Data Science Commons^™

Pim1 Promotes Hepatic Conversion By Suppressing Reprogramming-Induced Ferroptosis And Cell Cycle Arrest, Yangyang Yuan, Chenwei Wang, Xuran Zhuang, Shaofeng Lin, Miaomiao Luo, Wankun Deng, Jiaqi Zhou, Lihui Liu, Lina Mao, Wenbo Peng, Jian Chen, Qiangsong Wang, Yilai Shu, Yu Xue, Pengyu Huang

Faculty, Staff and Student Publications

Protein kinase-mediated phosphorylation plays a critical role in many biological processes. However, the identification of key regulatory kinases is still a great challenge. Here, we develop a trans-omics-based method, central kinase inference, to predict potentially key kinases by integrating quantitative transcriptomic and phosphoproteomic data. Using known kinases associated with anti-cancer drug resistance, the accuracy of our method denoted by the area under the curve is 5.2% to 29.5% higher than Kinase-Substrate Enrichment Analysis. We further use this method to analyze trans-omic data in hepatocyte maturation and hepatic reprogramming of human dermal fibroblasts, uncovering 5 kinases as regulators in the two …

Biomolecular Condensation: A New Phase In Cancer Research, Anupam K Chakravarty, Daniel J Mcgrail, Thomas M Lozanoski, Brandon S Dunn, David J H Shih, Kara M Cirillo, Sueda H Cetinkaya, Wenjin Jim Zheng, Gordon B Mills, S Stephen Yi, Daniel F Jarosz, Nidhi Sahni

Faculty, Staff and Student Publications

Multicellularity was a watershed development in evolution. However, it also meant that individual cells could escape regulatory mechanisms that restrict proliferation at a severe cost to the organism: cancer. From the standpoint of cellular organization, evolutionary complexity scales to organize different molecules within the intracellular milieu. The recent realization that many biomolecules can "phase-separate" into membraneless organelles, reorganizing cellular biochemistry in space and time, has led to an explosion of research activity in this area. In this review, we explore mechanistic connections between phase separation and cancer-associated processes and emerging examples of how these become deranged in malignancy.

SIGNIFICANCE: One …

Developing Positive Thermal Coefficient (Ptc) Heaters For Solar Electric Cooking, Katarina Ivana Brekalo, Andrew Shepherd

Physics

Positive Thermal Coefficients, PTCs, are materials that abruptly change in resistance in response to changes in temperature. The purpose of this experiment is to explore the viability of using the switching type ceramic PTC thermistor as a replacement for current resistive heaters. These types of PTCs have a nonlinear change in resistance with increases in temperature. This device will be used as a temperature-controlling heating element intended to power an Insulated Solar Electric Cooker (ISEC). The ISEC is designed to cook meals throughout the day for impacted communities as an alternative cooking method that doesn’t require biofuel as an energy …

Modern Approaches And Theoretical Extensions To The Multivariate Kolmogorov Smirnov Test, Gonzalo Hernando

Theses and Dissertations

Most statistical tests are fully developed for univariate data, but when inference is required for multivariate data, univariate tests risk information loss and interpretability. This research 1) derives and extends the multivariate Komolgorov Smirnov test for 2 and into m-dimensions, 2) derives small sample critical values for the KS test that are not reliant on sample size simulations or correlation between variables, 3) extends large sample estimations and current KS implementations, and 4) provides sample size and power calculations in order to enable experimental design with respect to testing for differences in distributions. Through extensive simulation, we demonstrate that our …

Improving Country Conflict And Peace Modeling: Datasets, Imputations, And Hierarchical Clustering, Benjamin D. Leiby

Theses and Dissertations

Many disparate datasets exist that provide country attributes covering political, economic, and social aspects. Unfortunately, this data often does not include all countries nor is the data complete for those countries included, as measured by the dataset’s missingness. This research addresses these dataset shortfalls in predicting country instability by considering country attributes in all aspects as well as in greater thresholds of missingness. First, a structured summary of past research is presented framed by a developed casual taxonomy and functional ontology. Additionally, a novel imputation technique for very large datasets is presented to account for moderate missingness in the expanded …

Implementing Github Actions Continuous Integration To Reduce Error Rates In Ecological Data Collection, Albert Y. Kim, Valentine Herrmann, Ross Barreto, Brianna Calkins, Erika Gonzalez-Akre, Daniel J. Johnson, Jennifer A. Jordan, Lukas Magee, Ian R. Mcgregor, Nicolle Montero, Karl Novak, Teagan Rogers, Jessica Shue, Kristina J. Anderson-Teixeira

Statistical and Data Sciences: Faculty Publications

Accurate field data are essential to understanding ecological systems and forecasting their responses to global change. Yet, data collection errors are common, and data analysis often lags far enough behind its collection that many errors can no longer be corrected, nor can anomalous observations be revisited. Needed is a system in which data quality assurance and control (QA/QC), along with the production of basic data summaries, can be automated immediately following data collection.

