Physical Sciences and Mathematics Commons^™

Automatic Segmentation Of Sinkholes Using A Convolutional Neural Network, Muhammad Usman Rafique, Junfeng Zhu, Nathan Jacobs

Faculty, Staff, and Affiliated Publications--KGS

Sinkholes are the most abundant surface features in karst areas worldwide. Understanding sinkhole occurrences and characteristics is critical for studying karst aquifers and mitigating sinkhole-related hazards. Most sinkholes appear on the land surface as depressions or cover collapses and are commonly mapped from elevation data, such as digital elevation models (DEMs). Existing methods for identifying sinkholes from DEMs often require two steps: locating surface depressions and separating sinkholes from non-sinkhole depressions. In this study, we explored deep learning to directly identify sinkholes from DEM data and aerial imagery. A key contribution of our study is an evaluation of various ways …

Automatic Segmentation Of Sinkholes Using A Convolutional Neural Network, Muhammad Usman Rafique, Junfeng Zhu, Nathan Jacobs

Computer Science Faculty Publications

Sinkholes are the most abundant surface features in karst areas worldwide. Understanding sinkhole occurrences and characteristics is critical for studying karst aquifers and mitigating sinkhole-related hazards. Most sinkholes appear on the land surface as depressions or cover collapses and are commonly mapped from elevation data, such as digital elevation models (DEMs). Existing methods for identifying sinkholes from DEMs often require two steps: locating surface depressions and separating sinkholes from non-sinkhole depressions. In this study, we explored deep learning to directly identify sinkholes from DEM data and aerial imagery. A key contribution of our study is an evaluation of various ways …

Recent Advances In Wearable Sensing Technologies, Alfredo J. Perez, Sherali Zeadally

Information Science Faculty Publications

Wearable sensing technologies are having a worldwide impact on the creation of novel business opportunities and application services that are benefiting the common citizen. By using these technologies, people have transformed the way they live, interact with each other and their surroundings, their daily routines, and how they monitor their health conditions. We review recent advances in the area of wearable sensing technologies, focusing on aspects such as sensor technologies, communication infrastructures, service infrastructures, security, and privacy. We also review the use of consumer wearables during the coronavirus disease 19 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus …

Bone Quality And Fractures In Women With Osteoporosis Treated With Bisphosphonates For 1 To 14 Years, Hartmut H. Malluche, Jin Chen, Florence Lima, Lucas J. Liu, Marie-Claude Monier-Faugere, David A. Pienkowski

Internal Medicine Faculty Publications

Oral bisphosphonates are the primary medication for osteoporosis, but concerns exist regarding potential bone-quality changes or low-energy fractures. This cross-sectional study used artificial intelligence methods to analyze relationships among bisphosphonate treatment duration, a wide variety of bone-quality parameters, and low-energy fractures. Fourier transform infrared spectroscopy and histomorphometry quantified bone-quality parameters in 67 osteoporotic women treated with oral bisphosphonates for 1 to 14 years. Artificial intelligence methods established two models relating bisphosphonate treatment duration to bone-quality changes and to low-energy clinical fractures. The model relating bisphosphonate treatment duration to bone quality demonstrated optimal performance when treatment durations of 1 to 8 …

Telomere Roles In Fungal Genome Evolution And Adaptation, Mostafa Rahnama, Baohua Wang, Jane Dostart, Olga Novikova, Daniel Yackzan, Andrew T. Yackzan, Haley Bruss, Maray Baker, Haven Jacob, Xiaofei Zhang, April Lamb, Alex Stewart, Melanie Heist, Joey Hoover, Patrick Calie, Li Chen, Jinze Liu, Mark L. Farman

Plant Pathology Faculty Publications

Telomeres form the ends of linear chromosomes and usually comprise protein complexes that bind to simple repeated sequence motifs that are added to the 3′ ends of DNA by the telomerase reverse transcriptase (TERT). One of the primary functions attributed to telomeres is to solve the “end-replication problem” which, if left unaddressed, would cause gradual, inexorable attrition of sequences from the chromosome ends and, eventually, loss of viability. Telomere-binding proteins also protect the chromosome from 5′ to 3′ exonuclease action, and disguise the chromosome ends from the double-strand break repair machinery whose illegitimate action potentially generates catastrophic chromosome aberrations. Telomeres …

