Digital Commons Network^™

Model-Based Deep Autoencoders For Clustering Single-Cell Rna Sequencing Data With Side Information, Xiang Lin

Dissertations

Clustering analysis has been conducted extensively in single-cell RNA sequencing (scRNA-seq) studies. scRNA-seq can profile tens of thousands of genes' activities within a single cell. Thousands or tens of thousands of cells can be captured simultaneously in a typical scRNA-seq experiment. Biologists would like to cluster these cells for exploring and elucidating cell types or subtypes. Numerous methods have been designed for clustering scRNA-seq data. Yet, single-cell technologies develop so fast in the past few years that those existing methods do not catch up with these rapid changes and fail to fully fulfil their potential. For instance, besides profiling transcription …

Head, Heart, And Hands: A Relationships First Approach To Indigenizing And Decolonizing Education, Sherra Lee C. Robinson

The Dissertation in Practice at Western University

Student engagement within District X is at an all-time low. As District X strives for more equitable learning opportunities, they also work to serve the unique and varying needs of students despite the rising physical and mental health concerns, particularly in the wake of the COVID-19 pandemic that shook students and adults alike, resulting in a global collective trauma and led to the shutdown of schools worldwide in March 2020. These issues are especially prevalent within our most underfunded and underserved populations, such as Indigenous populations. As Canadians, Indigenous relations and calls to adopt Indigenous ways of knowing and being …

Data-Centric Image Super-Resolution In Magnetic Resonance Imaging: Challenges And Opportunities, Mamata Shrestha

Graduate Theses and Dissertations

Super-resolution has emerged as a crucial research topic in the field of Magnetic Resonance Imaging (MRI) where it plays an important role in understanding and analysis of complex, qualitative, and quantitative characteristics of tissues at high resolutions. Deep learning techniques have been successful in achieving state-of-the-art results for super-resolution. These deep learning-based methods heavily rely on a substantial amount of data. Additionally, they require a pair of low-resolution and high-resolution images for supervised training which is often unavailable. Particularly in MRI super-resolution, it is often impossible to have low-resolution and high-resolution training image pairs. To overcome this, existing methods for …

Shift Variant Image Deconvolution Using Deep Learning, Arnab Ghosh

Theses

Image Deconvolution is a well-studied problem that seeks to restore the original sharp image from a blurry image formed in the imaging system. The Point Spread function(PSF) of a particular system can be used to infer the original sharp image given the blurred image. However, such a problem is usually simplified by making the shift-invariant assumption over the Field of View (FOV). Realistic systems are shift-variant; the optical system’s point spread function depends on the position of the object point from the principal axis. For example, asymmetrical lenses can cause space variant aberration. In this paper, we first simulate our …

Deep Learning With Effective Hierarchical Attention Mechanisms In Perception Of Autonomous Vehicles, Qiuxiao Chen

All Graduate Theses and Dissertations, Fall 2023 to Present

Autonomous vehicles need to gather and understand information from their surroundings to drive safely. Just like how we look around and understand what's happening on the road, these vehicles need to see and make sense of dynamic objects like other cars, pedestrians, and cyclists, and static objects like crosswalks, road barriers, and stop lines.

In this dissertation, we aim to figure out better ways for computers to understand their surroundings in the 3D object detection task and map segmentation task. The 3D object detection task automatically spots objects in 3D (like cars or cyclists) and the map segmentation task automatically …

Melanoma Detection Based On Deep Learning Networks, Sanjay Devaraneni

Electronic Theses, Projects, and Dissertations

Our main objective is to develop a method for identifying melanoma enabling accurate assessments of patient’s health. Skin cancer, such as melanoma can be extremely dangerous if not detected and treated early. Detecting skin cancer accurately and promptly can greatly increase the chances of survival. To achieve this, it is important to develop a computer-aided diagnostic support system. In this study a research team introduces a sophisticated transfer learning model that utilizes Resnet50 to classify melanoma. Transfer learning is a machine learning technique that takes advantage of trained models, for similar tasks resulting in time saving and enhanced accuracy by …

