Data Science Commons^™

Genetic Correlations Between Alzheimer’S Disease And Gut Microbiome Genera, Davis Cammann, Yimei Lu, Melika J Cummings, Mark L Zhang, Joan Manuel Cue, Jenifer Do, Jeffrey Ebersole, Xiangning Chen, Edwin C Oh, Jeffrey L Cummings, Jingchun Chen

Faculty, Staff and Student Publications

A growing body of evidence suggests that dysbiosis of the human gut microbiota is associated with neurodegenerative diseases like Alzheimer's disease (AD) via neuroinflammatory processes across the microbiota-gut-brain axis. The gut microbiota affects brain health through the secretion of toxins and short-chain fatty acids, which modulates gut permeability and numerous immune functions. Observational studies indicate that AD patients have reduced microbiome diversity, which could contribute to the pathogenesis of the disease. Uncovering the genetic basis of microbial abundance and its effect on AD could suggest lifestyle changes that may reduce an individual's risk for the disease. Using the largest genome-wide …

Hsc-Independent Definitive Hematopoiesis Persists Into Adult Life, Michihiro Kobayashi, Haichao Wei, Takashi Yamanashi, Nathalia Azevedo Portilho, Samuel Cornelius, Noemi Valiente, Chika Nishida, Haizi Cheng, Augusto Latorre, W Jim Zheng, Joonsoo Kang, Jun Seita, David J Shih, Jia Qian Wu, Momoko Yoshimoto

Faculty, Staff and Student Publications

It is widely believed that hematopoiesis after birth is established by hematopoietic stem cells (HSCs) in the bone marrow and that HSC-independent hematopoiesis is limited only to primitive erythro-myeloid cells and tissue-resident innate immune cells arising in the embryo. Here, surprisingly, we find that significant percentages of lymphocytes are not derived from HSCs, even in 1-year-old mice. Instead, multiple waves of hematopoiesis occur from embryonic day 7.5 (E7.5) to E11.5 endothelial cells, which simultaneously produce HSCs and lymphoid progenitors that constitute many layers of adaptive T and B lymphocytes in adult mice. Additionally, HSC lineage tracing reveals that the contribution …

Using California Harmful Algae Risk Mapping To Predict Sea Lion Strandings, Florybeth La Valle, Sydney Socquet

Seaver College Research And Scholarly Achievement Symposium

Domoic acid (DA) is a toxin produced by marine diatoms of the genus Pseudo-nitzschia (Pn) and bioaccumulates in California sea lions (Zalophus californianus). DA toxicosis can cause neurological issues and death, and the rate at which Z. californianus become stranded due to this condition has been increasing since it was first diagnosed in a marine mammal in 1998. We compared geotemporal data of sea lion strandings with data from the California Harmful Algae Risk Mapping (C-HARM) Model to analyze patterns that may indicate when and where a sea lion stranding due to DA toxicosis will occur. C-HARM geographically visualizes the …

Fraud Pattern Detection For Nft Markets, Andrew Leppla, Jorge Olmos, Jaideep Lamba

SMU Data Science Review

Non-Fungible Tokens (NFTs) enable ownership and transfer of digital assets using blockchain technology. As a relatively new financial asset class, NFTs lack robust oversight and regulations. These conditions create an environment that is susceptible to fraudulent activity and market manipulation schemes. This study examines the buyer-seller network transactional data from some of the most popular NFT marketplaces (e.g., AtomicHub, OpenSea) to identify and predict fraudulent activity. To accomplish this goal multiple features such as price, volume, and network metrics were extracted from NFT transactional data. These were fed into a Multiple-Scale Convolutional Neural Network that predicts suspected fraudulent activity based …

Self-Learning Algorithms For Intrusion Detection And Prevention Systems (Idps), Juan E. Nunez, Roger W. Tchegui Donfack, Rohit Rohit, Hayley Horn

