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 …

Quantum-Enhanced Disaster Assessment And Management (Quandam) System – A Perspective, Mohammed Sahil Nakhuda, Shweta Vincent Dr., Om Prakash Kumar Dr.

Manipal Journal of Science and Technology

Efficient disaster response hinges on the rapid identification of damaged structures post-natural disasters. This literature review surveys diverse solutions, emphasizing merits, drawbacks, and performance metrics. Techniques such as deep learning with pre-trained models, transfer learning with CNNs, and incremental learning with SVMs are scrutinized for their computational demands and adaptability. Ensemble learning, CNNs, attention-based models, transformer networks, and hybrid approaches offer distinct advantages like heightened accuracy and resource efficiency. Challenges, including computational complexity and cost, accompany these methods. Additionally, we propose a framework termed Quantum-Enhanced Disaster Assessment and Management (QuanDAM) which encompasses the usage of Artificial Intelligence (AI) predictive modelling, …

Determining The Presence And Size Of Shoulder Lesions In Sows Using Computer Vision, Shubham Bery, Tami M. Brown-Bandl, Bradley T. Jones, Gary A. Rohrer, Sudhendu Raj Sharma

Department of Biological Systems Engineering: Papers and Publications

Shoulder sores predominantly arise in breeding sows and often result in untimely culling. Reported prevalence rates vary significantly, spanning between 5% and 50% depending upon the type of crate flooring inside a farm, the animal’s body condition, or an existing injury that causes lameness. These lesions represent not only a welfare concern but also have an economic impact due to the labor needed for treatment and medication. The objective of this study was to evaluate the use of computer vision techniques in detecting and determining the size of shoulder lesions. A Microsoft Kinect V2 camera captured the top-down depth and …

Deep Learning In Bioinformatics, Malik Yousef, Jens Allmer

Turkish Journal of Biology

Deep learning is a powerful machine learning technique that can learn from large amounts of data using multiple layers of artificial neural networks. This paper reviews some applications of deep learning in bioinformatics, a field that deals with analyzing and interpreting biological data. We first introduce the basic concepts of deep learning and then survey the recent advances and challenges of applying deep learning to various bioinformatics problems, such as genome sequencing, gene expression analysis, protein structure prediction, drug discovery, and disease diagnosis. We also discuss future directions and opportunities for deep learning in bioinformatics. We aim to provide an …

Using Artificial Intelligence To Diagnose Demented In The Elderly, Ohood Fadil Alwan

Al-Esraa University College Journal for Engineering Sciences

In addition to possible other symptoms, memory loss and impairment are the hallmarks of Demented or Alzheimer’s disease (AD). Despite the fact that dementia is incurable and has a significant negative impact on patients' lives, an early diagnosis can help start the right treatment and prevent additional brain damage. Over the years, machine learning techniques have been used to classify AD; nevertheless, the efficacy of the results depends on the use of multi-step classifiers and manually created features. Thanks to recent advances in deep learning, patterns may now be classified using neural networks' final stage. In order to diagnose dementia …

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 …

Deep Learning Uncertainty Quantification For Clinical Text Classification, Alina Peluso, Ioana Danciu, Hong-Jun Yoon, Jamaludin Mohd Yusof, Tanmoy Bhattacharya, Adam Spannaus, Noah Schaefferkoetter, Eric B. Durbin, Xiao-Cheng Wu, Antoinette Stroup, Jennifer Doherty, Stephen Schwartz, Charles Wiggins, Linda Coyle, Lynne Penberthy, Georgia D. Tourassi, Shang Gao

School of Public Health Faculty Publications

INTRODUCTION: Machine learning algorithms are expected to work side-by-side with humans in decision-making pipelines. Thus, the ability of classifiers to make reliable decisions is of paramount importance. Deep neural networks (DNNs) represent the state-of-the-art models to address real-world classification. Although the strength of activation in DNNs is often correlated with the network's confidence, in-depth analyses are needed to establish whether they are well calibrated. METHOD: In this paper, we demonstrate the use of DNN-based classification tools to benefit cancer registries by automating information extraction of disease at diagnosis and at surgery from electronic text pathology reports from the US National …

