. Here, we constructed a comprehensive spatial proteomics functional annotation knowledgebase, scProAtlas (https://relab.xidian.edu.cn/scProAtlas/#/), …

Aspdb: An Integrative Knowledgebase Of Human Protein Isoforms From Experimental And Ai-Predicted Structures, Yuntao Yang, Himansu Kumar, Yuhan Xie, Zhao Li, Rongbin Li, Wenbo Chen, Chiamaka S Diala, Meer A Ali, Yi Xu, Albon Wu, Sayed-Rzgar Hosseini, Erfei Bi, Hongyu Zhao, Pora Kim, W Jim Zheng

Faculty, Staff and Student Publications

Alternative splicing is a crucial cellular process in eukaryotes, enabling the generation of multiple protein isoforms with diverse functions from a single gene. To better understand the impact of alternative splicing on protein structures, protein-protein interaction and human diseases, we developed ASpdb (https://biodataai.uth.edu/ASpdb/), a comprehensive database integrating experimentally determined structures and AlphaFold 2-predicted models for human protein isoforms. ASpdb includes over 3400 canonical isoforms, each represented by both experimentally resolved and predicted structures, and >7200 alternative isoforms with AlphaFold 2 predictions. In addition to detailed splicing events, 3D structures, sequence variations and functional annotations, ASpdb uniquely offers comparative analyses and …

Metsdb: A Knowledgebase Of Cancer Metastasis At Bulk, Single-Cell And Spatial Levels, Sijia Wu, Jiajin Zhang, Yanfei Wang, Xinyu Qin, Zhaocan Zhang, Zhennan Lu, Pora Kim, Xiaobo Zhou, Liyu Huang

Faculty, Staff and Student Publications

Cancer metastasis, the process by which tumour cells migrate and colonize distant organs from a primary site, is responsible for the majority of cancer-related deaths. Understanding the cellular and molecular mechanisms underlying this complex process is essential for developing effective metastasis prevention and therapy strategies. To this end, we systematically analysed 1786 bulk tissue samples from 13 cancer types, 988 463 single cells from 17 cancer types, and 40 252 spots from 45 spatial slides across 10 cancer types. The results of these analyses are compiled in the metsDB database, accessible at https://relab.xidian.edu.cn/metsDB/. This database provides insights into alterations in …

Crisprofft: Comprehensive Database Of Crispr/Cas Off-Targets, Grant Wang, Xiaona Liu, Aoqi Wang, Jianguo Wen, Pora Kim, Qianqian Song, Xiaona Liu, Xiaobo Zhou

Faculty, Staff and Student Publications

The CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated protein) programmable nuclease system continues to evolve, with in vivo therapeutic gene editing increasingly applied in clinical settings. However, off-target effects remain a significant challenge, hindering its broader clinical application. To enhance the development of gene-editing therapies and the accuracy of prediction algorithms, we developed CRISPRoffT (https://ccsm.uth.edu/CRISPRoffT/). Users can access a comprehensive repository of off-target regions predicted and validated by a diverse range of technologies across various cell lines, Cas enzyme variants, engineered sgRNAs (single guide RNAs) and CRISPR editing systems. CRISPRoffT integrates results of off-target analysis from 74 studies, encompassing …

On Solving Differential Equations Describing The Ecology Of Shallow Lakes: A Comparison Of Classical And Modern Computational Methods Through Python, Vruddhi Kapre, Jeffrey R. Anderson, Alessandro Maria Selvitella

Spora: A Journal of Biomathematics

In this exposition paper, we describe some computational methodologies to solve numerically differential equations modeling the shallow lake ecosystem, with particular focus on the dynamics of the phosphorus. We describe in detail Python implementations of classical algorithms, like Runge-Kutta, and more modern approaches, including physics-informed neural networks.

On The Sharpness Of A Korn’S Inequality For Piecewise H1 Space And Its Applications, Qingguo Hong, Young Ju Lee, Jinchao Xu

Mathematics and Statistics Faculty Research & Creative Works

In this paper, we investigate the sharpness of a Korn's inequality for piecewise H1 space and its applications. We first revisit a Korn's inequality for the piecewise H1 space based on general polygonal or polyhedral decompositions of the domain. We express the Korn's inequality with minimal jump terms. Then we prove that such minimal jump conditions are sharp for achieving the Korn's inequality. The sharpness of the Korn's inequality and explicitly given minimal conditions can be used to test whether any given finite element spaces satisfy Korn's inequality, immediately as well as to build or modify nonconforming finite elements for …

Successfully Navigating The Disruption Ai Will Bring To Survey Research, David M. Rothschild, Trent D. Buskirk, Stephanie Eckman, D. Sunshine Hillygus, Frauke Kreuter, David Lazer