Here, we implement and test a system to satisfy these needs. For two annual tree mortality censuses and a dendrometer band survey at two forest research sites, …

Data-Centric Machine Learning For Speech And Audio, Ali Raza Syed

Dissertations, Theses, and Capstone Projects

There is growing recognition of the importance of data-centric methods for building machine learning systems. Data-centric methods assume a fixed model and iterate over the data to improve system performance. This is in contrast to traditional model-centric approaches, which assume a fixed dataset and iterate over models for the same ends. Data-centric machine learning is driven by the observation that, beyond the size of the training data, model performance depends on factors such as the quality of the annotations, and whether the data are representative of conditions in which models will be deployed. This is particularly of interest in the …

The Interaction Of Different Primary Producers And Physical And Chemical Dynamics Of An Urban Shallow Lake, Majid Sahin

Dissertations, Theses, and Capstone Projects

An artificial urban shallow lake, Prospect Park Lake (PPL), is situated on a terminal moraine in Brooklyn New York, and supplied with municipal water treated with ortho-phosphates. The constant input of the phosphate nutrient is the primary source of eutrophication in the lake. The numerous pools along the water course houses various aquatic phototrophs, which influence the water quality and the state of the system, driving conditions into favoring the survival of their species. In the first half of the dissertation, the focus of the project is on analyzing how the different primary producers in different regions of PPL affect …

Finite Gaussian Neurons: Defending Against Adversarial Attacks By Making Neural Networks Say "I Don’T Know", Felix Grezes

Dissertations, Theses, and Capstone Projects

In this work, I introduce the Finite Gaussian Neuron (FGN), a novel neuron architecture for artificial neural networks aimed at protecting against adversarial attacks.
Since 2014, artificial neural networks have been known to be vulnerable to adversarial attacks, which can fool the network into producing wrong or nonsensical outputs by making humanly imperceptible alterations to inputs. While defenses against adversarial attacks have been proposed, they usually involve retraining a new neural network from scratch, a costly task.

My works aims to:
- easily convert existing models to Finite Gaussian Neuron architecture,
- while preserving the existing model's behavior on real …

Analyzing Fluctuation Of Topics And Public Sentiment Through Social Media Data, Haoyue Liu

Dissertations

Over the past decade years, Internet users were expending rapidly in the world. They form various online social networks through such Internet platforms as Twitter, Facebook and Instagram. These platforms provide a fast way that helps their users receive and disseminate information and express personal opinions in virtual space. When dealing with massive and chaotic social media data, how to accurately determine what events or concepts users are discussing is an interesting and important problem.

This dissertation work mainly consists of two parts. First, this research pays attention to mining the hidden topics and user interest trend by analyzing real-world …

Efficient And Scalable Triangle Centrality Algorithms In The Arkouda Framework, Joseph Thomas Patchett

Theses

Graph data structures provide a unique challenge for both analysis and algorithm development. These data structures are irregular in that memory accesses are not known a priori and accesses to these structures tend to lack locality.

Despite these challenges, graph data structures are a natural way to represent relationships between entities and to exhibit unique features about these relationships. The network created from these relationships can create unique local structures that can describe the behavior between members of these structures. Graphs can be analyzed in a number of different ways including at a high level in community detection and at …

Evaluation Of Vicinity-Based Hidden Markov Models For Genotype Imputation, Su Wang, Miran Kim, Xiaoqian Jiang, Arif Ozgun Harmanci

Faculty, Staff and Student Publications

BACKGROUND: The decreasing cost of DNA sequencing has led to a great increase in our knowledge about genetic variation. While population-scale projects bring important insight into genotype-phenotype relationships, the cost of performing whole-genome sequencing on large samples is still prohibitive. In-silico genotype imputation coupled with genotyping-by-arrays is a cost-effective and accurate alternative for genotyping of common and uncommon variants. Imputation methods compare the genotypes of the typed variants with the large population-specific reference panels and estimate the genotypes of untyped variants by making use of the linkage disequilibrium patterns. Most accurate imputation methods are based on the Li-Stephens hidden Markov …

Assessing Age-Specific Vaccination Strategies And Post-Vaccination Reopening Policies For Covid-19 Control Using Seir Modeling Approach, Xia Wang, Hulin Wu, Sanyi Tang

Faculty, Staff and Student Publications

As the availability of COVID-19 vaccines, it is badly needed to develop vaccination guidelines to prioritize the vaccination delivery in order to effectively stop COVID-19 epidemic and minimize the loss. We evaluated the effect of age-specific vaccination strategies on the number of infections and deaths using an SEIR model, considering the age structure and social contact patterns for different age groups for each of different countries. In general, the vaccination priority should be given to those younger people who are active in social contacts to minimize the number of infections, while the vaccination priority should be given to the elderly …

Multidisciplinarity In Data Science Curricula, Hossana Twinomurinzi, Siyabonga Mhlongo, Kelvin J. Bwalya, Tebogo Bokaba, Steven Mbeya

