Data Science Commons^™

Identifying Candidate Genes And Drug Targets For Alzheimer’S Disease By An Integrative Network Approach Using Genetic And Brain Region-Specific Proteomic Data, Andi Liu, Astrid M Manuel, Yulin Dai, Brisa S Fernandes, Nitesh Enduru, Peilin Jia, Zhongming Zhao

Faculty, Staff and Student Publications

Genome-wide association studies (GWAS) have identified more than 75 genetic variants associated with Alzheimer's disease (ad). However, how these variants function and impact protein expression in brain regions remain elusive. Large-scale proteomic datasets of ad postmortem brain tissues have become available recently. In this study, we used these datasets to investigate brain region-specific molecular pathways underlying ad pathogenesis and explore their potential drug targets. We applied our new network-based tool, Edge-Weighted Dense Module Search of GWAS (EW_dmGWAS), to integrate ad GWAS statistics of 472 868 individuals with proteomic profiles from two brain regions from two large-scale ad cohorts [parahippocampal gyrus …

Video-Urodynamics Efficacy Of Sacral Neuromodulation For Neurogenic Bladder Guided By Three-Dimensional Imaging Ct And C-Arm Fluoroscopy: A Single-Center Prospective Study, Shuaishuai Shan, Wen Zhu, Guoxian Zhang, Qinyong Zhang, Yingyu Che, Jianguo Wen, Qingwei Wang

Faculty, Staff and Student Publications

To assess the efficacy of sacral neuromodulation (SNM) for neurogenic bladder (NB), guided by intraoperative three-dimensional imaging of sacral computed tomography (CT) and mobile C-arm fluoroscopy through video-urodynamics examination. We enrolled 52 patients with NB who underwent conservative treatment with poor results between September 2019 and June 2021 and prospectively underwent SNM guided by intraoperative three-dimensional imaging of sacral CT and mobile C-arm fluoroscopy. Video-urodynamics examination, voiding diary, quality of life questionnaire, overactive bladder symptom scale (OABSS) scoring, and bowel dysfunction exam were completed and recorded at baseline, at SNM testing, and at 6-month follow-up phases. Finally, we calculated the …

Molecular Pathways Enhance Drug Response Prediction Using Transfer Learning From Cell Lines To Tumors And Patient-Derived Xenografts, Yi-Ching Tang, Reid T Powell, Assaf Gottlieb

Faculty, Staff and Student Publications

Computational models have been successful in predicting drug sensitivity in cancer cell line data, creating an opportunity to guide precision medicine. However, translating these models to tumors remains challenging. We propose a new transfer learning workflow that transfers drug sensitivity predicting models from large-scale cancer cell lines to both tumors and patient derived xenografts based on molecular pathways derived from genomic features. We further compute feature importance to identify pathways most important to drug response prediction. We obtained good performance on tumors (AUROC = 0.77) and patient derived xenografts from triple negative breast cancers (RMSE = 0.11). Using feature importance, …

Phishing Detection Using Natural Language Processing And Machine Learning, Apurv Mittal, Dr Daniel Engels, Harsha Kommanapalli, Ravi Sivaraman, Taifur Chowdhury

SMU Data Science Review

Phishing emails are a primary mode of entry for attackers into an organization. A successful phishing attempt leads to unauthorized access to sensitive information and systems. However, automatically identifying phishing emails is often difficult since many phishing emails have composite features such as body text and metadata that are nearly indistinguishable from valid emails. This paper presents a novel machine learning-based framework, the DARTH framework, that characterizes and combines multiple models, with one model for each composite feature, that enables the accurate identification of phishing emails. The framework analyses each composite feature independently utilizing a multi-faceted approach using Natural Language …

Classification Of Breast Cancer Histopathological Images Using Semi-Supervised Gans, Balaji Avvaru, Nibhrat Lohia, Sowmya Mani, Vijayasrikanth Kaniti