Innovative Computational Methods For Pharmaceutical Problem Solving A Review Part I: The Drug Development Process, Heather R. Campbell, Robert A. Lodder

Pharmaceutical Sciences Faculty Publications

Computational methods have provided pharmaceutical scientists and engineers a means to go beyond what's possible with experimental testing alone. Providing a means to study active pharmaceutical ingredients (API), excipients, and drug interactions at or near-atomic levels. This paper provides a review of this and other innovative computational methods used for solving pharmaceutical problems throughout the drug development process. Part one of two this paper will emphasize the role of computational methods and game theory in solving pharmaceutical challenges.

Innovative Computational Methods For Pharmaceutical Problem Solving A Review Part Ii: Serious Gaming, Heather R. Campbell, Robert A. Lodder

Pharmaceutical Sciences Faculty Publications

Serious gaming has begun to take a foothold in pharmaceutical problem-solving. Companies such as Akili's Interactive are seeing success in the form of positive clinical trial results and FDA approval of digital therapeutics. Academic researchers have begun exploring novel uses for serious gaming in the way of protein design and more with promising results. This paper provides a review of such topics in addition to topics of game repurposing- repurposing a game originally intended for entertainment into a serious game-such as Minecraft and America's Army. Reviewing these topics this paper shows the utility of serious gaming as a tool for …

Awegnn: Auto-Parametrized Weighted Element-Specific Graph Neural Networks For Molecules., Timothy Szocinski, Duc Duy Nguyen, Guo-Wei Wei

Mathematics Faculty Publications

While automated feature extraction has had tremendous success in many deep learning algorithms for image analysis and natural language processing, it does not work well for data involving complex internal structures, such as molecules. Data representations via advanced mathematics, including algebraic topology, differential geometry, and graph theory, have demonstrated superiority in a variety of biomolecular applications, however, their performance is often dependent on manual parametrization. This work introduces the auto-parametrized weighted element-specific graph neural network, dubbed AweGNN, to overcome the obstacle of this tedious parametrization process while also being a suitable technique for automated feature extraction on these internally complex …

Algebraic Graph-Assisted Bidirectional Transformers For Molecular Property Prediction, Dong Chen, Kaifu Gao, Duc Duy Nguyen, Xin Chen, Yi Jiang, Guo-Wei Wei, Feng Pan

Mathematics Faculty Publications

The ability of molecular property prediction is of great significance to drug discovery, human health, and environmental protection. Despite considerable efforts, quantitative prediction of various molecular properties remains a challenge. Although some machine learning models, such as bidirectional encoder from transformer, can incorporate massive unlabeled molecular data into molecular representations via a self-supervised learning strategy, it neglects three-dimensional (3D) stereochemical information. Algebraic graph, specifically, element-specific multiscale weighted colored algebraic graph, embeds complementary 3D molecular information into graph invariants. We propose an algebraic graph-assisted bidirectional transformer (AGBT) framework by fusing representations generated by algebraic graph and bidirectional transformer, as well as …

Mathematical Modeling Of The Candida Albicans Yeast To Hyphal Transition Reveals Novel Control Strategies, David J. Wooten, Jorge Gómez Tejeda Zañudo, David Murrugarra, Austin M. Perry, Anna Dongari-Bagtzoglou, Reinhard Laubenbacher, Clarissa J. Nobile, Réka Albert

Mathematics Faculty Publications

Candida albicans, an opportunistic fungal pathogen, is a significant cause of human infections, particularly in immunocompromised individuals. Phenotypic plasticity between two morphological phenotypes, yeast and hyphae, is a key mechanism by which C. albicans can thrive in many microenvironments and cause disease in the host. Understanding the decision points and key driver genes controlling this important transition and how these genes respond to different environmental signals is critical to understanding how C. albicans causes infections in the host. Here we build and analyze a Boolean dynamical model of the C. albicans yeast to hyphal transition, integrating …