SMU Data Science Review

Today, there is an increased risk to data privacy and information security due to cyberattacks that compromise data reliability and accessibility. New machine learning models are needed to detect and prevent these cyberattacks. One application of these models is cybersecurity threat detection and prevention systems that can create a baseline of a network's traffic patterns to detect anomalies without needing pre-labeled data; thus, enabling the identification of abnormal network events as threats. This research explored algorithms that can help automate anomaly detection on an enterprise network using Canadian Institute for Cybersecurity data. This study demonstrates that Neural Networks with Bayesian …

Deep Learning For Online Fashion: A Novel Solution For The Retail E-Commerce Industry, Zachary O. Harris, Gowtham G. Katta, Robert Slater, Joseph L. Woodall Iv

SMU Data Science Review

The online shopping experience for clothing can be further enhanced by implementing Deep Learning techniques, such as Computer Vision and personalized recommendation systems. Automation, as a principle, can be applied to solving problems surrounding efficacy, efficiency, and security. It also provides a layer of abstraction for the user during the online shopping experience. This research aims to apply Deep Learning methods and principles of automation to augment the e-commerce fashion market in a novel way. After using these methods, it was found that Convolutional Autoencoders and Item-to-Item Based Recommenders may be used to accurately and precisely recommend articles of clothing …

Movement, Behavior, And Trophic Ecology Of A Pelagic Predator Guild In The Eastern Tropical Pacific Ocean, Ryan Keith Logan

All HCAS Student Capstones, Theses, and Dissertations

Pelagic apex predators exert strong influences on ecological communities, and often support valuable commercial or recreational fisheries worldwide. Yet, due to their rarity and pelagic lifestyle, many species, such as billfishes, have proven particularly difficult to study at resolutions necessary to define dynamics of recovery from fishery interaction, physical interaction with environmental features and prey exploitation, and competitive interactions among other billfish predators. This leads to a paucity of knowledge on billfish ecology and habitat use, and hinders management efforts. With the ever-improving and miniaturization of technology and oceanographic datasets, the ability to define and quantify these interactions of fish …

Genetic Control Of Rna Editing In Neurodegenerative Disease, Sijia Wu, Qiuping Xue, Mengyuan Yang, Yanfei Wang, Pora Kim, Xiaobo Zhou, Liyu Huang

Faculty, Staff and Student Publications

A-to-I RNA editing diversifies human transcriptome to confer its functional effects on the downstream genes or regulations, potentially involving in neurodegenerative pathogenesis. Its variabilities are attributed to multiple regulators, including the key factor of genetic variants. To comprehensively investigate the potentials of neurodegenerative disease-susceptibility variants from the view of A-to-I RNA editing, we analyzed matched genetic and transcriptomic data of 1596 samples across nine brain tissues and whole blood from two large consortiums, Accelerating Medicines Partnership-Alzheimer's Disease and Parkinson's Progression Markers Initiative. The large-scale and genome-wide identification of 95 198 RNA editing quantitative trait loci revealed the preferred genetic effects …

Global Scientific Trends On Healthy Eating From 2002 To 2021: A Bibliometric And Visualized Analysis, Te Fang, Hongyi Cao, Yue Wang, Yang Gong, Zhongqing Wang

Faculty, Staff and Student Publications

Diet has been recognized as a vital risk factor for non-communicable diseases (NCDs), climate changes, and increasing population, which has been reflected by a rapidly growing body of the literature related to healthy eating. To reveal a panorama of the topics related to healthy eating, this study aimed to characterize and visualize the knowledge structure, hotspots, and trends in this field over the past two decades through bibliometric analyses. Publications related to healthy eating between 1 January 2002 and 31 December 2021 were retrieved and extracted from the Web of Science database. The characteristics of articles including publication years, journals, …

A Scoping Review Of Digital Health Interventions For Combating Covid-19 Misinformation And Disinformation, Katarzyna Czerniak, Raji Pillai, Abhi Parmar, Kavita Ramnath, Joseph Krocker, Sahiti Myneni

Faculty, Staff and Student Publications

OBJECTIVE: We provide a scoping review of Digital Health Interventions (DHIs) that mitigate COVID-19 misinformation and disinformation seeding and spread.