Uavs And Deep Neural Networks: An Alternative Approach To Monitoring Waterfowl At The Site Level, Zachary J. Loken

LSU Master's Theses

Understanding how waterfowl respond to habitat restoration and management activities is crucial for evaluating and refining conservation delivery programs. However, site-specific waterfowl monitoring is challenging, especially in heavily forested systems such as the Mississippi Alluvial Valley (MAV)—a primary wintering region for ducks in North America. I hypothesized that using uncrewed aerial vehicles (UAVs) coupled with deep learning-based methods for object detection would provide an efficient and effective means for surveying non-breeding waterfowl on difficult-to-access restored wetland sites. Accordingly, during the winters of 2021 and 2022, I surveyed wetland restoration easements in the MAV using a UAV equipped with a dual …

Spoken Language Processing And Modeling For Aviation Communications, Aaron Van De Brook

Doctoral Dissertations and Master's Theses

With recent advances in machine learning and deep learning technologies and the creation of larger aviation-specific corpora, applying natural language processing technologies, especially those based on transformer neural networks, to aviation communications is becoming increasingly feasible. Previous work has focused on machine learning applications to natural language processing, such as N-grams and word lattices. This thesis experiments with a process for pretraining transformer-based language models on aviation English corpora and compare the effectiveness and performance of language models transfer learned from pretrained checkpoints and those trained from their base weight initializations (trained from scratch). The results suggest that transformer language …

Faster, Cheaper, And Better Cfd: A Case For Machine Learning To Augment Reynolds-Averaged Navier-Stokes, John Peter Romano Ii

Mechanical & Aerospace Engineering Theses & Dissertations

In recent years, the field of machine learning (ML) has made significant advances, particularly through applying deep learning (DL) algorithms and artificial intelligence (AI). The literature shows several ways that ML may enhance the power of computational fluid dynamics (CFD) to improve its solution accuracy, reduce the needed computational resources and reduce overall simulation cost. ML techniques have also expanded the understanding of underlying flow physics and improved data capture from experimental fluid dynamics.

This dissertation presents an in-depth literature review and discusses ways the field of fluid dynamics has leveraged ML modeling to date. The author selects and describes …

Automatic Cardiac Mri Image Segmentation And Mesh Generation, Ziyuan Li

McKelvey School of Engineering Theses & Dissertations

Segmenting and reconstructing cardiac anatomical structures from magnetic resonance (MR) images is essential for the quantitative measurement and automatic diagnosis of cardiovascular diseases [1]. However, manual evaluation of the time-series cardiac MRI (CMRI) obtained during routine clinical care are laborious, inefficient, and tends to produce biased and non-reproducible results [2]. This thesis proposes an end-to-end pipeline for automatically segmenting short-axis (SAX) CMRI images and generating high-quality 2D and 3D meshes suitable for finite element analysis. The main advantage of our approach is that it can not only work as a stand-alone pipeline for the automatic CMR image segmentation and mesh …

Self-Supervised Pretraining And Transfer Learning On Fmri Data With Transformers, Sean Paulsen

Dartmouth College Ph.D Dissertations

Transfer learning is a machine learning technique founded on the idea that knowledge acquired by a model during “pretraining” on a source task can be transferred to the learning of a target task. Successful transfer learning can result in improved performance, faster convergence, and reduced demand for data. This technique is particularly desirable for the task of brain decoding in the domain of functional magnetic resonance imaging (fMRI), wherein even the most modern machine learning methods can struggle to decode labelled features of brain images. This challenge is due to the highly complex underlying signal, physical and neurological differences between …

Towards Non-Vascular Fundus Image Analysis And Disease Detection, Saeid Motevali

Computer Science Dissertations

Assessment of retinal fundus image is very informative and preventive in early ocular disease detection. This non-invasive assessment of fundus images also helps in the early diagnosis of vascular diseases. This unique combination help in the early diagnosis of diseases. Applying image enhancement techniques with advanced Deep learning techniques helps to overcome such a challenging problem. Most Deep learning models give a diagnosis without attention to underlying pathological abnormalities. In this thesis, we tried to solve the problem in the same way as ophthalmologists and experts in the field approach the problem. We created models that can detect an Optic …

