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2023

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Articles 4411 - 4440 of 9781

Full-Text Articles in Engineering

A Graph-Based Approach For Adaptive Serious Games, Nidhi G. Patel May 2023

A Graph-Based Approach For Adaptive Serious Games, Nidhi G. Patel

Theses and Dissertations

Traditional education systems are based on the one-size-fits-all approach, which lacks personalization, engagement, and flexibility necessary to meet the diverse needs and learning styles of students. This encouraged researchers to focus on exploring automated, personalized instructional systems to enhance students’ learning experiences. Motivated by this remark, this thesis proposes a personalized instructional system using a graph method to enhance a player’s learning process by preventing frustration and avoiding a monotonous experience. Our system uses a directional graph, called an action graph, for representing solutions to in-game problems based on possible player actions. Through our proposed algorithm, a serious game integrated …


Method Of Evanescently Coupling Whispering Gallery Mode Optical Resonators Using Liquids, Hengky Chandrahalim, Kyle T. Bodily May 2023

Method Of Evanescently Coupling Whispering Gallery Mode Optical Resonators Using Liquids, Hengky Chandrahalim, Kyle T. Bodily

AFIT Patents

The present invention relates to evanescently coupling whispering gallery mode optical resonators having a liquid coupling as well as methods of making and using same. The aforementioned evanescently coupling whispering gallery mode optical resonators having a liquid couplings provide increased tunability and sensing selectivity over current same. The aforementioned. Applicants’ method of making evanescent-wave coupled optical resonators can be achieved while having coupling gap dimensions that can be fabricated using standard photolithography. Thus economic, rapid, and mass production of coupled WGM resonators-based lasers, sensors, and signal processors for a broad range of applications can be realized.


Targeted Adversarial Attacks Against Neural Network Trajectory Predictors, Kaiyuan Tan May 2023

Targeted Adversarial Attacks Against Neural Network Trajectory Predictors, Kaiyuan Tan

McKelvey School of Engineering Graduate Student Theses & Dissertations

Trajectory prediction is an integral component of modern autonomous systems as it allows for envisioning future intentions of nearby moving agents. Due to the lack of other agents' dynamics and control policies, deep neural network (DNN) models are often employed for trajectory forecasting tasks. Although there exists an extensive literature on improving the accuracy of these models, there is a very limited number of works studying their robustness against adversarially crafted input trajectories. To bridge this gap, in this paper, we propose a targeted adversarial attack against DNN models for trajectory forecasting tasks. We call the proposed attack TA4TP for …


Real-Time Suitable Predictive Control Using Spat Information From Automated Traffic Lights, Pradeep Bhat, Bo Chen May 2023

Real-Time Suitable Predictive Control Using Spat Information From Automated Traffic Lights, Pradeep Bhat, Bo Chen

Michigan Tech Publications

Traffic intersections throughout the United States combine fixed, semi-actuated, and fully actuated intersections. In the case of the semi-actuated and actuated intersections, uncertainties are considered in phase duration. These uncertainties are due to car waiting queues and pedestrian crossing. Intelligent transportation systems deployed in traffic infrastructure can communicate Signal and Phase Timing messages (SPaT) to vehicles approaching intersections. In the connected and automated vehicle ecosystem, the fuel savings potential has been explored. Prior studies have predominantly focused on fixed time control for the driver. However, in the case of actuated signals, there is a different and significant challenge due to …


High-Throughput Phenotyping Of Plant Leaf Morphological, Physiological, And Biochemical Traits On Multiple Scales Using Optical Sensing, Huichun Zhang, Lu Wang, Xiuliang Jin, Liming Bian, Yufeng Ge May 2023

High-Throughput Phenotyping Of Plant Leaf Morphological, Physiological, And Biochemical Traits On Multiple Scales Using Optical Sensing, Huichun Zhang, Lu Wang, Xiuliang Jin, Liming Bian, Yufeng Ge

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Acquisition of plant phenotypic information facilitates plant breeding, sheds light on gene action, and can be applied to optimize the quality of agricultural and forestry products. Because leaves often show the fastest responses to external environmental stimuli, leaf phenotypic traits are indicators of plant growth, health, and stress levels. Combination of new imaging sensors, image processing, and data analytics permits measurement over the full life span of plants at high temporal resolution and at several organizational levels from organs to individual plants to field populations of plants. We review the optical sensors and associated data analytics used for measuring morphological, …