Energy Harvesting Techniques For Internet Of Things (Iot), Teodora Sanislav, George Dan Mois, Sherali Zeadally, Silviu Corneliu Folea

Information Science Faculty Publications

The rapid growth of the Internet of Things (IoT) has accelerated strong interests in the development of low-power wireless sensors. Today, wireless sensors are integrated within IoT systems to gather information in a reliable and practical manner to monitor processes and control activities in areas such as transportation, energy, civil infrastructure, smart buildings, environment monitoring, healthcare, defense, manufacturing, and production. The long-term and self-sustainable operation of these IoT devices must be considered early on when they are designed and implemented. Traditionally, wireless sensors have often been powered by batteries, which, despite allowing low overall system costs, can negatively impact the …

Limitations Of Transformers On Clinical Text Classification, Shang Gao, Mohammed Alawad, Michael Todd Young, John Gounley, Noah Schaefferkoetter, Hong-Jun Yoon, Xiao-Cheng Wu, Eric B. Durbin, Jennifer Doherty, Antoinette Stroup, Linda Coyle, Georgia D. Tourassi

Kentucky Cancer Registry Faculty Publications

Bidirectional Encoder Representations from Transformers (BERT) and BERT-based approaches are the current state-of-the-art in many natural language processing (NLP) tasks; however, their application to document classification on long clinical texts is limited. In this work, we introduce four methods to scale BERT, which by default can only handle input sequences up to approximately 400 words long, to perform document classification on clinical texts several thousand words long. We compare these methods against two much simpler architectures -- a word-level convolutional neural network and a hierarchical self-attention network -- and show that BERT often cannot beat these simpler baselines when classifying …

Non-Transgenic Crispr-Mediated Knockout Of Entire Ergot Alkaloid Gene Clusters In Slow-Growing Asexual Polyploid Fungi, Simona Florea, Jolanta Jaromczyk, Christopher L. Schardl

Computer Science Faculty Publications

The Epichloë species of fungi include seed-borne symbionts (endophytes) of cool-season grasses that enhance plant fitness, although some also produce alkaloids that are toxic to livestock. Selected or mutated toxin-free endophytes can be introduced into forage cultivars for improved livestock performance. Long-read genome sequencing revealed clusters of ergot alkaloid biosynthesis (EAS) genes in Epichloë coenophiala strain e19 from tall fescue (Lolium arundinaceum) and Epichloë hybrida Lp1 from perennial ryegrass (Lolium perenne). The two homeologous clusters in E. coenophiala—a triploid hybrid species—were 196 kb (EAS1) and 75 kb (EAS2), and …

Challenges When Identifying Migration From Geo-Located Twitter Data, Caitrin Armstrong, Ate Poorthuis, Matthew Zook, Derek Ruths, Thomas Soehl

Geography Faculty Publications

Given the challenges in collecting up-to-date, comparable data on migrant populations the potential of digital trace data to study migration and migrants has sparked considerable interest among researchers and policy makers. In this paper we assess the reliability of one such data source that is heavily used within the research community: geolocated tweets. We assess strategies used in previous work to identify migrants based on their geolocation histories. We apply these approaches to infer the travel history of a set of Twitter users who regularly posted geolocated tweets between July 2012 and June 2015. In a second step we hand-code …

Vehicle-Life Interaction In Fog-Enabled Smart Connected And Autonomous Vehicles, Bushra Feroz, Amjad Mehmood, Hafsa Maryam, Sherali Zeadally, Carsten Maple, Munam Ali Shah

Information Science Faculty Publications

Traffic accidents have become a major issue for researchers, academia, government and vehicle manufacturers over the last few years. Many accidents and emergency situations frequently occur on the road. Unfortunately, accidents lead to health injuries, destruction of some infrastructure, bad traffic flow, and more importantly these events cause deaths of hundreds of thousands of people due to not getting treatment in time. Thus, we need to develop an efficient and smart emergency system to ensure the timely arrival of an ambulance service to the place of the accident in order to provide timely medical help to those injured. In addition, …

Literature Retrieval For Precision Medicine With Neural Matching And Faceted Summarization, Jiho Noh, Ramakanth Kavuluru