Deep Learning Image Analysis To Isolate And Characterize Different Stages Of S-Phase In Human Cells, Kevin A. Boyd, Rudranil Mitra, John Santerre, Christopher L. Sansam

SMU Data Science Review

Abstract. This research used deep learning for image analysis by isolating and characterizing distinct DNA replication patterns in human cells. By leveraging high-resolution microscopy images of multiple cells stained with 5-Ethynyl-2′-deoxyuridine (EdU), a replication marker, this analysis utilized Convolutional Neural Networks (CNNs) to perform image segmentation and to provide robust and reliable classification results. First multiple cells in a field of focus were identified using a pretrained CNN called Cellpose. After identifying the location of each cell in the image a python script was created to crop out each cell into individual .tif files. After careful annotation, a CNN was …

Deep Generative Sculpting Models For Single Image 3d Reconstruction, Jason Jennings

Computer Science and Engineering Dissertations

In the field of computer vision, learning representations of images is an important task. This dissertation introduces deep generative sculpting models (DGSM), deep learning models that learn 3D representations of objects from 2D images. DGSMs use convolutional networks combined with a differentiable renderer to attempt to "sculpt" a base 3D mesh, such as a sphere, to faithfully represent an object in the scene, and render it to reconstruct the input image. The core methodology revolves around the encoding of the input image into latent variables. These variables are decoded into interpretable scene parameters, describing the object's translation, rotation, scale, texture, …

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 …

Statistical And Deep Learning Models For Reference Evapotranspiration Time Series Forecasting: A Comparison Of Accuracy, Complexity, And Data Efficiency, Arman Ahmadi, Andre Daccache, Mojtaba Sadegh, Richard L. Snyder

Civil Engineering Faculty Publications and Presentations

Reference evapotranspiration (ETo) is an essential variable in agricultural water resources management and irrigation scheduling. An accurate and reliable forecast of ETo facilitates effective decision-making in agriculture. Although numerous studies assessed various methodologies for ETo forecasting, an in-depth multi-dimensional analysis evaluating different aspects of these methodologies is missing. This study systematically evaluates the complexity, computational cost, data efficiency, and accuracy of ten models that have been used or could potentially be used for ETo forecasting. These models range from well-known statistical forecasting models like seasonal autoregressive integrated moving average (SARIMA) to state-of-the-art deep learning (DL) algorithms like temporal fusion transformer …

Sc-Fuse: A Feature Fusion Approach For Unpaved Road Detection From Remotely Sensed Images, Aniruddh Saxena

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Road network extraction from remote sensing imagery is crucial for numerous applications, ranging from autonomous navigation to urban and rural planning. A particularly challenging aspect is the detection of unpaved roads, often underrepresented in research and data. These roads display variability in texture, width, shape, and surroundings, making their detection quite complex. This thesis addresses these challenges by creating a specialized dataset and introducing the SC-Fuse model.

Our custom dataset comprises high resolution remote sensing imagery which primarily targets unpaved roads of the American Midwest. To capture the diverse seasonal variation and their impact, the dataset includes images from different …

Mgmt Promoter Methylation Status Prediction Using Mri Scans? An Extensive Experimental Evaluation Of Deep Learning Models, Numan Saeed, Muhammad Ridzuan, Hussain Alasmawi, Ikboljon Sobirov, Mohammad Yaqub

Computer Vision Faculty Publications

The number of studies on deep learning for medical diagnosis is expanding, and these systems are often claimed to outperform clinicians. However, only a few systems have shown medical efficacy. From this perspective, we examine a wide range of deep learning algorithms for the assessment of glioblastoma - a common brain tumor in older adults that is lethal. Surgery, chemotherapy, and radiation are the standard treatments for glioblastoma patients. The methylation status of the MGMT promoter, a specific genetic sequence found in the tumor, affects chemotherapy's effectiveness. MGMT promoter methylation improves chemotherapy response and survival in several cancers. MGMT promoter …