SMU Data Science Review

Breast cancer is diagnosed more frequently than skin cancer in women in the United States. Most breast cancer cases are diagnosed in women, while children and men are less likely to develop the disease. Various tissues in the breast grow uncontrollably, resulting in breast cancer. Different treatments analyze microscopic histopathology images for diagnosis that help accurately detect cancer cells. Deep learning is one of the evolving techniques to classify images where accuracy depends on the volume and quality of labeled images. This study used various pre-trained models to train the histopathological images and analyze these models to create a new …

Short Term Forecasting Of Solar Radiation, Ashwin Thota, Bradley Blanchard, Lijju Mathew, Paritosh Rai, Sid Swarupananda

SMU Data Science Review

This paper details how to predict solar radiation at a location for the next few hours using machine learning techniques like Facebook’s Prophet, and Amazon’s DeepAR+. Multiple techniques like AutoRegressive (ARIMA) and Exponential Smoothing (ES) have been used to forecast solar radiation, but they lack accuracy and are not scalable. Whereas Prophet, and Amazon’s DeepAR+ are scalable, accurate, and easily integrated into other machine learning techniques. This will be the first time where the combination of these techniques along with Linear Regression, Random Forest, XGBoost and Decision Tree will be leveraged to forecast solar radiation for the short term. Predicting …

Using Natural Language Processing To Increase Modularity And Interpretability Of Automated Essay Evaluation And Student Feedback, Chris Roche, Nathan Deinlein, Darryl Dawkins, Faizan Javed

SMU Data Science Review

For English teachers and students who are dissatisfied with the one-size-fits-all approach of current Automated Essay Scoring (AES) systems, this research uses Natural Language Processing (NLP) techniques that provide a focus on configurability and interpretability. Unlike traditional AES models which are designed to provide an overall score based on pre-trained criteria, this tool allows teachers to tailor feedback based upon specific focus areas. The tool implements a user-interface that serves as a customizable rubric. Students’ essays are inputted into the tool either by the student or by the teacher via the application’s user-interface. Based on the rubric settings, the tool …

Stock Forecasts With Lstm And Web Sentiment, Michael Burgess, Faizan Javed, Nnenna Okpara, Chance Robinson

SMU Data Science Review

Traditional time-series techniques, such as auto-regressive and moving average models, can have difficulties when applied to stock data due to the randomness inherent to the markets. In this study, Long Short-Term Memory Recurrent Neural Networks, or LSTMs, have been applied to pricing data along with sentiment scores derived from web sources such as Twitter and other financial media outlets. The project team utilized this approach to complement the technical indicators observed at the end of each trading day for three stocks from the NASDAQ stock exchange over a 12-year span. A common benchmark to assess model performance on time series …

Predicting Insulin Pump Therapy Settings, Riccardo L. Ferraro, David Grijalva, Alex Trahan

SMU Data Science Review

Millions of people live with diabetes worldwide [7]. To mitigate some of the many symptoms associated with diabetes, an estimated 350,000 people in the United States rely on insulin pumps [17]. For many of these people, how effectively their insulin pump performs is the difference between sleeping through the night and a life threatening emergency treatment at a hospital. Three programmed insulin pump therapy settings governing effective insulin pump function are: Basal Rate (BR), Insulin Sensitivity Factor (ISF), and Carbohydrate Ratio (ICR). For many people using insulin pumps, these therapy settings are often not correct, given their physiological needs. While …

Classification Of Pixel Tracks To Improve Track Reconstruction From Proton-Proton Collisions, Kebur Fantahun, Jobin Joseph, Halle Purdom, Nibhrat Lohia

SMU Data Science Review

In this paper, machine learning techniques are used to reconstruct particle collision pathways. CERN (Conseil européen pour la recherche nucléaire) uses a massive underground particle collider, called the Large Hadron Collider or LHC, to produce particle collisions at extremely high speeds. There are several layers of detectors in the collider that track the pathways of particles as they collide. The data produced from collisions contains an extraneous amount of background noise, i.e., decays from known particle collisions produce fake signal. Particularly, in the first layer of the detector, the pixel tracker, there is an overwhelming amount of background noise that …

