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 …

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 …

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 …

Understanding The Impact Of Trade Policy Effect Uncertainty On Firm-Level Innovation Investment: A Deep Learning Approach, Daniel Chang, Nan Hu, Peng Liang, Morgan Swink

Research Collection School Of Computing and Information Systems

Integrating the real options perspective and resource dependence theory, this study examines how firms adjust their innovation investments to trade policy effect uncertainty (TPEU), a less studied type of firm specific, perceived environmental uncertainty in which managers have difficulty predicting how potential policy changes will affect business operations. To develop a text-based, context-dependent, time-varying measure of firm-level perceived TPEU, we apply Bidirectional Encoder Representations from Transformers (BERT), a state-of-the-art deep learning approach. We apply BERT to analyze the texts of mandatory Management Discussion and Analysis (MD&A) sections of annual reports for a sample of 22,669 firm-year observations from 3,181 unique …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

On The Sustainability Of Deep Learning Projects: Maintainers' Perspective, Junxiao Han, Jiakun Liu, David Lo, Chen Zhi, Yishan Chen, Shuiguang Deng

Research Collection School Of Computing and Information Systems

Deep learning (DL) techniques have grown in leaps and bounds in both academia and industry over the past few years. Despite the growth of DL projects, there has been little study on how DL projects evolve, whether maintainers in this domain encounter a dramatic increase in workload and whether or not existing maintainers can guarantee the sustained development of projects. To address this gap, we perform an empirical study to investigate the sustainability of DL projects, understand maintainers' workloads and workloads growth in DL projects, and compare them with traditional open-source software (OSS) projects. In this regard, we first investigate …

A Comprehensive Survey Of Complex Brain Network Representation, Haoteng Tang, Guixiang Ma, Yanfu Zhang, Kai Ye, Lei Guo, Guodong Liu, Qi Huang, Yalin Wang, Olusola Ajilore, Alex D. Leow

Computer Science Faculty Publications and Presentations

Highlights

• Major traditional and deep learning methods on brain network representation are overviewed.

• Brain network datasets and algorithm implementation tools are summarized.

• Promising research directions in brain network analysis are discussed.

Abstract

Recent years have shown great merits in utilizing neuroimaging data to understand brain structural and functional changes, as well as its relationship to different neurodegenerative diseases and other clinical phenotypes. Brain networks, derived from different neuroimaging modalities, have attracted increasing attention due to their potential to gain system-level insights to characterize brain dynamics and abnormalities in neurological conditions. Traditional methods aim to pre-define multiple topological features of brain …

Optimized Uncertainty Estimation For Vision Transformers: Enhancing Adversarial Robustness And Performance Using Selective Classification, Erik Pautsch, John Li, Silvio Rizzi, George K. Thiruvathukal, Maria Pantoja

Computer Science: Faculty Publications and Other Works

Deep Learning models often exhibit undue confidence when encountering out-of-distribution (OOD) inputs, misclassifying with high confidence. The ideal outcome, in these cases, would be an "I do not know" verdict. We enhance the trustworthiness of our models through selective classification, allowing the model to abstain from making predictions when facing uncertainty. Rather than a singular prediction, the model offers a prediction distribution, enabling users to gauge the model’s trustworthiness and determine the need for human intervention. We assess uncertainty in two baseline models: a Convolutional Neural Network (CNN) and a Vision Transformer (ViT). By leveraging these uncertainty values, we minimize …

Understanding The Impact Of Trade Policy Effect Uncertainty On Firm-Level Innovation Investment: A Deep Learning Approach, Daniel. Chen, Nan Hu, Peng. Liang, Morgan. Swink