Information Technology & Decision Sciences Faculty Publications

Surveys are a core methodological tool in government, industry, and academia, providing essential data for theory development and evidence-based decision-making. As artificial intelligence continues its rapid advancement, it stands to fundamentally transform the entire survey lifecycle - from design and administration to analytics and reporting. Previous transitions to new technologies, such as telephone, internet, and non-probability surveys, led to divisions within the survey research community with real consequences for both the trajectory of research and trust in the industry. We believe the survey community should take proactive steps now to avoid similar challenges with AI integration. Specifically, our paper examines …

Empirical Vulnerability Function Development Based On The Damage Caused By The 2014 Chiang Rai Earthquake, Thailand, Patcharavadee Hong, Masashi Matsuoka

Institute for Innovation & Entrepreneurship Publications

Seismic hazards in Thailand are frequently overlooked in disaster management planning, leading to insufficient research and significant economic losses during earthquake events. The 2014 Chiang Rai earthquake exposed critical vulnerabilities in Thailand's building practices due to widespread non-compliance with building codes and limited preparedness. This exposure prompted the development of empirical vulnerability functions using loss data from 15,031 damaged residences. The study analyzed government compensation records, which were standardized using replacement cost metrics. Three distinct models were developed through probabilistic and possibilistic modeling approaches. Residual analysis demonstrated the superior performance of the possibilistic approach, with the Possibilistic-based Vulnerability Function achieving …

Predicting Superconducting Critical Temperature From Composition-Derived Features: A Transparent Linear And Regularized Regression Study, Md Ahiduzzaman

Data Science and Data Mining

We study prediction of superconducting critical temperature (Tc) from 81 composition-derived descriptors across 21,263 materials. To keep the analysis transparent and repro- ducible, we focus on linear models: Ordinary Least Squares (OLS), Ridge, Lasso, and Elastic Net (ENet). All models share a single evaluation protocol (5-fold cross-validation with standardized inputs) and are compared on RMSE, MAE, and R2. On this feature set, OLS attains the best cross-validated performance (RMSE = 17.6 K, MAE = 13.3 K , R2 = 0.735), with Lasso/ENet essentially tied next (RMSE ≈ 17.7 K , R2 ≈ 0.734); Ridge underperforms (RMSE = 18.9 K , …

Comparative Analysis Of Lasso, Ridge, And Elastic Net For Variable Selection In High-Dimensional Maize Data, Md Ahiduzzaman

Data Science and Data Mining

In high-dimensional genomic data analysis, traditional linear regression techniques often struggle due to the presence of a large number of predictor variables relative to observations. Penalized regression methods such as LASSO, Ridge, and Elastic Net have emerged as effective solutions by imposing regularization, which helps in managing multicollinearity and enhancing prediction accuracy. This study applies these techniques to the Maize dataset to model the time to male flowering, selecting relevant genetic markers as predictors. Our findings suggest that Elastic Net is particularly effective for high-dimensional data with correlated variables, achieving a balance between prediction accuracy and variable selection. The results …

Landslide At River's Edge: Alum Bluff, Apalachicola River, Florida, Joann Mossa, Yin-Hsuen Chen

Center for Geospatial Science, Education & Analytics Faculty Publications

When rivers impinge on the steep bluffs of valley walls, dynamic changes stem from a combination of fluvial and mass wasting processes. This study identifies the geomorphic changes, drivers, and timing of a landslide adjacent to the Apalachicola River at Alum Bluff, the tallest natural geological exposure in Florida at similar to 40 m, comprising horizontal sediments of mixed lithology. We used hydrographic surveys from 1960 and 2010, two sets of LiDAR from 2007 and 2018, historical aerial, drone, and ground photography, and satellite imagery to interpret changes at this bluff and river bottom. Evidence of slope failure includes a …

Technology-Facilitated Abuse (Tfa): Analyzing Trends, Tactics, And Victim Responses On Reddit, Solomon G. Dandekar

Computer Science and Engineering Theses - Archive

The increasing integration of technology into daily life has provided numerous benefits but also significant risks, particularly when exploited by malicious actors in cases of technology facilitated abuse (TFA). Per- petrators can misuse technology to monitor, control, and intimidate their partners, random strangers, etc. exacerbating cycles of abuse. From location tracking and cellphone surveillance to smart device manipula- tion, spyware, and doxing, digital tools have become powerful instruments for coercion and control. This research project investigates the role of technology in stalking and harassment by analyzing discussions on a relevant subreddit where victims share their experiences, strategies for coping, and …

Scalable Approaches Towards Characterizing And Mitigating Emerging Phishing Scams, Sayak Saha Roy