Institute for Biomedical Informatics Faculty Publications

Information retrieval (IR) for precision medicine (PM) often involves looking for multiple pieces of evidence that characterize a patient case. This typically includes at least the name of a condition and a genetic variation that applies to the patient. Other factors such as demographic attributes, comorbidities, and social determinants may also be pertinent. As such, the retrieval problem is often formulated as ad hoc search but with multiple facets (e.g., disease, mutation) that may need to be incorporated. In this paper, we present a document reranking approach that combines neural query-document matching and text summarization toward such retrieval scenarios. Our …

A User Study Of A Wearable System To Enhance Bystanders’ Facial Privacy, Alfredo J. Perez, Sherali Zeadally, Scott Griffith, Luis Y. Matos Garcia, Jaouad A. Mouloud

Information Science Faculty Publications

The privacy of users and information are becoming increasingly important with the growth and pervasive use of mobile devices such as wearables, mobile phones, drones, and Internet of Things (IoT) devices. Today many of these mobile devices are equipped with cameras which enable users to take pictures and record videos anytime they need to do so. In many such cases, bystanders’ privacy is not a concern, and as a result, audio and video of bystanders are often captured without their consent. We present results from a user study in which 21 participants were asked to use a wearable system called …

Secure Authentication And Privacy-Preserving Techniques In Vehicular Ad-Hoc Networks (Vanets), Dakshnamoorthy Manivannan, Shafika Showkat Moni, Sherali Zeadally

Computer Science Faculty Publications

In the last decade, there has been growing interest in Vehicular Ad Hoc NETworks (VANETs). Today car manufacturers have already started to equip vehicles with sophisticated sensors that can provide many assistive features such as front collision avoidance, automatic lane tracking, partial autonomous driving, suggestive lane changing, and so on. Such technological advancements are enabling the adoption of VANETs not only to provide safer and more comfortable driving experience but also provide many other useful services to the driver as well as passengers of a vehicle. However, privacy, authentication and secure message dissemination are some of the main issues that …

Integrated Multiparametric Radiomics And Informatics System For Characterizing Breast Tumor Characteristics With The Oncotypedx Gene Assay, Michael A. Jacobs, Christopher B. Umbricht, Vishwa S. Parekh, Riham H. El Khouli, Leslie Cope, Katarzyna J. Macura, Susan Harvey, Antonio C. Wolff

Radiology Faculty Publications

Optimal use of multiparametric magnetic resonance imaging (mpMRI) can identify key MRI parameters and provide unique tissue signatures defining phenotypes of breast cancer. We have developed and implemented a new machine-learning informatic system, termed Informatics Radiomics Integration System (IRIS) that integrates clinical variables, derived from imaging and electronic medical health records (EHR) with multiparametric radiomics (mpRad) for identifying potential risk of local or systemic recurrence in breast cancer patients. We tested the model in patients (n = 80) who had Estrogen Receptor positive disease and underwent OncotypeDX gene testing, radiomic analysis, and breast mpMRI. The IRIS method was trained …

Timing Of Maximal Weight Reduction Following Bariatric Surgery: A Study In Chinese Patients, Ting Xu, Chen Wang, Hongwei Zhang, Xiaodong Han, Weijie Liu, Junfeng Han, Haoyong Yu, Jin Chen, Pin Zhang, Jianzhong Di

Computer Science Faculty Publications

Introduction: Bariatric surgery is a well-received treatment for obesity with maximal weight loss at 12–36 months postoperatively. We investigated the effect of early bariatric surgery on weight reduction of Chinese patients in accordance with their preoperation characteristics.

Materials and Methods: Altogether, 409 patients with obesity from a prospective cohort in a single bariatric center were enrolled retrospectively and evaluated for up to 4 years. Measurements obtained included surgery type, duration of diabetic condition, besides the usual body mass index data tuple. Weight reduction was expressed as percent total weight loss (%TWL) and percent excess weight loss (%EWL).