Evaluation Of Temperature-Index And Energy-Balance Snow Models For Hydrological Applications In Operational Water Supply Forecasts, Tian Gan, David G. Tarboton, Tseganeh Z. Gichamo May 2023

Evaluation Of Temperature-Index And Energy-Balance Snow Models For Hydrological Applications In Operational Water Supply Forecasts, Tian Gan, David G. Tarboton, Tseganeh Z. Gichamo

Civil and Environmental Engineering Faculty Publications

In the western United States, snow accumulation, storage, and ablation affect seasonal runoff. Thus, the prediction of snowmelt is essential to improve the reliability of water supply forecasts to guide water allocation and operational decisions. The current method used at the Colorado Basin River Forecast Center (CBRFC) couples the SNOW-17 temperature index snow model and the Sacramento Soil Moisture Accounting (SAC-SMA) runoff model in a lumped approach. Limitations in parameter transferability and calibration requirements for changing conditions with the temperature-index model motivated this research, in which new avenues were investigated to assess and prototype the application of an energy-balance snow …


Modern Practices For Responsive Web Design And Web Accessibility, Keyaun Washington May 2023

Modern Practices For Responsive Web Design And Web Accessibility, Keyaun Washington

Honors Program: Senior Projects (Public)

Responsive web design and web accessibility play crucial roles in ensuring an optimal user experience on the web. By designing websites with responsiveness and accessibility in mind, more opportunities are opened up for a wider audience to access and interact with our content. Through modern practices, responsive web design allows websites to reach several different devices ranging from compact smartwatches to expansive television screens. Designing for accessibility provides accommodations for individuals with impairments while also providing benefits for individuals without impairments. However, designing for responsiveness and accessibility can present challenges; a poor attempt at providing accessibility features can worsen a …


Stump Grinder Project, Wyatt Hopper May 2023

Stump Grinder Project, Wyatt Hopper

Honors Program: Senior Projects (Public)

This project covers the analysis of a Portable Stump Grinder device sponsored by private investors known as Gary and Carol Sherman, two farmers out of Lincoln, Nebraska. The ultimate goal of this project, in terms of the work we were assigned, was to provide the foundation work for future engineering teams to design and build the stump grinder for Gary and Carol Sherman.


Reflectance Quantitative Polarized Light Imaging For Microstructural Evaluation Of Musculoskeletal Soft Tissues, Leanne Elizabeth Iannucci May 2023

Reflectance Quantitative Polarized Light Imaging For Microstructural Evaluation Of Musculoskeletal Soft Tissues, Leanne Elizabeth Iannucci

McKelvey School of Engineering Graduate Student Theses & Dissertations

Musculoskeletal soft tissue injury is common and can lead to debilitating pain, loss of tissue function, and overall decrease in quality of life. Proper biomechanical function of musculoskeletal soft tissues is dictated by their hierarchically organized collagenous extracellular matrices, which are disrupted in periods of disease or injury. To best understand dynamic structure-function relationships of these tissues in normal and pathological conditions, it is imperative to be able to visualize collagen microstructure using a quantitative, high spatiotemporal resolution imaging modality. The innate birefringence associated with collagen fibers permits the use of biomedical polarimetry techniques to probe collagen in a specific …


Confined Growth Of Perovskite Stabilized By Strain Engineering, Xucheng Tao May 2023

Confined Growth Of Perovskite Stabilized By Strain Engineering, Xucheng Tao

McKelvey School of Engineering Graduate Student Theses & Dissertations

Halide perovskite has been extensively studied for its excellent optoelectronic properties. In this project, we want to explore some range of band gap that conventional 2D materials could not have. To overcome this challenge, we aimed to produce two-dimensional (2D) perovskites with large scale which is suitable for device fabrication and improve its stability using strain engineering. To prepare such 2D perovskite, we tried 2D transformation first and then decided to use confined growth to optimize result. For strain engineering, we employed sputtered nickel as an external stressor.