MATERIALS AND METHODS: We applied our search protocol to PubMed, PsychINFO, and Web of Science to screen 1666 articles. The 17 articles included in this paper are experimental and interventional studies that developed and tested public consumer-facing DHIs. We examined these DHIs to understand digital features, incorporation of theory, the role of healthcare professionals, end-user experience, and implementation issues.

RESULTS: The majority of studies (n = 11) used social media in DHIs, but there was a lack of platform-agnostic generalizability. …

Infinite-Dimensional Stochastic Transforms And Reproducing Kernel Hilbert Space, Myung-Sin Song, Palle Jorgensen, James Feng Tian

SIUE Faculty Research, Scholarship, and Creative Activity

By way of concrete presentations, we construct two infinite-dimensional transforms at the crossroads of Gaussian fields and reproducing kernel Hilbert spaces (RKHS), thus leading to a new infinite-dimensional Fourier transform in a general setting of Gaussian processes. Our results serve to unify existing tools from infinite-dimensional analysis.

Chatgpt As Metamorphosis Designer For The Future Of Artificial Intelligence (Ai): A Conceptual Investigation, Amarjit Kumar Singh (Library Assistant), Dr. Pankaj Mathur (Deputy Librarian)

Library Philosophy and Practice (e-journal)

Abstract

Purpose: The purpose of this research paper is to explore ChatGPT’s potential as an innovative designer tool for the future development of artificial intelligence. Specifically, this conceptual investigation aims to analyze ChatGPT’s capabilities as a tool for designing and developing near about human intelligent systems for futuristic used and developed in the field of Artificial Intelligence (AI). Also with the helps of this paper, researchers are analyzed the strengths and weaknesses of ChatGPT as a tool, and identify possible areas for improvement in its development and implementation. This investigation focused on the various features and functions of ChatGPT that …

A Gene Regulatory Network Approach Harmonizes Genetic And Epigenetic Signals And Reveals Repurposable Drug Candidates For Multiple Sclerosis, Astrid M Manuel, Yulin Dai, Peilin Jia, Leorah A Freeman, Zhongming Zhao

Faculty, Staff and Student Publications

Multiple sclerosis (MS) is a complex dysimmune disorder of the central nervous system. Genome-wide association studies (GWAS) have identified 233 genetic variations associated with MS at the genome-wide significant level. Epigenetic studies have pinpointed differentially methylated CpG sites in MS patients. However, the interplay between genetic risk factors and epigenetic regulation remains elusive. Here, we employed a network model to integrate GWAS summary statistics of 14 802 MS cases and 26 703 controls with DNA methylation profiles from 140 MS cases and 139 controls and the human interactome. We identified differentially methylated genes by aggregating additive effects of differentially methylated …

Text And Data Mining Applications For Teaching Music Bibliography, Taylor Greene, Laurie Sampsel

Library Presentations, Posters, and Audiovisual Materials

Text and data mining (TDM) is a process of increasing interdisciplinary potential and one with many practical applications for music graduate students. TDM, however, remains a topic rarely introduced in the music bibliography course. Understandably, talk of artificial intelligence, algorithms, and programming languages are intimidating to music students, but thanks to software applications, knowledge about these computer science topics are not required to participate in research using TDM. This presentation explores ways to introduce digital humanities to music students through TDM.

In our presentation, we will discuss two approaches to incorporating TDM into the music bibliography course, focusing on two …

Uncertainty Quantification In Federated Learning For Persistent Post-Traumatic Headache, Byungmoo Brian Kim

Theses and Dissertations

A post-traumatic headache (PTH), resulting from a mild traumatic brain injury (mTBI), potentially develops into persistent post-traumatic headache (PPTH). Although no known cure for PPTH exists, research has shown that receiving treatment at earlier stages of PTH lowers the risk of patients developing PPTH. Previous studies have shown machine learning (ML) models capable of predicting a patient’s PTH progression, but none have considered the issue of protecting patient privacy. Due to patient privacy, ML models only have access to data within the institution. Federated learning (FL) harnesses data from separate institutions without sacrificing patient privacy as institutions can run ML …

Identifying A Clinical Informatics Or Electronic Health Record Expert Witness For Medical Professional Liability Cases, Dean F Sittig, Adam Wright

Faculty, Staff and Student Publications

BACKGROUND: The health care field is experiencing widespread electronic health record (EHR) adoption. New medical professional liability (i.e., malpractice) cases will likely involve the review of data extracted from EHRs as well as EHR workflows, audit logs, and even the potential role of the EHR in causing harm.