Determining The Presence And Size Of Shoulder Lesions In Sows Using Computer Vision, Shubham Bery, Tami M. Brown-Brandl, Bradley T. Jones, Gary A. Rohrer, Sudhendu Raj Sharma

Department of Biological Systems Engineering: Papers and Publications

Shoulder sores predominantly arise in breeding sows and often result in untimely culling. Reported prevalence rates vary significantly, spanning between 5% and 50% depending upon the type of crate flooring inside a farm, the animal’s body condition, or an existing injury that causes lameness. These lesions represent not only a welfare concern but also have an economic impact due to the labor needed for treatment and medication. The objective of this study was to evaluate the use of computer vision techniques in detecting and determining the size of shoulder lesions. A Microsoft Kinect V2 camera captured the top-down depth and …

Distxplore: Distribution-Guided Testing For Evaluating And Enhancing Deep Learning Systems, Longtian Wang, Xiaofei Xie, Xiaoning Du, Meng Tian, Qing Guo, Zheng Yang, Chao Shen

Research Collection School Of Computing and Information Systems

Deep learning (DL) models are trained on sampled data, where the distribution of training data differs from that of real-world data (i.e., the distribution shift), which reduces the model's robustness. Various testing techniques have been proposed, including distribution-unaware and distribution-aware methods. However, distribution-unaware testing lacks effectiveness by not explicitly considering the distribution of test cases and may generate redundant errors (within same distribution). Distribution-aware testing techniques primarily focus on generating test cases that follow the training distribution, missing out-of-distribution data that may also be valid and should be considered in the testing process. In this paper, we propose a novel …

Better Pay Attention Whilst Fuzzing, Shunkai Zhu, Jingyi Wang, Jun Sun, Jie Yang, Xingwei Lin, Liyi Zhang, Peng Cheng

Research Collection School Of Computing and Information Systems

Fuzzing is one of the prevailing methods for vulnerability detection. However, even state-of-the-art fuzzing methods become ineffective after some period of time, i.e., the coverage hardly improves as existing methods are ineffective to focus the attention of fuzzing on covering the hard-to-trigger program paths. In other words, they cannot generate inputs that can break the bottleneck due to the fundamental difficulty in capturing the complex relations between the test inputs and program coverage. In particular, existing fuzzers suffer from the following main limitations: 1) lacking an overall analysis of the program to identify the most “rewarding” seeds, and 2) lacking …

Probabilistic Multivariate Time Series Forecasting And Robust Uncertainty Quantification With Applications In Electricity Price Prediction, Jie Han

Industrial, Manufacturing, and Systems Engineering Dissertations

Electricity price forecasting (EPF) is a crucial task for market participants seeking informed decisions in day-ahead electricity markets. The increasing penetration of stochastic renewable energy and the deregulation of electricity markets pose challenges to electricity price forecasting. Given the dependence of electricity prices on stochastic factors such as weather conditions, market dynamics, and customer behaviors, deterministic forecasting methods offer limited insight into the potential future states of energy prices in highly stochastic markets. In this study, a transformer-based electricity price forecasting (TDEPF) model was developed, utilizing a two-step training process and demonstrating superior performance compared to typical RNN models. Subsequently, …

Constructing Large Open-Source Corpora And Leveraging Language Models For Simulink Toolchain Testing And Analysis, Sohil Lal Shrestha

Computer Science and Engineering Dissertations

In several safety-critical industries such as automotive, aerospace, healthcare, and industrial automation, MATLAB/Simulink has emerged as the de-facto standard tool for system modeling and analysis, model compilation into executable code, and code deployment onto embedded hardware. Within the context of cyber-physical system (CPS) development, it is imperative to both rigorously test the development tools, such as MathWorks’ Simulink, and understand modeling practices and model evolution. The existing body of work faces limitations primarily stemming from two factors: (1) contemporary testing methodologies often prove inefficient in identifying critical toolchain bugs due to a paucity of explicit toolchain specifications and (2) there …

