Engineering Commons^™

Language Models For Rare Disease Information Extraction: Empirical Insights And Model Comparisons, Shashank Gupta

Theses and Dissertations--Computer Science

End-to-end relation extraction (E2ERE) is a crucial task in natural language processing (NLP) that involves identifying and classifying semantic relationships between entities in text. This thesis compares three paradigms for end-to-end relation extraction (E2ERE) in biomedicine, focusing on rare diseases with discontinuous and nested entities. We evaluate Named Entity Recognition (NER) to Relation Extraction (RE) pipelines, sequence-to-sequence models, and generative pre-trained transformer (GPT) models using the RareDis information extraction dataset. Our findings indicate that pipeline models are the most effective, followed closely by sequence-to-sequence models. GPT models, despite having eight times as many parameters, perform worse than sequence-to-sequence models and …

Machine-Learning-Powered Cyber-Physical Systems, Enrico Casella

Theses and Dissertations--Computer Science

In the last few years, we witnessed the revolution of the Internet of Things (IoT) paradigm and the consequent growth of Cyber-Physical Systems (CPSs). IoT devices, which include a plethora of smart interconnected sensors, actuators, and microcontrollers, have the ability to sense physical phenomena occurring in an environment and provide copious amounts of heterogeneous data about the functioning of a system. As a consequence, the large amounts of generated data represent an opportunity to adopt artificial intelligence and machine learning techniques that can be used to make informed decisions aimed at the optimization of such systems, thus enabling a variety …

A Secure And Distributed Architecture For Vehicular Cloud And Protocols For Privacy-Preserving Message Dissemination In Vehicular Ad Hoc Networks, Hassan Mistareehi

Theses and Dissertations--Computer Science

Given the enormous interest in self-driving cars, Vehicular Ad hoc NETworks (VANETs) are likely to be widely deployed in the near future. Cloud computing is also gaining widespread deployment. Marriage between cloud computing and VANETs would help solve many of the needs of drivers, law enforcement agencies, traffic management, etc. The contributions of this dissertation are summarized as follows: A Secure and Distributed Architecture for Vehicular Cloud: Ensuring security and privacy is an important issue in the vehicular cloud; if information exchanged between entities is modified by a malicious vehicle, serious consequences such as traffic congestion and accidents can …

Personalized Point Of Interest Recommendations With Privacy-Preserving Techniques, Longyin Cui

Theses and Dissertations--Computer Science

Location-based services (LBS) have become increasingly popular, with millions of people using mobile devices to access information about nearby points of interest (POIs). Personalized POI recommender systems have been developed to assist users in discovering and navigating these POIs. However, these systems typically require large amounts of user data, including location history and preferences, to provide personalized recommendations.

The collection and use of such data can pose significant privacy concerns. This dissertation proposes a privacy-preserving approach to POI recommendations that address these privacy concerns. The proposed approach uses clustering, tabular generative adversarial networks, and differential privacy to generate synthetic user …

Deep Learning-Based Intrusion Detection Methods For Computer Networks And Privacy-Preserving Authentication Method For Vehicular Ad Hoc Networks, Ayesha Dina

Theses and Dissertations--Computer Science

The incidence of computer network intrusions has significantly increased over the last decade, partially attributed to a thriving underground cyber-crime economy and the widespread availability of advanced tools for launching such attacks. To counter these attacks, researchers in both academia and industry have turned to machine learning (ML) techniques to develop Intrusion Detection Systems (IDSes) for computer networks. However, many of the datasets use to train ML classifiers for detecting intrusions are not balanced, with some classes having fewer samples than others. This can result in ML classifiers producing suboptimal results. In this dissertation, we address this issue and present …

Peer-To-Peer Energy Trading In Smart Residential Environment With User Behavioral Modeling, Ashutosh Timilsina

Theses and Dissertations--Computer Science

Electric power systems are transforming from a centralized unidirectional market to a decentralized open market. With this shift, the end-users have the possibility to actively participate in local energy exchanges, with or without the involvement of the main grid. Rapidly reducing prices for Renewable Energy Technologies (RETs), supported by their ease of installation and operation, with the facilitation of Electric Vehicles (EV) and Smart Grid (SG) technologies to make bidirectional flow of energy possible, has contributed to this changing landscape in the distribution side of the traditional power grid.

