Physical Sciences and Mathematics Commons^™

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 …

Multi-Modal Medical Imaging Analysis With Modern Neural Networks, Gongbo Liang

Theses and Dissertations--Computer Science

Medical imaging is an important non-invasive tool for diagnostic and treatment purposes in medical practice. However, interpreting medical images is a time consuming and challenging task. Computer-aided diagnosis (CAD) tools have been used in clinical practice to assist medical practitioners in medical imaging analysis since the 1990s. Most of the current generation of CADs are built on conventional computer vision techniques, such as manually defined feature descriptors. Deep convolutional neural networks (CNNs) provide robust end-to-end methods that can automatically learn feature representations. CNNs are a promising building block of next-generation CADs. However, applying CNNs to medical imaging analysis tasks is …

“Distance Learning” In The Ninth Century?: Micro-Cluster Analysis Of The Epistolary Network Of Alcuin After 796, William James Mattingly

Theses and Dissertations--History

Scholars of eighth- and ninth-century education have assumed that intellectuals did not write works of Scriptural interpretation until that intellectual had a firm foundation in the seven liberal arts.This ensured that anyone who embarked on work of Scriptural interpretation would have the required knowledge and methods to read and interpret Scripture correctly. The potential for theological error and the transmission of those errors was too great unless the interpreter had the requisite training. This dissertation employs computistical methods, specifically the techniques of social network mapping and cluster analysis, to study closely the correspondence of Alcuin, a late-eighth- and early-ninth-century scholar …

Estimating Free-Flow Speed With Lidar And Overhead Imagery, Armin Hadzic

Theses and Dissertations--Computer Science

Understanding free-flow speed is fundamental to transportation engineering in order to improve traffic flow, control, and planning. The free-flow speed of a road segment is the average speed of automobiles unaffected by traffic congestion or delay. Collecting speed data across a state is both expensive and time consuming. Some approaches have been presented to estimate speed using geometric road features for certain types of roads in limited environments. However, estimating speed at state scale for varying landscapes, environments, and road qualities has been relegated to manual engineering and expensive sensor networks. This thesis proposes an automated approach for estimating free-flow …

Deep Neural Architectures For End-To-End Relation Extraction, Tung Tran

Theses and Dissertations--Computer Science

The rapid pace of scientific and technological advancements has led to a meteoric growth in knowledge, as evidenced by a sharp increase in the number of scholarly publications in recent years. PubMed, for example, archives more than 30 million biomedical articles across various domains and covers a wide range of topics including medicine, pharmacy, biology, and healthcare. Social media and digital journalism have similarly experienced their own accelerated growth in the age of big data. Hence, there is a compelling need for ways to organize and distill the vast, fragmented body of information (often unstructured in the form of natural …

Fault Identification On Electrical Transmission Lines Using Artificial Neural Networks, Christopher W. Asbery

Theses and Dissertations--Electrical and Computer Engineering

Transmission lines are designed to transport large amounts of electrical power from the point of generation to the point of consumption. Since transmission lines are built to span over long distances, they are frequently exposed to many different situations that can cause abnormal conditions known as electrical faults. Electrical faults, when isolated, can cripple the transmission system as power flows are directed around these faults therefore leading to other numerous potential issues such as thermal and voltage violations, customer interruptions, or cascading events. When faults occur, protection systems installed near the faulted transmission lines will isolate these faults from the …

Structural And Lexical Methods For Auditing Biomedical Terminologies, Rashmie Abeysinghe

Theses and Dissertations--Computer Science

Biomedical terminologies serve as knowledge sources for a wide variety of biomedical applications including information extraction and retrieval, data integration and management, and decision support. Quality issues of biomedical terminologies, if not addressed, could affect all downstream applications that use them as knowledge sources. Therefore, Terminology Quality Assurance (TQA) has become an integral part of the terminology management lifecycle. However, identification of potential quality issues is challenging due to the ever-growing size and complexity of biomedical terminologies. It is time-consuming and labor-intensive to manually audit them and hence, automated TQA methods are highly desirable. In this dissertation, systematic and scalable …

Temporal Data Extraction And Query System For Epilepsy Signal Analysis, Yan Huang

Theses and Dissertations--Computer Science

The 2016 Epilepsy Innovation Institute (Ei2) community survey reported that unpredictability is the most challenging aspect of seizure management. Effective and precise detection, prediction, and localization of epileptic seizures is a fundamental computational challenge. Utilizing epilepsy data from multiple epilepsy monitoring units can enhance the quantity and diversity of datasets, which can lead to more robust epilepsy data analysis tools. The contributions of this dissertation are two-fold. One is the implementation of a temporal query for epilepsy data; the other is the machine learning approach for seizure detection, seizure prediction, and seizure localization. The three key components of our temporal …

A Comparative Analysis Of Reinforcement Learning Applied To Task-Space Reaching With A Robotic Manipulator With And Without Gravity Compensation, Jonathan Fugal

Theses and Dissertations--Electrical and Computer Engineering

Advances in computing power in recent years have facilitated developments in autonomous robotic systems. These robotic systems can be used in prosthetic limbs, wearhouse packaging and sorting, assembly line production, as well as many other applications. Designing these autonomous systems typically requires robotic system and world models (for classical control based strategies) or time consuming and computationally expensive training (for learning based strategies). Often these requirements are difficult to fulfill. There are ways to combine classical control and learning based strategies that can mitigate both requirements. One of these ways is to use a gravity compensated torque control with reinforcement …

Text Mining Methods For Analyzing Online Health Information And Communication, Sifei Han

Theses and Dissertations--Computer Science

The Internet provides an alternative way to share health information. Specifically, social network systems such as Twitter, Facebook, Reddit, and disease specific online support forums are increasingly being used to share information on health related topics. This could be in the form of personal health information disclosure to seek suggestions or answering other patients' questions based on their history. This social media uptake gives a new angle to improve the current health communication landscape with consumer generated content from social platforms. With these online modes of communication, health providers can offer more immediate support to the people seeking advice. Non-profit …

Orthogonal Recurrent Neural Networks And Batch Normalization In Deep Neural Networks, Kyle Eric Helfrich

Theses and Dissertations--Mathematics

Despite the recent success of various machine learning techniques, there are still numerous obstacles that must be overcome. One obstacle is known as the vanishing/exploding gradient problem. This problem refers to gradients that either become zero or unbounded. This is a well known problem that commonly occurs in Recurrent Neural Networks (RNNs). In this work we describe how this problem can be mitigated, establish three different architectures that are designed to avoid this issue, and derive update schemes for each architecture. Another portion of this work focuses on the often used technique of batch normalization. Although found to be successful …

Unitary And Symmetric Structure In Deep Neural Networks, Kehelwala Dewage Gayan Maduranga

Theses and Dissertations--Mathematics

Recurrent neural networks (RNNs) have been successfully used on a wide range of sequential data problems. A well-known difficulty in using RNNs is the vanishing or exploding gradient problem. Recently, there have been several different RNN architectures that try to mitigate this issue by maintaining an orthogonal or unitary recurrent weight matrix. One such architecture is the scaled Cayley orthogonal recurrent neural network (scoRNN), which parameterizes the orthogonal recurrent weight matrix through a scaled Cayley transform. This parametrization contains a diagonal scaling matrix consisting of positive or negative one entries that can not be optimized by gradient descent. Thus the …