Computer Science and Engineering Dissertations - Archive

Phishing scams are among the most dangerous and persistent forms of cybercrime, leveraging social engineering to exploit human behavior and obtain sensitive information, leading to widespread identity theft and data breaches. In the past year, these attacks have resulted in financial losses exceeding $10 billion in the United States alone. As phishing scams continue to evolve, they have not only expanded in scale but also grown in sophistication, spreading rapidly across social media and employing adversarial techniques to evade detection by anti-scam tools. The situation is further exacerbated by the availability of advanced phishing kits, and more recently, generative AI, …

Handwritten Digit Recognition Using Machine Learning Classifiers, Md Ahiduzzaman

Data Science and Data Mining

This project explores and compares the performance of various machine learning classifiers for handwritten digit recognition using the MNIST dataset. The classifiers include Logistic Regression, k-Nearest Neighbors, and Convolutional Neural Networks. Each classifier is evaluated based on accuracy, precision, recall, F1-score, and confusion matrix analysis.

Comparative Analysis Of Machine Learning Models For Glioblastoma Survival., Muna Awel

All Graduate Theses, Dissertations, and Other Capstone Projects

Glioblastoma multiforme (GBM) remains one of the most lethal brain tumors, necessitating improved survival prediction models that integrate clinical and molecular data. This study develops a comprehensive machine learning pipeline leveraging TCGA-derived multi-omics datasets to predict binary survival outcomes. The framework integrates four classifiers Logistic Regression, Random Forest, XGBoost, and Support Vector Machine (SVM) and includes rigorous preprocessing with MCAR testing, KNN imputation, feature scaling, and hyperparameter optimization via GridSearchCV. SMOTE was applied to mitigate class imbalance and enhance model robustness for minority survival classes. Comparative performance analyses revealed Random Forest and XGBoost as top performers, achieving the highest recall …

Hybrid Agentic System For Schema-Aware Nl2sql Generation, David Omondi Onyango

All Graduate Theses, Dissertations, and Other Capstone Projects

The natural language to SQL (NL2SQL) task enables non-expert users to interact with relational databases via natural language interfaces. However, NL2SQL frameworks often rely on Large Language Models (LLMs), raising concerns about computational overhead, data privacy, and deployment in resource-limited environments. To address these issues, we propose a hybrid schema-aware agentic system using Small Language Models (SLMs) as primary agents, with a selective LLM fallback mechanism. The LLM activates only when errors are detected in SLM-generated queries, reducing inference costs. Experiments on the BIRD benchmark dataset show our system achieves an execution accuracy of 53.91% and validation efficiency score of …

A Study Of Three Modern Asian Lacquers Using Surface Metrology And Data Science/Analytics, H. David Sheets, Ravines Patrick, Marianne Webb

Computer and Data Science Faculty Publications

No abstract provided.

Elephant Presence Detection For Early-Warning In Kenya: A Cnn Transfer-Learning Approach, Pascaline Jerotich

All Graduate Theses, Dissertations, and Other Capstone Projects

In Kenya, conflicts between humans and elephants often lead to destruction of crops, lower family income, and put people and elephants at risk at the border of developing farms. Fences, patrols, and manual camera inspection are all expensive and take too long to be useful. This research creates an affordable early warning system that uses transfer learning with convolutional neural networks to find elephants in images. There are two label of elephant and non-elephant wildlife which are a public wildlife corpus of approximately 40,000 photographs of binary task. Cleaning of the dataset was done to ensure high quality and consistency. …

The Integration Of Big Data In Fintech: Review Of Enhancing Financial Services Through Advanced Technologies, Soudeh Pazouki, Mohammad B. Jamshidi, Mirarmia Jalali, Arya Tafreshi

Management Faculty Publications

Big data analytics is revolutionizing the FinTech industry, offering new opportunities for real-time decision-making, personalized financial services, and improved risk management. By leveraging advanced technologies like machine learning and artificial intelligence, financial institutions can efficiently detect fraud, predict market trends, and create innovative solutions tailored to customer needs. Big data also plays a critical role in promoting financial inclusion through alternative credit scoring models, providing access to credit for underserved populations and fostering broader participation in the financial system.

However, the integration of big data into FinTech is not without its challenges. Issues such as data privacy concerns, regulatory complexities, …

Random Graph Models For Dual Graphs, Anne Friedman

Scripps Senior Theses

This paper aims to better characterize dual graphs derived from state districting maps by developing random graph models that replicate their structural properties. Dual graphs provide a simplified way to represent districting maps, making it computationally feasible to analyze their structure. These representations enable researchers, legislators, and courts to assess district compactness, detect signs of gerrymandering, and generate alternative districting plans. A deeper understanding of the structural patterns of these dual graphs can help researchers choose or design more effective algorithms for redistricting analysis. The random graph models developed in this study serve as testbeds for evaluating algorithmic approaches to …