Cov-Inception: Covid-19 Detection Tool Using Chest X-Ray, Aswini Thota, Ololade Awodipe, Rashmi Patel

SMU Data Science Review

Since the pandemic started, researchers have been trying to find a way to detect COVID-19 which is a cost-effective, fast, and reliable way to keep the economy viable and running. This research details how chest X-ray radiography can be utilized to detect the infection. This can be for implementation in Airports, Schools, and places of business. Currently, Chest imaging is not a first-line test for COVID-19 due to low diagnostic accuracy and confounding with other viral pneumonia. Different pre-trained algorithms were fine-tuned and applied to the images to train the model and the best model obtained was fine-tuned InceptionV3 model …

Predicting Twitch.Tv Donations Using Sentiment Analysis, Alexander J. Gilbert, Jason Herbaugh, Feby Cheruvathoor, Ben Williams, Alex Tozzo

SMU Data Science Review

Twitch.tv streamers have a rare opportunity to receive immediate feedback from their audience through a real-time chat log that is rife with sentiment information. Tools that can help a streamer understand how they need to influence their audience can be useful in increasing the donations and subscriptions they earn. Although millions around the world stream on Twitch, only a minuscule fraction of these streamers earn a living streaming alone. This paper aimed to provide muchneeded guidance to enable more streamers to succeed. We used stream logs, known as VODs (video on demand), which can be easily accessed through Twitch’s API …

Hierarchical Neural Networks (Hnn): Using Tensorflow To Build Hnn, Rick Fontenot, Joseph Lazarus, Puri Rudick, Anthony Sgambellone

SMU Data Science Review

This research demonstrates the use of TensorFlow to build a Hierarchical Neural Network (HNN). Constructing and engineering neural networks to maximize accuracy and efficiency is an active field of research in machine learning. HNN, along with several other applications of split networks have been developed as recently as 2017. However, implementations thus far have required custom-built and coded HNNs. The research conducted here uses TensorFlow to validate this structure by building entirely separate neural nets with logical relations between the output of one net and the inputs of the nets that are downstream. Research has shown that Hierarchical Neural Networks …

Examining Bias In Jury Selection For Criminal Trials In Dallas County, Megan Ball, Brandon Birmingham, Matt Farrow, Katherine Mitchell, Bivin Sadler, Lynne Stokes

SMU Data Science Review

One of the hallmarks of the American judicial system is the concept of trial by jury, and for said trial to consist of an impartial jury of your peers. Several landmark legal cases in the history of the United States have challenged this notion of equal representation by jury—most notably Batson v. Kentucky, 476 U.S. 79 (1986). Most of the previous research, focus, and legal precedence has centered around peremptory challenges and attempting to prove if bias was suspected in excluding certain jurors from serving. Few studies, however, focus on examining challenges for cause based on self-reported biases from the …

Application Of Probabilistic Ranking Systems On Women’S Junior Division Beach Volleyball, Cameron Stewart, Michael Mazel, Bivin Sadler

SMU Data Science Review

Women’s beach volleyball is one of the fastest growing collegiate sports today. The increase in popularity has come with an increase in valuable scholarship opportunities across the country. With thousands of athletes to sort through, college scouts depend on websites that aggregate tournament results and rank players nationally. This project partnered with the company Volleyball Life, who is the current market leader in the ranking space of junior beach volleyball players. Utilizing the tournament information provided by Volleyball Life, this study explored replacements to the current ranking systems, which are designed to aggregate player points from recent tournament placements. Three …

Market Segmentation And Recency Frequency Monetary Value Analysis For A Freemium Mobile Game, Satvik Ajmera, Taylor Bonar, Dylan Scott, Carol Miu, Alana Manuel

SMU Data Science Review

Bricks ‘N Balls is a freemium game that relies on in-app purchases and ad monetization from users to be profitable at no upfront cost to the players. This study explores how in-game data analytics and purchase data can be used to segment players. Features taken into consideration for segmentation include past purchasing habits along with the players interactions within the missions. This study uses the Recency Frequency Monetary Value (RFM) framework to extract insights on player purchasing behavior to segment players into clusters and predict how much users will spend in the future.