So far, we have produced multilayer polycrystalline perovskites material close to atomic …


Single-Molecule Super-Resolution Imaging Of Geobacter Sulfurreducens Under Anaerobic Conditions, Ziyi Hu May 2023

Single-Molecule Super-Resolution Imaging Of Geobacter Sulfurreducens Under Anaerobic Conditions, Ziyi Hu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Geobacter sulfurreducens are anaerobic bacteria capable of making electrical contacts with other organisms and extracellular electron acceptors. The challenge of imaging live Geobacter bacteria is maintaining anaerobic conditions during the imaging process. In this thesis, we augment a single-molecule localization microscope (SMLM) with a home-built anaerobic imaging chamber and use constant argon bubbling to maintain oxygen-free imaging conditions. To validate the imaging protocol, we use the transient binding of Nile red to resolve the spherical morphology of lipid-coated glass spheres with nanoscale resolution. However, when imaging Geobacter, the distribution of Nile red localizations is non-uniform, both between different cells …


Columbus, Nebraska: Southern Housing Development Design Proposal, Ryan Weyers, Caiden Dynek, Alex Papa, Brexton Robertson, Kaden Perala May 2023

Columbus, Nebraska: Southern Housing Development Design Proposal, Ryan Weyers, Caiden Dynek, Alex Papa, Brexton Robertson, Kaden Perala

Honors Program: Senior Projects (Public)

The following paper proposes the design and creation of a new housing development in the city of Columbus, Nebraska in a lot to the south of the city and directly north of the Columbus wastewater treatment plant. The goal of this proposal is to provide readers with confidence that our company is the most qualified to complete the project and will create the safest, most comfortable, most efficient, and most cost-effective final design. This proposal seeks to offer a solution to the lack of affordable housing for the growing workforce in Columbus. In order to arrive at this solution, each …


Stability Impacts Of Sandia Frequency Shift Anti-Islanding On A Grid-Connected Inverter, Daniel Mendoza May 2023

Stability Impacts Of Sandia Frequency Shift Anti-Islanding On A Grid-Connected Inverter, Daniel Mendoza

Electrical and Computer Engineering Master's Theses

Most renewable energy generation connected to the distribution level of the electric grid is connected through an inverter. To prevent an unintentional islanding condition, these inverters employ a variety of anti-islanding protection schemes. The Sandia Frequency Shift (SFS) method of anti-islanding protection is considered to be the most effective scheme built into grid-connected inverters. Much of what makes it so effective is the postive feedback loop that it creates when the inverter’s connection to the bulk power system is lost. However, this same positive feedback can have negative impacts on the stability of the inverter even when it is connected …


Comparison Of Control Parameters For Roller Blinds, Hani Alkhatib, Philippe Lemarchand, Brian Norton, Dominic O'Sullivan May 2023

Comparison Of Control Parameters For Roller Blinds, Hani Alkhatib, Philippe Lemarchand, Brian Norton, Dominic O'Sullivan

Articles

Roller blinds can reduce the heating and cooling building energy consumption required to maintain thermal comfort. The effectiveness of roller blinds is influenced by the strategies and input parameters for their control. This study is the first to identify the most effective of seven alternative control parameters to control roller blinds. It further defines the benefits from using paired control parameters to maximise energy savings and optimise occupants’ comfort. For the particular case studies and conditions examined, it is concluded that operating roller blinds using indoor air temperature as a single control parameter with rule-based controller provided, 16 %, 19 …


Piezoelectric And Conductive Polymer Based Flexible Devices Enabling Cardiovascular Health Sensing And Energy Harvesting, Andrew Closson May 2023

Piezoelectric And Conductive Polymer Based Flexible Devices Enabling Cardiovascular Health Sensing And Energy Harvesting, Andrew Closson

Dartmouth College Ph.D Dissertations

Piezoelectric materials show great promise for low-power wearable and implantable sensing, but their rigidity makes it challenging to integrate them with biological tissue. To address this, researchers have started exploring polymer-based functional materials that offer flexibility and are suitable for interfacing with the human body. However, these materials are still in their early stages, and a framework is necessary to illustrate how these materials, in conjunction with novel fabrication techniques and device designs, can enable the development of multi-functional sensing and energy harvesting devices.

This thesis utilizes highly scalable fabrication methods for functional polymers to build and test a flexible …


The Efficacy Of Conservation Practices In Reducing Floods And Improving Water Quality, Shivendra Srivastava, Andrea D. Basche, Elbert Traylor, Tirthankar Roy May 2023

The Efficacy Of Conservation Practices In Reducing Floods And Improving Water Quality, Shivendra Srivastava, Andrea D. Basche, Elbert Traylor, Tirthankar Roy