OBJECTIVES: Reviewing printed versions of a patient's EHRs can be difficult due to differences in printed versus on-screen presentations, redundancies, and the way printouts are often grouped by document or information type rather than chronologically. Simply recreating an accurate timeline often requires experts with training and experience in designing, developing, using, and …

Mining For Equitable Health: Assessing The Impact Of Missing Data In Electronic Health Records, Emily Getzen, Lyle Ungar, Danielle Mowery, Xiaoqian Jiang, Qi Long

Faculty, Staff and Student Publications

Electronic health records (EHR) are collected as a routine part of healthcare delivery, and have great potential to be utilized to improve patient health outcomes. They contain multiple years of health information to be leveraged for risk prediction, disease detection, and treatment evaluation. However, they do not have a consistent, standardized format across institutions, particularly in the United States, and can present significant analytical challenges- they contain multi-scale data from heterogeneous domains and include both structured and unstructured data. Data for individual patients are collected at irregular time intervals and with varying frequencies. In addition to the analytical challenges, EHR …

A Hierarchical Strategy To Minimize Privacy Risk When Linking “De-Identified” Data In Biomedical Research Consortia, Lucila Ohno-Machado, Xiaoqian Jiang, Tsung-Ting Kuo, Shiqiang Tao, Luyao Chen, Pritham M Ram, Guo-Qiang Zhang, Hua Xu

Faculty, Staff and Student Publications

Linking data across studies offers an opportunity to enrich data sets and provide a stronger basis for data-driven models for biomedical discovery and/or prognostication. Several techniques to link records have been proposed, and some have been implemented across data repositories holding molecular and clinical data. Not all these techniques guarantee appropriate privacy protection; there are trade-offs between (a) simple strategies that can be associated with data that will be linked and shared with any party and (b) more complex strategies that preserve the privacy of individuals across parties. We propose an intermediary, practical strategy to support linkage in studies that …

Institutional Design And Policy Responsiveness In Us States, Scott J. Lacombe

Government: Faculty Publications

There is significant disagreement on the moderating role of institutions on policy responsive- ness, yet overwhelmingly research in state politics has focused on single institutions. This project leverages a new aggregate scale of state institutions to evaluate if the collective insti- tutional context moderates the influence of public opinion on policy. I use a recently released latent scale of institutional context and find that high levels of accountability pressure strongly strengthen public opinion’s influence on policy for both economic and social policy, while the strength of a state’s checks and balance system is largely unrelated to policy responsiveness. These results …

Wearables For In-Situ Monitoring Of Cognitive States: Challenges And Opportunities, Meera Radhakrishnan, Thivya Kandappu, Manoj Gulati, Archan Misra

Research Collection School Of Computing and Information Systems

We propose using wrist and ear-based sensing, via multiple novel and complementary modalities, to unobtrusively infer activity-aware, complex cognitive and affective states (such as confusion, boredom, and recall failure) of individuals. While state-of-the-art wearable devices are predominantly used (a) independently, with limited coordination among multiple devices, and (b) to capture macro-level physical activity and physiological state, we seek to expand the ambit of unobtrusive wearable sensing to capture the cognitive states while performing commonplace physical activities. Such states typically manifest via fine-grained, almost unobservable, microscopic head, face, and eye movements. We identify some of these fine-grained physical markers that serve …