Trading energy among users in a decentralized fashion has been referred …

Multi-Agent Learning For Game-Theoretical Problems, Kshitija Taywade

Theses and Dissertations--Computer Science

Multi-agent systems are prevalent in the real world in various domains. In many multi-agent systems, interaction among agents is inevitable, and cooperation in some form is needed among agents to deal with the task at hand. We model the type of multi-agent systems where autonomous agents inhabit an environment with no global control or global knowledge, decentralized in the true sense. In particular, we consider game-theoretical problems such as the hedonic coalition formation games, matching problems, and Cournot games. We propose novel decentralized learning and multi-agent reinforcement learning approaches to train agents in learning behaviors and adapting to the environments. …

Hard-Hearted Scrolls: A Noninvasive Method For Reading The Herculaneum Papyri, Stephen Parsons

Theses and Dissertations--Computer Science

The Herculaneum scrolls were buried and carbonized by the eruption of Mount Vesuvius in A.D. 79 and represent the only classical library discovered in situ. Charred by the heat of the eruption, the scrolls are extremely fragile. Since their discovery two centuries ago, some scrolls have been physically opened, leading to some textual recovery but also widespread damage. Many other scrolls remain in rolled form, with unknown contents. More recently, various noninvasive methods have been attempted to reveal the hidden contents of these scrolls using advanced imaging. Unfortunately, their complex internal structure and lack of clear ink contrast has prevented …

Image Geo-Localization With Cross-Attention, Connor Greenwell

Theses and Dissertations--Computer Science

The problem of estimating the location from which un-geotagged photographs were captured has been well studied by the computer vision community in recent years. The central proposal of this thesis is to define a common framework within which existing approaches can be constructed and evaluated, and to introduce a new method under this framework which uses cross-attention between the query image and a database of satellite imagery with known geotags. Our experiments fit within three broad categories: 1) evaluating the ability of image localization approaches to generalize to unseen regions; 2) examining performance changes under various reference database resolutions, scales, …

Design, Development And Benchmarking Of Machine Learning Algorithms In Biomedical Applications, Qi Sun

Theses and Dissertations--Computer Science

Machine learning algorithms are becoming the most effective methods for knowledge discovery from high dimensional datasets. Machine learning seeks to construct predictive models through the analysis of large-scale heterogeneous data. While machine learning has been widely used in many domains including computer vision, natural language processing, product recommendation, its application in biomedical science for clinical diagnosis and treatment is only emerging. However, the wealthy amount of data in the biomedical domain offers not only challenges but also opportunities for machine learning. In this dissertation, we focus on three biomedical applications from vastly different domains to understand the opportunities and challenges …

Improving Network Policy Enforcement Using Natural Language Processing And Programmable Networks, Pinyi Shi

Theses and Dissertations--Computer Science

Computer networks are becoming more complex and challenging to operate, manage, and protect. As a result, Network policies that define how network operators should manage the network are becoming more complex and nuanced. Unfortunately, network policies are often an undervalued part of network design, leaving network operators to guess at the intent of policies that are written and fill in the gaps where policies don’t exist. Organizations typically designate Policy Committees to write down the network policies in the policy documents using high-level natural languages. The policy documents describe both the acceptable and unacceptable uses of the network. Network operators …

Protocols And Architecture For Privacy-Preserving Authentication And Secure Message Dissemination In Vehicular Ad Hoc Networks, Shafika Showkat Moni

Theses and Dissertations--Computer Science

The rapid development in the automotive industry and wireless communication technologies have enhanced the popularity of Vehicular ad hoc networks (VANETs). Today, the automobile industry is developing sophisticated sensors that can provide a wide range of assistive features, including accident avoidance, automatic lane tracking, semi-autonomous driving, suggested lane changes, and more. VANETs can provide drivers a safer and more comfortable driving experience, as well as many other useful services by leveraging such technological advancements. Even though this networking technology enables smart and autonomous driving, it also introduces a plethora of attack vectors. However, the main issues to be sorted out …

An Automated Framework To Debug System-Level Concurrency Failures, Tarannum Shaila Zaman

Theses and Dissertations--Computer Science

The ever-increasing parallelism in computer systems has made software more prone to concurrency failures, causing problems during both pre- and post-development. Debugging concurrent programs is difficult because of the non-deterministic behavior and the specific sequences of interleaving in the execution flow. Debugging is a technique where programmers reproduce the bug, identify the root cause, and then take necessary steps to remove the bug from the system. The failure information may come from the bug reports of the testing phase or the production runs. In both cases, there should be steps taken to reproduce and localize the failure. However, reproducing and …

Scalable Approaches For Auditing The Completeness Of Biomedical Ontologies, Fengbo Zheng

Theses and Dissertations--Computer Science

An ontology provides a formalized representation of knowledge within a domain. In biomedicine, ontologies have been widely used in modern biomedical applications to enable semantic interoperability and facilitate data exchange. Given the important roles that biomedical ontologies play, quality issues such as incompleteness, if not addressed, can affect the quality of downstream ontology-driven applications. However, biomedical ontologies often have large sizes and complex structures. Thus, it is infeasible to uncover potential quality issues through manual effort. In this dissertation, we introduce automated and scalable approaches for auditing the completeness of biomedical ontologies. We mainly focus on two incompleteness issues -- …