Research Collection School Of Computing and Information Systems

Integrating the real options perspective and resource dependence theory, this study examines how firms adjust their innovation investments to trade policy effect uncertainty (TPEU), a less studied type of firm specific, perceived environmental uncertainty in which managers have difficulty predicting how potential policy changes will affect business operations. To develop a text-based, context-dependent, time-varying measure of firm-level perceived TPEU, we apply Bidirectional Encoder Representations from Transformers (BERT), a state-of-the-art deep learning approach. We apply BERT to analyze the texts of mandatory Management Discussion and Analysis (MD&A) sections of annual reports for a sample of 22,669 firm-year observations from 3,181 unique …

Prediction Of Rockburst Intensity Grade Based On Convolutional Neural Network, Li Kangnan, Wu Yaqin, Du Feng, Zhang Xiang, Wang Yiqiao

Coal Geology & Exploration

Rockburst is one of the urgent problems to be addressed in the process of deep resource extraction. In order to predict the rockburst disasters safely and efficiently, a rockburst intensity grade prediction model (MICE-CNN) based on the Multiple Imputation by Chained Equations (MICE) and Convolutional Neural Network (CNN) was proposed. Specifically, a predictive indicator system was established based on the main influencing factors and the acquisition conditions of rockburst. A total of 120 sets of raw data from rockburst cases were collected, with the outliers processed by pauta criterion. Then, the missing data were interpolated with the four interpolation models …

Deep Learning For Plant Bioinformatics: An Explainable Gradient-Based Approach For Disease Detection, Muhammad Shoaib, Babar Shah, Nasir Sayed, Farman Ali, Rafi Ullah, Irfan Hussain

All Works

Emerging in the realm of bioinformatics, plant bioinformatics integrates computational and statistical methods to study plant genomes, transcriptomes, and proteomes. With the introduction of high-throughput sequencing technologies and other omics data, the demand for automated methods to analyze and interpret these data has increased. We propose a novel explainable gradient-based approach EG-CNN model for both omics data and hyperspectral images to predict the type of attack on plants in this study. We gathered gene expression, metabolite, and hyperspectral image data from plants afflicted with four prevalent diseases: powdery mildew, rust, leaf spot, and blight. Our proposed EG-CNN model employs a …

Contemporary Art Authentication With Large-Scale Classification, Todd Dobbs, Abdullah-Al-Raihan Nayeem, Isaac Cho, Zbigniew Ras

Computer Science Faculty and Staff Publications

Art authentication is the process of identifying the artist who created a piece of artwork and is manifested through events of provenance, such as art gallery exhibitions and financial transactions. Art authentication has visual influence via the uniqueness of the artist’s style in contrast to the style of another artist. The significance of this contrast is proportional to the number of artists involved and the degree of uniqueness of an artist’s collection. This visual uniqueness of style can be captured in a mathematical model produced by a machine learning (ML) algorithm on painting images. Art authentication is not always possible …

Cognitive Digital Modelling For Hyperspectral Image Classification Using Transfer Learning Model, Mohammad Shabaz, Mukesh Soni

Turkish Journal of Electrical Engineering and Computer Sciences

Deep convolutional neural networks can fully use the intrinsic relationship between features and improve the separability of hyperspectral images, which has received extensive in recent years. However, the need for a large number of labelled samples to train deep network models limits the application of such methods. The idea of transfer learning is introduced into remote sensing image classification to reduce the need for the number of labelled samples. In particular, the situation in which each class in the target picture only has one labelled sample is investigated. In the target domain, the number of training samples is enlarged by …

Infrared Imaging Segmentation Employing An Explainable Deep Neural Network, Xinfei Liao, Dan Wang, Zairan Li, Nilanjan Dey, Rs Simon, Fuqian Shi

Turkish Journal of Electrical Engineering and Computer Sciences

Explainable AI (XAI) improved by a deep neural network (DNN) of a residual neural network (ResNet) and long short-term memory networks (LSTMs), termed XAIRL, is proposed for segmenting foot infrared imaging datasets. First, an infrared sensor imaging dataset is acquired by a foot infrared sensor imaging device and preprocessed. The infrared sensor image features are then defined and extracted with XAIRL being applied to segment the dataset. This paper compares and discusses our results with XAIRL. Evaluation indices are applied to perform various measurements for foot infrared image segmentation including accuracy, precision, recall, F1 score, intersection over union (IoU), Dice …