Department of Civil and Environmental Engineering: Faculty Publications

Conservation practices such as crop rotation, filter strips, and constructed wetlands are nature-based approaches intended to safeguard natural resources in agricultural landscapes. In this study, we reviewed the literature on how conservation practices, both at watershed and field scales, have been proven to subdue flood peaks, surface runoff, soil erosion, sediment transport, and nutrient loss. We classified different conservation practices based on the mode of their application (i.e., in-field, edge-of-field, and structural practices) and described what prior research efforts have concluded about the efficacy of different practices. At the field scale, practices such as reduced or no-till farming, grassed waterways, …


Enabling The Integration Of Sustainable Design Methodological Frameworks And Computational Life Cycle Assessment Tools Into Product Development Practice, Tejaswini Chatty May 2023

Enabling The Integration Of Sustainable Design Methodological Frameworks And Computational Life Cycle Assessment Tools Into Product Development Practice, Tejaswini Chatty

Dartmouth College Ph.D Dissertations

Environmental sustainability has gained critical importance in product development (PD) due to increased regulation, market competition, and consumer awareness, leading companies to set ambitious climate targets . To meet these goals, PD practitioners (engineers and designers) are often left to adapt their practices to reduce the impacts of the products they manufacture. Literature review and interviews with practitioners show that they highly valued using quantitative life cycle assessment (LCA) results to inform decision making.

LCA is a technique to measure the environmental impacts across various stages of a product life cycle. Existing LCA software tools, however, are designed for dedicated …


Evaluating The Potential Of Geopolymer Concrete As A Sustainable Alternative For Thin White-Topping Pavement, Sathvik S. Chandra, Pshtiwan Shakor, Sarwar Mohmmad, Bankole O. Awuzie, Atul K. Singh, Abishek Rauniyar, M Karakouzian May 2023

Evaluating The Potential Of Geopolymer Concrete As A Sustainable Alternative For Thin White-Topping Pavement, Sathvik S. Chandra, Pshtiwan Shakor, Sarwar Mohmmad, Bankole O. Awuzie, Atul K. Singh, Abishek Rauniyar, M Karakouzian

Civil and Environmental Engineering and Construction Faculty Research

Introduction:

The construction industry uses a large quantity of natural materials in the production of concrete. Although attempts to incorporate green materials in concrete began years ago, not every building uses such materials today, and roadways, particularly, still rely on unsustainable materials.

Methods:

Therefore, this study used alternative materials, including fly ash, manufactured sand aggregates, and different molarities of alkaline activators, to incorporate waste byproducts in a geopolymer concrete white-topping pavement layer. Recent developments have led to the emergence of geopolymers as distinct classes of materials. In the 1990s, fly ash-based geopolymers became more popular than other kinds, as they …


Validity Of Fitbit And Garmin Devices While Ascending And Descending Flights Of Stairs, Alan Garcia May 2023

Validity Of Fitbit And Garmin Devices While Ascending And Descending Flights Of Stairs, Alan Garcia

UNLV Theses, Dissertations, Professional Papers, and Capstones

Two popular wearable fitness device brands are Fitbit and Garmin. The validity of Fitbit and Garmin’s wrist-worn devices in measuring step counts in various settings, such as walking up and down a staircase, is unclear. PURPOSE: To determine if four devices, the Fitbit Charge 2, Fitbit Versa 2, Garmin Fēnix 5 and Garmin Vívosmart HR+ record valid measures of step count when ascending and descending flights of stairs at three different speeds. METHODS: Twenty-eight participants (n=28) were tested individually. Two devices were randomly selected to be placed on each wrist. Participants climbed up and then down one, two, and three …


Robust Analog Circuit Parameter Optimization With Sampling-Efficient Reinforcement Learning, Jian Gao May 2023

Robust Analog Circuit Parameter Optimization With Sampling-Efficient Reinforcement Learning, Jian Gao

McKelvey School of Engineering Graduate Student Theses & Dissertations

Design automation of analog circuits has been a longstanding challenge in the integrated circuit field. Recently, multiple methods based on learning or optimization have demonstrated great promise in automating device sizing for analog circuits. However, they often ignore the strong susceptibility of analog circuits to process, voltage, and temperature (PVT) variations or suffer from low sampling efficiency to train algorithms. To address these critical limitations, this thesis proposes RoSE, the first Robust analog circuit parameter optimization framework with high Sampling Efficience by synergistically combining Bayesian Optimization (BO) and reinforcement learning (RL). Its core is to use the fast convergence of …