Routing And Applications Of Vehicular Named Data Networking, Bassma G. Aldahlan

Theses and Dissertations--Computer Science

Vehicular Ad hoc NETwork (VANET) allows vehicles to exchange important informationamong themselves and has become a critical component for enabling smart transportation.In VANET, vehicles are more interested in content itself than from which vehicle the contentis originated. Named Data Networking (NDN) is an Internet architecture that concentrateson what the content is rather than where the content is located. We adopt NDN as theunderlying communication paradigm for VANET because it can better address a plethora ofproblems in VANET, such as frequent disconnections and fast mobility of vehicles. However,vehicular named data networking faces the problem of how to efficiently route interestpackets and …

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 …

Automated Testing And Bug Reproduction Of Android Apps, Yu Zhao

Theses and Dissertations--Computer Science

The large demand of mobile devices creates significant concerns about the quality of mobile applications (apps). The corresponding increase in app complexity has made app testing and maintenance activities more challenging. During app development phase, developers need to test the app in order to guarantee its quality before releasing it to the market. During the deployment phase, developers heavily rely on bug reports to reproduce failures reported by users. Because of the rapid releasing cycle of apps and limited human resources, it is difficult for developers to manually construct test cases for testing the apps or diagnose failures from a …

Metadata Management For Clinical Data Integration, Ningzhou Zeng

Theses and Dissertations--Computer Science

Clinical data have been continuously collected and growing with the wide adoption of electronic health records (EHR). Clinical data have provided the foundation to facilitate state-of-art researches such as artificial intelligence in medicine. At the same time, it has become a challenge to integrate, access, and explore study-level patient data from large volumes of data from heterogeneous databases. Effective, fine-grained, cross-cohort data exploration, and semantically enabled approaches and systems are needed. To build semantically enabled systems, we need to leverage existing terminology systems and ontologies. Numerous ontologies have been developed recently and they play an important role in semantically enabled …

Algorithms For Achieving Fault-Tolerance And Ensuring Security In Cloud Computing Systems, Md. Tariqul Islam

Theses and Dissertations--Computer Science

Security and fault tolerance are the two major areas in cloud computing systems that need careful attention for its widespread deployment. Unlike supercomputers, cloud clusters are mostly built on low cost, unreliable, commodity hardware. Therefore, large-scale cloud systems often suffer from performance degradation, service outages, and sometimes node and application failures. On the other hand, the multi-tenant shared architecture, dynamism, heterogeneity, and openness of cloud computing make it susceptible to various security threats and vulnerabilities. In this dissertation, we analyze these problems and propose algorithms for achieving fault tolerance and ensuring security in cloud computing systems.

First, we perform a …

Image-Based Roadway Assessment Using Convolutional Neural Networks, Weilian Song

Theses and Dissertations--Computer Science

Road crashes are one of the main causes of death in the United States. To reduce the number of accidents, roadway assessment programs take a proactive approach, collecting data and identifying high-risk roads before crashes occur. However, the cost of data acquisition and manual annotation has restricted the effect of these programs. In this thesis, we propose methods to automate the task of roadway safety assessment using deep learning. Specifically, we trained convolutional neural networks on publicly available roadway images to predict safety-related metrics: the star rating score and free-flow speed. Inference speeds for our methods are mere milliseconds, enabling …

A Diverse Band-Aware Dynamic Spectrum Access Architecture For Connectivity In Rural Communities, Vijay K. Shah

Theses and Dissertations--Computer Science

Ubiquitous connectivity plays an important role in improving the quality of life in terms of economic development, health and well being, social justice and equity, as well as in providing new educational opportunities. However, rural communities which account for 46% of the world's population lacks access to proper connectivity to avail such societal benefits, creating a huge "digital divide" between the urban and rural areas. A primary reason is that the Information and Communication Technologies (ICT) providers have less incentives to invest in rural areas due to lack of promising revenue returns. Existing research and industrial attempts in providing connectivity …

Novel Applications Of Machine Learning In Bioinformatics, Yi Zhang

Theses and Dissertations--Computer Science

Technological advances in next-generation sequencing and biomedical imaging have led to a rapid increase in biomedical data dimension and acquisition rate, which is challenging the conventional data analysis strategies. Modern machine learning techniques promise to leverage large data sets for finding hidden patterns within them, and for making accurate predictions. This dissertation aims to design novel machine learning-based models to transform biomedical big data into valuable biological insights. The research presented in this dissertation focuses on three bioinformatics domains: splice junction classification, gene regulatory network reconstruction, and lesion detection in mammograms.