Enhancing The Classification Of Autism Spectrum Disorder From Rs-Fmri Functional Connectivity Data Using Temporal Information, Mihir Yashwant Ingole

Computer Science and Engineering Theses

Autism Spectrum Disorder (ASD) affects the patient’s cognitive development which leads to difficulties in social functioning, daily tasks, and independent living. This necessitates intervention at an early age to take preventive measures and provide vital care. Manual diagnosis methods like Autism Diagnostic Observation Schedule (ADOS) assessment adopts symptom-based criteria which typically manifest at a later age. To automate this process, correlations computed from BOLD (Blood Oxygen-level dependent) signals obtained through resting state functional magnetic resonance imaging (rs-fMRI) data of patients across sparse brain regions has been used recently as a measure of functional connectivity. The goal of this study is …

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 …

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 …

Customer Churn Prediction Using Composite Deep Learning Technique, Asad Khattak, Zartashia Mehak, Hussain Ahmad, Muhammad Usama Asghar, Muhammad Zubair Asghar, Aurangzeb Khan

All Works

Customer churn, a phenomenon that causes large financial losses when customers leave a business, makes it difficult for modern organizations to retain customers. When dissatisfied customers find their present company's services inadequate, they frequently migrate to another service provider. Machine learning and deep learning (ML/DL) approaches have already been used to successfully identify customer churn. In some circumstances, however, ML/DL-based algorithms lacks in delivering promising results for detecting client churn. Previous research on estimating customer churn revealed unexpected forecasts when utilizing machine learning classifiers and traditional feature encoding methodologies. Deep neural networks were also used in these efforts to extract …

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 …

Non-Invasive Arterial Blood Pressure Measurement And Spo2 Estimation Using Ppg Signal: A Deep Learning Framework, Yan Chu, Kaichen Tang, Yu Chun Hsu, Tongtong Huang, Dulin Wang, Wentao Li, Sean I. Savitz, Xiaoqian Jiang, Shayan Shams

Faculty Research, Scholarly, and Creative Activity

Background: Monitoring blood pressure and peripheral capillary oxygen saturation plays a crucial role in healthcare management for patients with chronic diseases, especially hypertension and vascular disease. However, current blood pressure measurement methods have intrinsic limitations; for instance, arterial blood pressure is measured by inserting a catheter in the artery causing discomfort and infection. Method: Photoplethysmogram (PPG) signals can be collected via non-invasive devices, and therefore have stimulated researchers’ interest in exploring blood pressure estimation using machine learning and PPG signals as a non-invasive alternative. In this paper, we propose a Transformer-based deep learning architecture that utilizes PPG signals to conduct …

A Comparative Study Of Yolo Models And A Transformer-Based Yolov5 Model For Mass Detection In Mammograms, Damla Coşkun, Dervi̇ş Karaboğa, Alper Baştürk, Bahri̇ye Akay, Özkan Ufuk Nalbantoğlu, Serap Doğan, İshak Paçal, Meryem Altin Karagöz

Turkish Journal of Electrical Engineering and Computer Sciences

Breast cancer is a prevalent form of cancer across the globe, and if it is not diagnosed at an early stage it can be life-threatening. In order to aid in its diagnosis, detection, and classification, computer-aided detection (CAD) systems are employed. You Only Look Once (YOLO)-based CAD algorithms have become very popular owing to their highly accurate results for object detection tasks in recent years. Therefore, the most popular YOLO models are implemented to compare the performance in mass detection with various experiments on the INbreast dataset. In addition, a YOLO model with an integrated Swin Transformer in its backbone …