Hybrid Modeling For Electrochemical Systems, Luis Alejandro Briceno-Mena

LSU Doctoral Dissertations

The discovery of new materials like catalysts, polymeric films, and biomolecules, is driven by industrial needs such as improving reaction or separation selectivity, enhancing therapeutic effects on medical treatments, or reducing costs of replacement. However, deployment of these advances in industrial applications is often hindered by the lack of models needed for design and optimization. Due to the novelty of materials and devices, experimental data and first principles' knowledge are scarce, making it hard to build models either via data-driven or knowledge based approaches. In this context, a way to efficiently combine domain knowledge with data could provide a pathway …

Named Entity Recognition From Biomedical Text, Maged Guirguis

Theses and Dissertations

As vast amounts of unstructured data are becoming available digitally, computer-based methods to extract relevant and meaningful information are needed. Named entity recognition (NER) is the task of identifying text spans that mention named entities, and to classify them into predefined categories. Despite the existence of numerous and well-versed NER methods, the bio-medical domain remains under-studied. The objective of this research is to identify an efficient technique for NER tasks from biomedical data. This is achieved by investigating using deep learning technologies namely pre-trained BERT [1] model and its variances SciBERT [2] and BioBERT [3]. Preprocessing the data before passing …

Multicollinearity Applied Stepwise Stochastic Imputation: A Large Dataset Imputation Through Correlation‑Based Regression, Benjamin D. Leiby, Darryl K. Ahner

Faculty Publications

This paper presents a stochastic imputation approach for large datasets using a correlation selection methodology when preferred commercial packages struggle to iterate due to numerical problems. A variable range-based guard rail modification is proposed that benefits the convergence rate of data elements while simultaneously providing increased confidence in the plausibility of the imputations. A large country conflict dataset motivates the search to impute missing values well over a common threshold of 20% missingness. The Multicollinearity Applied Stepwise Stochastic imputation methodology (MASS-impute) capitalizes on correlation between variables within the dataset and uses model residuals to estimate unknown values. Examination of the …

Automated Contouring And Planning In Radiation Therapy: What Is 'Clinically Acceptable'?, Hana Baroudi, Kristy K Brock, Wenhua Cao, Xinru Chen, Caroline Chung, Laurence E Court, Mohammad D El Basha, Maguy Farhat, Skylar Gay, Mary P Gronberg, Aashish Chandra Gupta, Soleil Hernandez, Kai Huang, David A Jaffray, Rebecca Lim, Barbara Marquez, Kelly Nealon, Tucker J Netherton, Callistus M Nguyen, Brandon Reber, Dong Joo Rhee, Ramon M Salazar, Mihir D Shanker, Carlos Sjogreen, Mckell Woodland, Jinzhong Yang, Cenji Yu, Yao Zhao

Faculty, Staff and Student Publications

Developers and users of artificial-intelligence-based tools for automatic contouring and treatment planning in radiotherapy are expected to assess clinical acceptability of these tools. However, what is 'clinical acceptability'? Quantitative and qualitative approaches have been used to assess this ill-defined concept, all of which have advantages and disadvantages or limitations. The approach chosen may depend on the goal of the study as well as on available resources. In this paper, we discuss various aspects of 'clinical acceptability' and how they can move us toward a standard for defining clinical acceptability of new autocontouring and planning tools.

Session11: Skip-Gcn : A Framework For Hierarchical Graph Representation Learning, Jackson Cates, Justin Lewis, Randy Hoover, Kyle Caudle

SDSU Data Science Symposium

Recently there has been high demand for the representation learning of graphs. Graphs are a complex data structure that contains both topology and features. There are first several domains for graphs, such as infectious disease contact tracing and social media network communications interactions. The literature describes several methods developed that work to represent nodes in an embedding space, allowing for classical techniques to perform node classification and prediction. One such method is the graph convolutional neural network that aggregates the node neighbor’s features to create the embedding. Another method, Walklets, takes advantage of the topological information stored in a graph …

2d Respiratory Sound Analysis To Detect Lung Abnormalities, Rafia Sharmin Alice, Kc Santosh