“Be A Pattern For The World”: The Development Of A Dark Patterns Detection Tool To Prevent Online User Loss, Jordan Donnelly, Alan Dowley, Yunpeng Liu, Yufei Su, Quanwei Sun, Lan Zeng, Andrea Curley, Damian Gordon, Paul Kelly, Dympna O'Sullivan, Anna Becevel

Articles

Dark Patterns are designed to trick users into sharing more information or spending more money than they had intended to do, by configuring online interactions to confuse or add pressure to the users. They are highly varied in their form, and are therefore difficult to classify and detect. Therefore, this research is designed to develop a framework for the automated detection of potential instances of web-based dark patterns, and from there to develop a software tool that will provide a highly useful defensive tool that helps detect and highlight these patterns.

Oral Nanomedicines For Sirna Delivery To Treat Inflammatory Bowel Disease, Jongyoon Shinn, Juyeon Lee, Seon Ah Lee, Seon Ju Lee, Ah Hyun Choi, Jung Seo Kim, Su Jin Kim, Hyo Jin Kim, Cherin Lee, Yejin Kim, Joohyeon Kim, Jonghee Choi, Byungchae Jung, Taeho Kim, Hyeontaek Nam, Hyungjun Kim, Yonghyun Lee

Faculty, Staff and Student Publications

RNA interference (RNAi) therapies have significant potential for the treatment of inflammatory bowel diseases (IBD). Although administering small interfering RNA (siRNA) via an oral route is desirable, various hurdles including physicochemical, mucus, and cellular uptake barriers of the gastrointestinal tract (GIT) impede both the delivery of siRNA to the target site and the action of siRNA drugs at the target site. In this review, we first discuss various physicochemical and biological barriers in the GI tract. Furthermore, we present recent strategies and the progress of oral siRNA delivery strategies to treat IBD. Finally, we consider the challenges faced in the …

Delineating Covid-19 Immunological Features Using Single-Cell Rna Sequencing, Wendao Liu, Johnathan Jia, Yulin Dai, Wenhao Chen, Guangsheng Pei, Qiheng Yan, Zhongming Zhao

Faculty, Staff and Student Publications

Understanding the molecular mechanisms of coronavirus disease 2019 (COVID-19) pathogenesis and immune response is vital for developing therapies. Single-cell RNA sequencing has been applied to delineate the cellular heterogeneity of the host response toward COVID-19 in multiple tissues and organs. Here, we review the applications and findings from over 80 original COVID-19 single-cell RNA sequencing studies as well as many secondary analysis studies. We describe that single-cell RNA sequencing reveals multiple features of COVID-19 patients with different severity, including cell populations with proportional alteration, COVID-19-induced genes and pathways, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection in single cells, and adaptation …

Self-Supervised Learning For Invariant Representations From Multi-Spectral And Sar Images, Pallavi Jain, Bianca Schoen Phelan, Robert J. Ross

Articles

Self-Supervised learning (SSL) has become the new state of the art in several domain classification and segmentation tasks. One popular category of SSL are distillation networks such as Bootstrap Your Own Latent (BYOL). This work proposes RS-BYOL, which builds on BYOL in the remote sensing (RS) domain where data are non-trivially different from natural RGB images. Since multi-spectral (MS) and synthetic aperture radar (SAR) sensors provide varied spectral and spatial resolution information, we utilise them as an implicit augmentation to learn invariant feature embeddings. In order to learn RS based invariant features with SSL, we trained RS-BYOL in two ways, …

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 …