Results: RYGB or …

Network Architecture For Generating A Labeled Overhead Image, Nathan Jacobs, Scott Workman

Computer Science Faculty Patents

A computer-implemented process is disclosed for generating a labeled overhead image of a geographical area. A plurality of ground level images of the geographical area is retrieved. A ground level feature map is generated, via a ground level convolutional neural network, based on features extracted from the plurality of ground level images. An overhead image of the geographical area is also retrieved. A joint feature map is generated, via an overhead convolutional neural network based on the ground level feature map and features extracted from the plurality of ground level images. Geospatial function values at a plurality of pixels of …

Β-Amyloid And Tau Drive Early Alzheimer's Disease Decline While Glucose Hypometabolism Drives Late Decline, Tyler C. Hammond, Xin Xing, Chris Wang, David Ma, Kwangsik Nho, Paul K. Crane, Fanny Elahi, David A. Ziegler, Gongbo Liang, Qiang Cheng, Lucille M. Yanckello, Nathan Jacobs, Ai-Ling Lin

Sanders-Brown Center on Aging Faculty Publications

Clinical trials focusing on therapeutic candidates that modify β-amyloid (Aβ) have repeatedly failed to treat Alzheimer’s disease (AD), suggesting that Aβ may not be the optimal target for treating AD. The evaluation of Aβ, tau, and neurodegenerative (A/T/N) biomarkers has been proposed for classifying AD. However, it remains unclear whether disturbances in each arm of the A/T/N framework contribute equally throughout the progression of AD. Here, using the random forest machine learning method to analyze participants in the Alzheimer’s Disease Neuroimaging Initiative dataset, we show that A/T/N biomarkers show varying importance in predicting AD development, with elevated biomarkers of Aβ …

Recent Shrinkage And Fragmentation Of Bluegrass Landscape In Kentucky, Bo Tao, Yanjun Yang, Jia Yang, S. Ray Smith, James F. Fox, Alex C. Ruane, Jinze Liu, Wei Ren

Plant and Soil Sciences Faculty Publications

The Bluegrass Region is an area in north-central Kentucky with unique natural and cultural significance, which possesses some of the most fertile soils in the world. Over recent decades, land use and land cover changes have threatened the protection of the unique natural, scenic, and historic resources in this region. In this study, we applied a fragmentation model and a set of landscape metrics together with the satellite-derived USDA Cropland Data Layer to examine the shrinkage and fragmentation of grassland in the Bluegrass Region, Kentucky during 2008–2018. Our results showed that recent land use change across the Bluegrass Region is …

Interactive Free-Viewpoint Video Generation, Yanru Wang, Zhihao Huang, Hao Zhu, Wei Li, Xun Cao, Ruigang Yang

Computer Science Faculty Publications

Background

Free-viewpoint video (FVV) is processed video content in which viewers can freely select the viewing position and angle. FVV delivers an improved visual experience and can also help synthesize special effects and virtual reality content. In this paper, a complete FVV system is proposed to interactively control the viewpoints of video relay programs through multimedia terminals such as computers and tablets.

Methods

The hardware of the FVV generation system is a set of synchronously controlled cameras, and the software generates videos in novel viewpoints from the captured video using view interpolation. The interactive interface is designed to visualize the …

Hierarchical Clustering Analyses Of Plasma Proteins In Subjects With Cardiovascular Risk Factors Identify Informative Subsets Based On Differential Levels Of Angiogenic And Inflammatory Biomarkers, Zachary Winder, Tiffany L. Sudduth, David W. Fardo, Qiang Cheng, Larry B. Goldstein, Peter T. Nelson, Frederick A. Schmitt, Gregory A. Jicha, Donna M. Wilcock

Sanders-Brown Center on Aging Faculty Publications

Agglomerative hierarchical clustering analysis (HCA) is a commonly used unsupervised machine learning approach for identifying informative natural clusters of observations. HCA is performed by calculating a pairwise dissimilarity matrix and then clustering similar observations until all observations are grouped within a cluster. Verifying the empirical clusters produced by HCA is complex and not well studied in biomedical applications. Here, we demonstrate the comparability of a novel HCA technique with one that was used in previous biomedical applications while applying both techniques to plasma angiogenic (FGF, FLT, PIGF, Tie-2, VEGF, VEGF-D) and inflammatory (MMP1, MMP3, MMP9, IL8, TNFα) protein data to …