African Conference on Information Systems and Technology

This paper sought to identify and compare disciplinary emphases in data science curricula across South Africa’s 26 public universities using a website scoping review method. The key findings reveal that only 12 of the 26 universities offer data science programmes that are publicly accessible on their websites. Of those 12, only 5 offer data science at the undergraduate level, and these undergraduate programmes are objectified (entirely leaning) to the science, technology, engineering, and mathematics (STEM) disciplines. Only seven of the universities offer a few non-STEM subjects with only one offering more non-STEM subjects compared to STEM subjects. The implications are …

Pancancer Analysis Of A Potential Gene Mutation Model In The Prediction Of Immunotherapy Outcomes, Lishan Yu, Caifeng Gong

Faculty, Staff and Student Publications

Background: Immune checkpoint blockade (ICB) represents a promising treatment for cancer, but predictive biomarkers are needed. We aimed to develop a cost-effective signature to predict immunotherapy benefits across cancers.

Methods: We proposed a study framework to construct the signature. Specifically, we built a multivariate Cox proportional hazards regression model with LASSO using 80% of an ICB-treated cohort (n = 1661) from MSKCC. The desired signature named SIGP was the risk score of the model and was validated in the remaining 20% of patients and an external ICB-treated cohort (n = 249) from DFCI.

Results: SIGP was based on …

Understanding Consumers' Use Experience On Electrically Heated Jacket: A Study On Online Review Using Topic Modeling, Md Nakib-Ul Hasan

LSU Doctoral Dissertations

The demand for heated jackets is anticipated to be fuelled by frequent temperature drops, severe winter weather, and increasing outdoor activities. Electrically heated jackets (EHJ) are primarily marketed through online distribution channels and expansion of online sales channels is expected to boost the global market. Consumers are increasingly relying on online reviews from other consumers to help them decide what to buy. Businesses also actively monitor and manage their online reviews to build trust in their brand and make it more likely that customers will buy. Traditional approaches for assessing customer behavior, such as market research surveys and focus groups, …

Controlling Multiple Covid-19 Epidemic Waves: An Insight From A Multi-Scale Model Linking The Behaviour Change Dynamics To The Disease Transmission Dynamics, Biao Tang, Weike Zhou, Xia Wang, Hulin Wu, Yanni Xiao

Faculty, Staff and Student Publications

COVID-19 epidemics exhibited multiple waves regionally and globally since 2020. It is important to understand the insight and underlying mechanisms of the multiple waves of COVID-19 epidemics in order to design more efficient non-pharmaceutical interventions (NPIs) and vaccination strategies to prevent future waves. We propose a multi-scale model by linking the behaviour change dynamics to the disease transmission dynamics to investigate the effect of behaviour dynamics on COVID-19 epidemics using game theory. The proposed multi-scale models are calibrated and key parameters related to disease transmission dynamics and behavioural dynamics with/without vaccination are estimated based on COVID-19 epidemic data (daily reported …

Developing Research Data Management Services In A Regional Comprehensive University: The Case Of Central Washington University, Ping Fu, Maurice Blackson, Maura Valentino

Library Scholarship

This study aims to analyze the needs of researchers in a regional comprehensive university for research data management services; discuss the options for developing a research data management program at the university; and then propose a phased three-year implementation plan for the university libraries. The method was to design a survey to collect information from researchers and assess and evaluate their needs for research data management services. The results show that researchers’ needs in a regional comprehensive university could be quite different from those of researchers in a research-intensive university. Also, the results verify the hypothesis that researchers in the …

Data Engineering Techniques And Designs With Music Generating Neural Networks, Noah Solomon

Honors Program Theses and Projects

The generation of music artificially is an interesting concept to many and has received a lot of attention in recent years. The advancement of neural networks has allowed for the creation of models that can seemingly generate music creatively to mimic a specific genre or composer. This project delved deep into the many ways to construct music generating neural networks and compared different model architectures and data engineering techniques. Three main types of models were implemented and the resulting generated music was evaluated with respect to the melody, note agreeableness, and rhythm. These models used the Bach Chorales corpus as …

Immuno-Genomic Profiling Of Biopsy Specimens Predicts Neoadjuvant Chemotherapy Response In Esophageal Squamous Cell Carcinoma, Shota Sasagawa, Hiroaki Kato, Koji Nagaoka, Changbo Sun, Motohiro Imano, Takao Sato, Todd A Johnson, Masashi Fujita, Kazuhiro Maejima, Yuki Okawa, Kazuhiro Kakimi, Takushi Yasuda, Hidewaki Nakagawa

Faculty, Staff and Student Publications

Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive cancers and is primarily treated with platinum-based neoadjuvant chemotherapy (NAC). Some ESCCs respond well to NAC. However, biomarkers to predict NAC sensitivity and their response mechanism in ESCC remain unclear. We perform whole-genome sequencing and RNA sequencing analysis of 141 ESCC biopsy specimens before NAC treatment to generate a machine-learning-based diagnostic model to predict NAC reactivity in ESCC and analyzed the association between immunogenomic features and NAC response. Neutrophil infiltration may play an important role in ESCC response to NAC. We also demonstrate that specific copy-number alterations and copy-number …