Non-Destructive Evaluation Of White Striping And Microbial Spoilage Of Broiler Breast Meat Using Structured-Illumination Reflectance Imaging, Ebenezer O. Olaniyi

Theses and Dissertations

Manual inspection is a prevailing practice for quality assessment of poultry meat, but it is labor-intensive, tedious, and subjective. This thesis aims to assess the efficacy of an emerging structured illumination reflectance imaging (SIRI) technique with machine learning approaches for assessing WS and microbial spoilage in broiler breast meat. Broiler breast meat samples were imaged by an in house-assembled SIRI platform under sinusoidal illumination. In first experiment, handcrafted texture features were extracted from direct component (DC, corresponding to conventional uniform illumination) and amplitude component (AC, unique to the use of sinusoidal illumination) images retrieved from raw SIRI pattern images build …

More Is Better Than One: The Effect Of Ensembling On Deep Learning Performance In Biochemical Prediction Problems, Jacob A. Stern

Theses and Dissertations

This thesis presents two papers addressing important biochemical prediction challenges. The first paper focuses on accurate protein distance predictions and introduces updates to the ProSPr network. We evaluate its performance in the Critical Assessment of techniques for Protein Structure Prediction (CASP14) competition, investigating its accuracy dependence on sequence length and multiple sequence alignment depth. The ProSPr network, an ensemble of three convolutional neural networks (CNNs), demonstrates superior performance compared to individual networks. The second paper addresses the issue of accurate ligand ranking in virtual screening for drug discovery. We propose MILCDock, a machine learning consensus docking tool that leverages predictions …

Physics-Augmented Modeling And Optimization Of Complex Systems: Healthcare Applications, Jianxin Xie

Doctoral Dissertations

The rapid advances in sensing technology have created a data-rich environment that tremendously

benefits predictive modeling and decision-making for complex systems. Harnessing

the full potential of this complexly-structured sensing data requires the development of

novel and reliable analytical models and tools for system informatics. Such advancements in

sensing present unprecedented opportunities to investigate system dynamics and optimize

decision-making processes for smart health. Nevertheless, sensing data is typically

characterized by high dimensionality and intricate structures. To fully unlock the potential of

this data, we significantly rely on innovative analytical methods and tools that can effectively

process information.

The objective of this …

Optimizing Collective Communication For Scalable Scientific Computing And Deep Learning, Jiali Li

Doctoral Dissertations

In the realm of distributed computing, collective operations involve coordinated communication and synchronization among multiple processing units, enabling efficient data exchange and collaboration. Scientific applications, such as simulations, computational fluid dynamics, and scalable deep learning, require complex computations that can be parallelized across multiple nodes in a distributed system. These applications often involve data-dependent communication patterns, where collective operations are critical for achieving high performance in data exchange. Optimizing collective operations for scientific applications and deep learning involves improving the algorithms, communication patterns, and data distribution strategies to minimize communication overhead and maximize computational efficiency.

Within the context of this …

Deep Learning Based Power System Stability Assessment For Reduced Wecc System, Yinfeng Zhao

Doctoral Dissertations

Power system stability is the ability of power system, for a giving initial operating condition, to reach a new operation condition with most of the system variables bounded in normal range after subjecting to a short or long disturbance. Traditional power system stability mainly uses time-domain simulation which is very time consuming and only appropriate for offline assessment.

Nowadays, with increasing penetration of inverter based renewable, large-scale distributed energy storage integration and operation uncertainty brought by weather and electricity market, system dynamic and operating condition is more dramatic, and traditional power system stability assessment based on scheduling may not be …

Deep Learning For Resource Constraint Devices, Sheikh Rufsan Reza

All Dissertations

The amount of Internet-of-things (IoT) devices is rapidly expanding. This also triggered the necessity of smart IoT devices which are capable of conducting any task by itself. Deep learning techniques are also booming due to the increased computing power and refined algorithms. The advantage of deep learning is that it can be tuned into any application without the manual feature extraction process. Now, the combination of deep learning with smart IoT devices/edge devices can result in any application that can be used in machine vision, vision inspection, autonomous vehicle, and many more. These applications can be automated which requires human …