Harnessing Artificial Intelligence Capabilities To Improve Cybersecurity, Sherali Zeadally, Erwin Adi, Zubair Baig, Imran A. Khan

Information Science Faculty Publications

Cybersecurity is a fast-evolving discipline that is always in the news over the last decade, as the number of threats rises and cybercriminals constantly endeavor to stay a step ahead of law enforcement. Over the years, although the original motives for carrying out cyberattacks largely remain unchanged, cybercriminals have become increasingly sophisticated with their techniques. Traditional cybersecurity solutions are becoming inadequate at detecting and mitigating emerging cyberattacks. Advances in cryptographic and Artificial Intelligence (AI) techniques (in particular, machine learning and deep learning) show promise in enabling cybersecurity experts to counter the ever-evolving threat posed by adversaries. Here, we explore AI's …

Enhancing Timeliness Of Drug Overdose Mortality Surveillance: A Machine Learning Approach, Patrick J. Ward, Peter J. Rock, Svetla Slavova, April M. Young, Terry L. Bunn, Ramakanth Kavuluru

Kentucky Injury Prevention and Research Center Faculty Publications

BACKGROUND: Timely data is key to effective public health responses to epidemics. Drug overdose deaths are identified in surveillance systems through ICD-10 codes present on death certificates. ICD-10 coding takes time, but free-text information is available on death certificates prior to ICD-10 coding. The objective of this study was to develop a machine learning method to classify free-text death certificates as drug overdoses to provide faster drug overdose mortality surveillance.

METHODS: Using 2017–2018 Kentucky death certificate data, free-text fields were tokenized and features were created from these tokens using natural language processing (NLP). Word, bigram, and trigram features were created …

Influence Spread In Two-Layer Interdependent Networks: Designed Single-Layer Or Random Two-Layer Initial Spreaders?, Hana Khamfroush, Nathaniel Hudson, Samuel Iloo, Mahshid R. Naeini

Computer Science Faculty Publications

Influence spread in multi-layer interdependent networks (M-IDN) has been studied in the last few years; however, prior works mostly focused on the spread that is initiated in a single layer of an M-IDN. In real world scenarios, influence spread can happen concurrently among many or all components making up the topology of an M-IDN. This paper investigates the effectiveness of different influence spread strategies in M-IDNs by providing a comprehensive analysis of the time evolution of influence propagation given different initial spreader strategies. For this study we consider a two-layer interdependent network and a general probabilistic threshold influence spread model …

From Invisibility To Readability: Recovering The Ink Of Herculaneum, Clifford Seth Parker, Stephen Parsons, Jack Bandy, Christy Chapman, Frederik Coppens, William Brent Seales

Computer Science Faculty Publications

The noninvasive digital restoration of ancient texts written in carbon black ink and hidden inside artifacts has proven elusive, even with advanced imaging techniques like x-ray-based micro-computed tomography (micro-CT). This paper identifies a crucial mistaken assumption: that micro-CT data fails to capture any information representing the presence of carbon ink. Instead, we show new experiments indicating a subtle but detectable signature from carbon ink in micro-CT. We demonstrate a new computational approach that captures, enhances, and makes visible the characteristic signature created by carbon ink in micro-CT. This previously "unseen" evidence of carbon inks, which can now successfully be made …

Sensitive Research, Practice And Design In Hci, Stevie Chancellor, Nazanin Andalibi, Lindsay Blackwell, David Nemer, Wendy Moncur

Information Science Faculty Publications

New research areas in HCI examine complex and sensitive research areas, such as crisis, life transitions, and mental health. Further, research in complex topics such as harassment and graphic content can leave researchers vulnerable to emotional and physical harm. There is a need to bring researchers together to discuss challenges across sensitive research spaces and environments. We propose a workshop to explore the methodological, ethical, and emotional challenges of sensitive research in HCI. We will actively recruit from diverse research environments (industry, academia, government, etc.) and methods areas (qualitative, quantitative, design practices, etc.) and identify commonalities in and encourage relationship-building …