SDSU Data Science Symposium

Abstract. In this paper, we analyze deep visual features from 2D data representation(s) of the respiratory sound to detect evidence of lung abnormalities. The primary motivation behind this is that visual cues are more important in decision-making than raw data (lung sound). Early detection and prompt treatments are essential for any future possible respiratory disorders, and respiratory sound is proven to be one of the biomarkers. In contrast to state-of-the-art approaches, we aim at understanding/analyzing visual features using our Convolutional Neural Networks (CNN) tailored Deep Learning Models, where we consider all possible 2D data such as Spectrogram, Mel-frequency Cepstral Coefficients …

Temporal Tensor Factorization For Multidimensional Forecasting, Jackson Cates, Karissa Scipke, Randy Hoover, Kyle Caudle

SDSU Data Science Symposium

In the era of big data, there is a need for forecasting high-dimensional time series that might be incomplete, sparse, and/or nonstationary. The current research aims to solve this problem for two-dimensional data through a combination of temporal matrix factorization (TMF) and low-rank tensor factorization. From this method, we propose an expansion of TMF to two-dimensional data: temporal tensor factorization (TTF). The current research aims to interpolate missing values via low-rank tensor factorization, which produces a latent space of the original multilinear time series. We then can perform forecasting in the latent space. We present experimental results of the proposed …

Emotion Classification Of Indonesian Tweets Using Bidirectional Lstm, Aaron K. Glenn, Phillip M. Lacasse, Bruce A. Cox

Faculty Publications

Emotion classification can be a powerful tool to derive narratives from social media data. Traditional machine learning models that perform emotion classification on Indonesian Twitter data exist but rely on closed-source features. Recurrent neural networks can meet or exceed the performance of state-of-the-art traditional machine learning techniques using exclusively open-source data and models. Specifically, these results show that recurrent neural network variants can produce more than an 8% gain in accuracy in comparison with logistic regression and SVM techniques and a 15% gain over random forest when using FastText embeddings. This research found a statistical significance in the performance of …

Hemoglobin Concentration Impacts Viscoelastic Hemostatic Assays In Icu Admitted Patients, David J Roh, Tiffany R Chang, Aditya Kumar, Devin Burke, Glenda Torres, Katherine Xu, Winni Yang, Azzurra Cottarelli, Ernest Moore, Angela Sauaia, Kirk Hansen, Angela Velazquez, Amelia Boehme, Athina Vrosgou, Shivani Ghoshal, Soojin Park, Sachin Agarwal, Jan Claassen, E Sander Connolly, Gebhard Wagener, Richard O Francis, Eldad Hod

Faculty, Staff and Student Publications

Objectives: Low hemoglobin concentration impairs clinical hemostasis across several diseases. It is unclear whether hemoglobin impacts laboratory functional coagulation assessments. We evaluated the relationship of hemoglobin concentration on viscoelastic hemostatic assays in intracerebral hemorrhage (ICH) and perioperative patients admitted to an ICU.

Design: Observational cohort study and separate in vitro laboratory study.

Setting: Multicenter tertiary referral ICUs.

Patients: Two acute ICH cohorts receiving distinct testing modalities: rotational thromboelastometry (ROTEM) and thromboelastography (TEG), and a third surgical ICU cohort receiving ROTEM were evaluated to assess the generalizability of findings across disease processes and testing platforms. A separate in vitro ROTEM laboratory …

Biological Correlates Of The Effects Of Auricular Point Acupressure On Pain, Chao Hsing Yeh, Nada Lukkahatai, Xinran Huang, Hulin Wu, Hongyu Wang, Jingyu Zhang, Xinyi Sun, Thomas J Smith

Faculty, Staff and Student Publications

BACKGROUND: To identify candidate inflammatory biomarkers for the underlying mechanism of auricular point acupressure (APA) on pain relief and examine the correlations among pain intensity, interference, and inflammatory biomarkers.

DESIGN: This is a secondary data analysis.

METHODS: Data on inflammatory biomarkers collected via blood samples and patient self-reported pain intensity and interference from three pilot studies (chronic low back pain, n = 61; arthralgia related to aromatase inhibitors, n = 20; and chemotherapy-induced neuropathy, n = 15) were integrated and analyzed. This paper reports the results based on within-subject treatment effects (change in scores from pre- to post-APA intervention) for …