Increasing The Efficiency And Accuracy Of Collective Intelligence Methods For Image Classification, Md Mahmudulla Hassan

Open Access Theses & Dissertations

Collective intelligence has emerged as a powerful methodology for annotating and classifying challenging data that pose difficulties for automated classifiers. It works by leveraging the concept of "wisdom of the crowds" which approximates a ground truth after aggregating experts' feedback and filtering out noise. However, challenges arise when certain applications, such as medical image classification, security threat detection, and financial fraud detection, demand accurate and reliable data annotation. The unreliability of experts due to inconsistent expertise and competencies, coupled with the associated cost and time-consuming judgment extraction, presents additional challenges.

Input aggregation is the process of consolidating and combining multiple …

The Development Of Artificial Intelligence-Based Tools For Expert Peer Review Of Radiotherapy Treatment Plans, Mary Gronberg

Dissertations & Theses (Open Access)

Creating a patient-specific radiation treatment plan is a time-consuming and operator-dependent manual process. The treatment planner adjusts the planning parameters in a trial-and-error fashion in an effort to balance the competing clinical objectives of tumor coverage and normal tissue sparing. Often, a plan is selected because it meets basic organ at risk dose thresholds for severe toxicity; however, it is evident that a plan with a decreased risk of normal tissue complication probability could be achieved. This discrepancy between “acceptable” and “best possible” plan is magnified if either the physician or treatment planner lacks focal expertise in the disease site. …

Evaluating Chatgpt For Recommendation: How Does The Ability To Converse Impact Recommendation?, Kyle Spurlock

Electronic Theses and Dissertations

Recommendation algorithms have become an absolute necessity in the modern world to avoid information overload. However, the interaction between the human and the system is largely superficial and without any real contact. If you are given poor recommendations, you have no choice but to sift through mountains of content on your own until the model learns to accommodate your tastes more. This is bad for business as well as the consumer. Recently, large language models like ChatGPT have seen a significant rise in popularity due to their ease of use and wide range of knowledge. It has now become nearly …

Insights Into The Application Of Deep Reinforcement Learning In Healthcare And Materials Science, Benjamin R. Smith

Doctoral Dissertations

Reinforcement learning (RL) is a type of machine learning designed to optimize sequential decision-making. While controlled environments have served as a foundation for RL research, due to the growth in data volumes and deep learning methods, it is now increasingly being applied to real-world problems. In our work, we explore and attempt to overcome challenges that occur when applying RL to solve problems in healthcare and materials science.

First, we explore how issues in bias and data completeness affect healthcare applications of RL. To understand how bias has already been considered in this area, we survey the literature for existing …

Deep Learning Models For Biomedical Data Analysis, Lucy Nwosu

All Dissertations

The field of biomedical data analysis is a vibrant area of research dedicated to extracting valuable insights from a wide range of biomedical data sources, including biomedical images and genomics data. The emergence of deep learning, an artificial intelligence approach, presents significant prospects for enhancing biomedical data analysis and knowledge discovery. This dissertation focused on exploring innovative deep-learning methods for biomedical image processing and gene data analysis.

During the COVID-19 pandemic, biomedical imaging data, including CT scans and chest x-rays, played a pivotal role in identifying COVID-19 cases by categorizing patient chest x-ray outcomes as COVID-19-positive or negative. While supervised …

Deep Learning Methods For Some Problems In Scientific Computing, Yuankai Teng

Theses and Dissertations

Deep learning has emerged as a powerful approach for solving complex problems in scientific computing due to the increasing availability of large-scale data and computational resources. This thesis explores the potential of deep learning methods for three specific problems in scientific computing: (i) reducing the dimensions of variables in function approximation, (ii) solving linear reaction-diffusion equations, and (iii) finding the parametric representations of parameters in the numerical schemes for solving time-dependent partial differential equations.