An In-Depth Analysis Of Domain Adaptation In Computer And Robotic Vision, Muhammad Hassan Tanveer, Zainab Fatima, Shehnila Zardari, David A. Guerra-Zubiaga

Faculty Articles

This review article comprehensively delves into the rapidly evolving field of domain adaptation in computer and robotic vision. It offers a detailed technical analysis of the opportunities and challenges associated with this topic. Domain adaptation methods play a pivotal role in facilitating seamless knowledge transfer and enhancing the generalization capabilities of computer and robotic vision systems. Our methodology involves systematic data collection and preparation, followed by the application of diverse assessment metrics to evaluate the efficacy of domain adaptation strategies. This study assesses the effectiveness and versatility of conventional, deep learning-based, and hybrid domain adaptation techniques within the domains of …

A Systematic Collection Of Medical Image Datasets For Deep Learning, Johann Li, Guangming Zhu, Cong Hua, Mingtao Feng, Basheer Bennamoun, Ping Li, Xiaoyuan Lu, Juan Song, Peiyi Shen, Xu Xu, Lin Mei, Liang Zhang, Syed A. A. Shah, Mohammed Bennamoun

Research outputs 2022 to 2026

The astounding success made by artificial intelligence in healthcare and other fields proves that it can achieve human-like performance. However, success always comes with challenges. Deep learning algorithms are data dependent and require large datasets for training. Many junior researchers face a lack of data for a variety of reasons. Medical image acquisition, annotation, and analysis are costly, and their usage is constrained by ethical restrictions. They also require several other resources, such as professional equipment and expertise. That makes it difficult for novice and non-medical researchers to have access to medical data. Thus, as comprehensively as possible, this article …

Sustainable Waste Management Through The Lens Of Artificial Intelligence: An In-Depth Review, Noha Emad El-Sayad, Shereen Zakaria

Journal of Engineering Research

One of the major issues facing the world, particularly developing countries, is waste management. “Waste” is any material that is not needed or has no intended use. Neglecting this waste endangers the safety of the public and causes harm, as it emits dangerous gases that have negative effects on human health. Egypt has made distinguished efforts to achieve the goals of Egypt Vision 2030 and the Sustainable Development Goals. These efforts, which have been implemented through massive government projects throughout the past few years and are set to be followed by more in the future, still require a lot of …

Multi-View Information Fusion Using Multi-View Variational Autoencoder To Predict Proximal Femoral Fracture Load, Chen Zhao, Joyce H. Keyak, Xuewei Cao, Qiuying Sha, Li Wu, Zhe Luo, Lan Juan Zhao, Qing Tian, Michael Serou, Chuan Qiu, Kuan Jui Su, Hui Shen, Hong Wen Deng, Weihua Zhou

Michigan Tech Publications, Part 2

Background: Hip fracture occurs when an applied force exceeds the force that the proximal femur can support (the fracture load or “strength”) and can have devastating consequences with poor functional outcomes. Proximal femoral strengths for specific loading conditions can be computed by subject-specific finite element analysis (FEA) using quantitative computerized tomography (QCT) images. However, the radiation and availability of QCT limit its clinical usability. Alternative low-dose and widely available measurements, such as dual energy X-ray absorptiometry (DXA) and genetic factors, would be preferable for bone strength assessment. The aim of this paper is to design a deep learning-based model to …

Sustainable Waste Management Through The Lens Of Artificial Intelligence: An In-Depth Review, Noha Emad El-Sayad, Shereen Zakaria

Journal of Engineering Research

One of the major issues facing the world, particularly developing countries, is waste management. “Waste” is any material that is not needed or has no intended use. Neglecting this waste endangers the safety of the public and causes harm, as it emits dangerous gases that have negative effects on human health. Egypt has made distinguished efforts to achieve the goals of Egypt Vision 2030 and the Sustainable Development Goals. These efforts, which have been implemented through massive government projects throughout the past few years and are set to be followed by more in the future, still require a lot of …