Two-Dimensional Field Effect Transistor, Yimeng Li May 2023

Two-Dimensional Field Effect Transistor, Yimeng Li

McKelvey School of Engineering Graduate Student Theses & Dissertations

As silicon-based field-effect transistors (FETs) approach their physical limits with channel lengths approaching 5 nm, the search for new semiconductor materials that can surpass this limit has become urgent. Two-dimensional layered semiconductor nanomaterials, represented by graphene, have emerged as promising candidates due to their unique physical, mechanical, and chemical properties. Unlike traditional silicon-based FETs, two dimensional (2D) layered nanomaterials are held together by van der Waals forces between layers, with no dangling bonds on the material surface, which can effectively address the short-channel effect issue faced by traditional silicon-based FETs. However, unlike traditional silicon-based FETs, which have matured fabrication systems, …


A General-Purpose Software Platform For Closed-Loop Neuromodulation, William Engelhardt May 2023

A General-Purpose Software Platform For Closed-Loop Neuromodulation, William Engelhardt

McKelvey School of Engineering Graduate Student Theses & Dissertations

Implementing closed-loop neuromodulation therapies is a challenging and expensive endeavor. It requires developing software capable of acquiring signals from a bio-signal amplifier, analysis of these signals, and initiation of precisely timed stimulation, all of which need to be accomplished in real-time with very low latency. Developing this software is difficult, as it requires a wide range of expertise ranging from interfacing with hardware to real-time signal processing. Even when successfully implementing such a system for one set of hardware, it often then only works within the laboratory that conceived it. This is because of the inherent heterogeneity in the devices …


Dual Color Optogenetic Control For Analyzing Cardiac Function In Drosophila, Jiantao Zhu May 2023

Dual Color Optogenetic Control For Analyzing Cardiac Function In Drosophila, Jiantao Zhu

McKelvey School of Engineering Graduate Student Theses & Dissertations

Prolonged consumption of carbohydrate-rich diets and immobile lifestyles frequently cause metabolic disorders and obesity and, as a result, may lead to progressive heart dysfunction among broad social groups of the population. Drosophila melanogaster serves as an essential model organism in cardiovascular disease research due to conserved physiological and genomic traits shared with humans, its genetic and molecular toolbox versatility, and cost-effective maintenance. Here, we combine optogenetics and optical coherence tomography to study cardiovascular function in D. melanogaster. A new optogenetic pacing system has been developed, employing a transgenic line carrying two opsins: ChR2 and NpHR2.0. A custom-built hardware setup …


Memristive Behavior And Its Applications In Different Materials., Mingyang Wu May 2023

Memristive Behavior And Its Applications In Different Materials., Mingyang Wu

McKelvey School of Engineering Graduate Student Theses & Dissertations

The huge amount of data calculation requires the next generation non-volatile memory (NVM) technology to have the characteristics of large storage capacity and fast read/write speed. The storage and computing are separated in the traditional von Neumann architecture-based hardware platforms. The data transport between information processing and storage are causing increasing time latency, which is called von Neumann Bottleneck. Memristor, as a basic circuit component, could combine perception, storage, and computing in a single component, which has a very wide range of application prospectives. In this paper, we investigate binary oxide memristor and 2D material memristor, including their structural design …


A Novel Mrna Delivery Strategy Employing Adenovirus Piggyback Mrna Binders Via Catcher/Tag Molecular Glue, Kexin Geng May 2023

A Novel Mrna Delivery Strategy Employing Adenovirus Piggyback Mrna Binders Via Catcher/Tag Molecular Glue, Kexin Geng

McKelvey School of Engineering Graduate Student Theses & Dissertations

mRNA-based therapeutics open a new era for the prevention and treatment of a wide range of diseases. However, existing mRNA delivery vehicles have limited repertoires for dendritic cell targeting and intranasal administration which are two paramount delivery pathways of significant advantages for treating cancer and infectious respiratory diseases. Adenovirus (Ad) with well-deciphered viral genomes and intensive-studied structure biology has been developed for DCs-targeted cancer vaccines and intranasal COVID vaccines. In light of these virtues, Ad presents as the “off-the-shelf” tool possessing well-defined manufacturable capabilities and translatable feasibility that perfectly complements the current limitations of mRNA delivery. In this study, we …


3-Dimensional Visualization Of Cardiac Plaque Mapping Data, Phan Ly Vy Nguyen May 2023