For the first problem, a novel deep learning architecture is developed for reducing the dimensions of variables in function approximation. The proposed method achieves state-of-the-art performance …

Automatic Classification And Segmentation Of Patterned Martian Ground Using Deep Learning Techniques, Ruthy Brito

Electronic Thesis and Dissertation Repository

Science autonomy onboard spacecraft can optimize image return by prioritizing downlink of meaningful data. Martian polygonally cracked ground is actively studied by planetary geologists and may be indicative of subsurface water. Filtering images containing these polygonal features can be used as a case study for science autonomy and to reduce the overhead associated with parsing through Martian surface images. This thesis demonstrates the use of deep learning techniques in the classification of Martian polygonally patterned ground from HiRISE images. Three tasks are considered, a binary classification to identify images containing polygons, multiclass classification distinguishing different polygon types and semantic segmentation …

Sarcasm Detection In English And Arabic Tweets Using Transformer Models, Rishik Lad

Computer Science Senior Theses

This thesis describes our approach toward the detection of sarcasm and its various types in English and Arabic Tweets through methods in deep learning. There are five problems we attempted: (1) detection of sarcasm in English Tweets, (2) detection of sarcasm in Arabic Tweets, (3) determining the type of sarcastic speech subcategory for English Tweets, (4) determining which of two semantically equivalent English Tweets is sarcastic, and (5) determining which of two semantically equivalent Arabic Tweets is sarcastic. All tasks were framed as classification problems, and our contributions are threefold: (a) we developed an English binary classifier system with RoBERTa, …

Ai-Enabled Online Plan Adaptation For Mr-Guided Stereotactic Ablative Radiotherapy (Sabr) Of Head And Neck Cancer, Yao Zhao

Dissertations & Theses (Open Access)

Head and neck cancer (HNC) is a prevalent cancer type worldwide. Stereotactic ablative radiotherapy (SABR) has emerged as an effective treatment for HNC, delivering highly conformal doses to the tumor target while sparing surrounding normal tissues with a sharp dose gradient. However, the accuracy of the treatment delivery is limited by setup errors, anatomical changes, and intra-/inter-fraction organ motion. The emergence of MR-guided adaptive radiotherapy (ART) has the potential to further improve the SABR of HNC, by providing superior visualization of soft tissue and enabling real-time plan adaptation based on the daily anatomical changes of patients. This novel technology has …

Patient Movement Monitoring Based On Imu And Deep Learning, Mohsen Sharifi Renani

Electronic Theses and Dissertations

Osteoarthritis (OA) is the leading cause of disability among the aging population in the United States and is frequently treated by replacing deteriorated joints with metal and plastic components. Developing better quantitative measures of movement quality to track patients longitudinally in their own homes would enable personalized treatment plans and hasten the advancement of promising new interventions. Wearable sensors and machine learning used to quantify patient movement could revolutionize the diagnosis and treatment of movement disorders. The purpose of this dissertation was to overcome technical challenges associated with the use of wearable sensors, specifically Inertial Measurement Units (IMUs), as a …

Deep Learning For Skin Photoaging, Gokul Srinivasan

Computer Science Senior Theses

Skin photoaging is the premature aging of skin that results from ultraviolet light exposure. It is a major risk factor for the development of skin cancer, among other malignant skin pathologies. Accordingly, understanding its etiology is important for both preventative and reparative clinical action. In this study, skin samples obtained from patients with ranging solar elastosis grades – a proxy for skin photoaging – were sequenced using next-generation sequencing techniques to further understand the genomic, epigenomic, and histological signs and signals of skin photoaging. The results of this study suggest that tissues with severe photoaging exhibit increases in the frequency …

Connecting Linguistic Expressions And Pain Relief Through Transformer Model Construction And Analysis, Sarah M. Chacko

Computer Science Senior Theses

Chronic pain is a widespread problem that significantly impacts quality of life. Overprescription and abuse of pain medication continues to be a major public health issue and can further burden patients due to a fragmented health care system. Previous research has suggested a possible psychological basis to pain and the potential for safer, non-pharmacological alternatives for pain relief. This project leverages language models to study chronic pain development and relief through psychological treatments, which will be assessed through responses to post-treatment interviews. A transformer-based natural language processing model is employed to identify connections between language expressions and pain on a …