A critical step in defining gene structures and mRNA …

Automated Network Security With Exceptions Using Sdn, Sergio A. Rivera Polanco

Theses and Dissertations--Computer Science

Campus networks have recently experienced a proliferation of devices ranging from personal use devices (e.g. smartphones, laptops, tablets), to special-purpose network equipment (e.g. firewalls, network address translation boxes, network caches, load balancers, virtual private network servers, and authentication servers), as well as special-purpose systems (badge readers, IP phones, cameras, location trackers, etc.). To establish directives and regulations regarding the ways in which these heterogeneous systems are allowed to interact with each other and the network infrastructure, organizations typically appoint policy writing committees (PWCs) to create acceptable use policy (AUP) documents describing the rules and behavioral guidelines that all campus network …

Metadata-Based Image Collecting And Databasing For Sharing And Analysis, Xi Wu

Theses and Dissertations--Computer Science

Data collecting and preparing is generally considered a crucial process in data science projects. Especially for image data, adding semantic attributes when preparing image data provides much more insights for data scientists. In this project, we aim to implement a general-purpose central image data repository that allows image researchers to collect data with semantic properties as well as data query. One of our researchers has come up with the specific challenge of collecting images with weight data of infants in least developed countries with limited internet access. The rationale is to predict infant weights based on image data by applying …

Relation Prediction Over Biomedical Knowledge Bases For Drug Repositioning, Mehmet Bakal

Theses and Dissertations--Computer Science

Identifying new potential treatment options for medical conditions that cause human disease burden is a central task of biomedical research. Since all candidate drugs cannot be tested with animal and clinical trials, in vitro approaches are first attempted to identify promising candidates. Likewise, identifying other essential relations (e.g., causation, prevention) between biomedical entities is also critical to understand biomedical processes. Hence, it is crucial to develop automated relation prediction systems that can yield plausible biomedical relations to expedite the discovery process. In this dissertation, we demonstrate three approaches to predict treatment relations between biomedical entities for the drug repositioning task …

Depth Enhancement And Surface Reconstruction With Rgb/D Sequence, Xinxin Zuo

Theses and Dissertations--Computer Science

Surface reconstruction and 3D modeling is a challenging task, which has been explored for decades by the computer vision, computer graphics, and machine learning communities. It is fundamental to many applications such as robot navigation, animation and scene understanding, industrial control and medical diagnosis. In this dissertation, I take advantage of the consumer depth sensors for surface reconstruction. Considering its limited performance on capturing detailed surface geometry, a depth enhancement approach is proposed in the first place to recovery small and rich geometric details with captured depth and color sequence. In addition to enhancing its spatial resolution, I present a …

Interactive Clinical Event Pattern Mining And Visualization Using Insurance Claims Data, Zhenhui Piao

Theses and Dissertations--Computer Science

With exponential growth on a daily basis, there is potentially valuable information hidden in complex electronic medical records (EMR) systems. In this thesis, several efficient data mining algorithms were explored to discover hidden knowledge in insurance claims data. The first aim was to cluster three levels of information overload(IO) groups among chronic rheumatic disease (CRD) patient groups based on their clinical events extracted from insurance claims data. The second aim was to discover hidden patterns using three renowned pattern mining algorithms: Apriori, frequent pattern growth(FP-Growth), and sequential pattern discovery using equivalence classes(SPADE). The SPADE algorithm was found to be the …

3d Human Face Reconstruction And 2d Appearance Synthesis, Yajie Zhao

Theses and Dissertations--Computer Science

3D human face reconstruction has been an extensive research for decades due to its wide applications, such as animation, recognition and 3D-driven appearance synthesis. Although commodity depth sensors are widely available in recent years, image based face reconstruction are significantly valuable as images are much easier to access and store.

In this dissertation, we first propose three image-based face reconstruction approaches according to different assumption of inputs.

In the first approach, face geometry is extracted from multiple key frames of a video sequence with different head poses. The camera should be calibrated under this assumption.

As the first approach is …

Retail Data Analytics Using Graph Database, Rashmi Priya

Theses and Dissertations--Computer Science

Big data is an area focused on storing, processing and visualizing huge amount of data. Today data is growing faster than ever before. We need to find the right tools and applications and build an environment that can help us to obtain valuable insights from the data. Retail is one of the domains that collects huge amount of transaction data everyday. Retailers need to understand their customer’s purchasing pattern and behavior in order to take better business decisions.

Market basket analysis is a field in data mining, that is focused on discovering patterns in retail’s transaction data. Our goal is …

Automated Tree-Level Forest Quantification Using Airborne Lidar, Hamid Hamraz

Theses and Dissertations--Computer Science

Traditional forest management relies on a small field sample and interpretation of aerial photography that not only are costly to execute but also yield inaccurate estimates of the entire forest in question. Airborne light detection and ranging (LiDAR) is a remote sensing technology that records point clouds representing the 3D structure of a forest canopy and the terrain underneath. We present a method for segmenting individual trees from the LiDAR point clouds without making prior assumptions about tree crown shapes and sizes. We then present a method that vertically stratifies the point cloud to an overstory and multiple understory tree …