3-Dimensional Visualization Of Cardiac Plaque Mapping Data, Phan Ly Vy Nguyen

McKelvey School of Engineering Graduate Student Theses & Dissertations

Atrial Fibrillation (AF) of one of the most prevalent cardiac arrythmia in humans, and also the most studied arrythmias due to its high association with cardiovascular morbidity and mortality. Diagnosis of AF, which is highly dependent on the observation of the irregular signal in the atria, is often challenging since AF is often asymptomatic at the onset. There has been a lot of effort in exploring different cardiac mapping techniques to understand the dynamics of AF for better intervention. This study aims at developing a MATLAB interface that assists the development of a cardiac plaque mapping data acquisition system in …


Preparing Non-Human Primates To Study Hand-Eye Coordination In Frontal Eye Fields (Fef) During Delayed Movement Task, Juliusz Cydzik May 2023

Preparing Non-Human Primates To Study Hand-Eye Coordination In Frontal Eye Fields (Fef) During Delayed Movement Task, Juliusz Cydzik

McKelvey School of Engineering Graduate Student Theses & Dissertations

ABSTRACT OF THE THESIS Preparing Non-Human Primates to Study Hand-Eye Coordination in Frontal Eye Fields (FEF) During Delayed Movement Task by Juliusz Cydzik Master of Science in Biomedical Engineering Washington University in St. Louis, 2023 Professor Lawrence Snyder, Chair Hand-eye coordination enables humans and non-human primates to use their hands and eyes to perform various tasks. We are interested in coordination at the systems level, where saccades and reaches are encoded. The parietal reach region (PRR), situated at the posterior end of the intraparietal sulcus (IPS) and overlapping portions of the medial intraparietal area (MIP) and V6a, is commonly attributed …


Data-Driven Platform And Digital Operations, Bing Bai May 2023

Data-Driven Platform And Digital Operations, Bing Bai

Olin Business School Graduate Student Theses and Dissertations

The objective of this dissertation is to study the emerging operations issues on data-driven platforms and digital operations. With the increasing availability of data and the development of information technologies, platforms process a large amount of data in order to efficiently make daily operational decisions. Understanding human behaviors and the human-algorithm connection is instrumental to the success of this process. In my research, I implement field experiments and use structural models to study in-warehouse worker behavior and out-of-warehouse customer behavior in the last mile of logistics.

In Chapter 1, “The Impacts of Algorithmic Work Assignment on Fairness Perceptions and Productivity: …


Reinforcement Learning-Based Resilience And Decision Making In Cyber-Physical Systems, Fisayo Sangoleye May 2023

Reinforcement Learning-Based Resilience And Decision Making In Cyber-Physical Systems, Fisayo Sangoleye

Electrical and Computer Engineering ETDs

Cyber-physical systems (CPS) transform how humans interact with technology by integrating sensing, computation, networking, and control with physical processes to facilitate smart services and innovative applications in our environments. Recent advances in CPS have led to rapid growth in the amount of information constantly generated by people, systems, and processes. Most of this information, however, is underutilized due to the lack of efficient information utilization and decision-making techniques. Also, the increasing interconnectivity of CPSs presents security risks that, if left unaddressed, could be highly disruptive to systems, processes, and economies. In this dissertation, we present a study and proposal of …


Pathformer: Interpretable And Powerful Graph Transformer For Gene Network Analysis, Qihang Zhao, Zehao Dong, Muhan Zhang, Philip Payne, Michael Province, Carlos Cruchaga, Tianyu Zhao, Yixin Chen, Fuhai Li May 2023

Pathformer: Interpretable And Powerful Graph Transformer For Gene Network Analysis, Qihang Zhao, Zehao Dong, Muhan Zhang, Philip Payne, Michael Province, Carlos Cruchaga, Tianyu Zhao, Yixin Chen, Fuhai Li

McKelvey School of Engineering Graduate Student Theses & Dissertations

Understanding which gene/pathway expression profiles are related to specific disease phenotypes has been a critical active research area in Bioinformatics. Although graph neural networks (GNNs) have achieved impressive performance on various graph-based real-world applications such as recommendation systems and social network analysis, applying GNNs in gene-network-based Bioinformatical tasks is still challenging due to the effectiveness issue and lack of interpretation methods. In this paper, we propose PathFormer, an interpretable graph Transformer (i.e. GNN), to effectively analyze gene networks and discover meaningful biomarkers/pathways. PathFormer is composed of a stack of PathFormer encoder layers and two subsequent interpretation machines. The PathFormer encoder …