Object Recognition With Deep Neural Networks In Low-End Systems, Lillian Davis

Mahurin Honors College Capstone Experience/Thesis Projects

Object recognition is an important area in computer vision. Object recognition has been advanced significantly by deep learning that unifies feature extraction and classification. In general, deep neural networks, such as Convolution Neural Networks (CNNs), are trained in high-performance systems. Aiming to extend the reach of deep learning to personal computing, I propose a study of deep learning-based object recognition in low-end systems, such as laptops. This research includes how differing layer configurations and hyperparameter values used in CNNs can either create or resolve the issue of overfitting and affect final accuracy levels of object recognition systems. The main contribution …

An Ai-Based Framework For Translating American Sign Language To English And Vice Versa, Vijayendra D. Avina, Md Amiruzzaman, Stefanie Amiruzzaman, Linh B. Ngo, M. Ali Akber Dewan

Computer Science Faculty Publications

Abstract: In this paper, we propose a framework to convert American Sign Language (ASL) to English and English to ASL. Within this framework, we use a deep learning model along with the rolling average prediction that captures image frames from videos and classifies the signs from the image frames. The classified frames are then used to construct ASL words and sentences to support people with hearing impairments. We also use the same deep learning model to capture signs from the people with deaf symptoms and convert them into ASL words and English sentences. Based on this framework, we developed a …

Affine Image Registration Of Arterial Spin Labeling Mri Using Deep Learning Networks, Zongpai Zhang, Huiyuan Yang, Yanchen Guo, Nicolas R. Bolo, Matcheri Keshavan, Eve Derosa, Adam K. Anderson, David C. Alsop, Lijun Yin, Weiying Dai

Computer Science Faculty Research & Creative Works

Convolutional neural networks (CNN) have demonstrated good accuracy and speed in spatially registering high signal-to-noise ratio (SNR) structural magnetic resonance imaging (sMRI) images. However, some functional magnetic resonance imaging (fMRI) images, e.g., those acquired from arterial spin labeling (ASL) perfusion fMRI, are of intrinsically low SNR and therefore the quality of registering ASL images using CNN is not clear. In this work, we aimed to explore the feasibility of a CNN-based affine registration network (ARN) for registration of low-SNR three-dimensional ASL perfusion image time series and compare its performance with that from the state-of-the-art statistical parametric mapping (SPM) algorithm. The …

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 …

Attention-Based Human Age Estimation From Face Images To Enhance Public Security, Md. Ashiqur Rahman, Shuhena S. Aonty, Kaushik Deb, Iqbal H. Sarker

Research outputs 2022 to 2026

Age estimation from facial images has gained significant attention due to its practical applications such as public security. However, one of the major challenges faced in this field is the limited availability of comprehensive training data. Moreover, due to the gradual nature of aging, similar-aged faces tend to share similarities despite their race, gender, or location. Recent studies on age estimation utilize convolutional neural networks (CNN), treating every facial region equally and disregarding potentially informative patches that contain age-specific details. Therefore, an attention module can be used to focus extra attention on important patches in the image. In this study, …

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 …

Perceptual Cue-Guided Adaptive Image Downscaling For Enhanced Semantic Segmentation On Large Document Images, Chulwoo Pack, Leen-Kiat Soh, Elizabeth Lorang

School of Computing: Faculty Publications

Image downscaling is an essential operation to reduce spatial complexity for various applications and is becoming increasingly important due to the growing number of solutions that rely on memory-intensive approaches, such as applying deep convolutional neural networks to semantic segmentation tasks on large images. Although conventional content-independent image downscaling can efficiently reduce complexity, it is vulnerable to losing perceptual details, which are important to preserve. Alternatively, existing content-aware downscaling severely distorts spatial structure and is not effectively applicable for segmentation tasks involving document images. In this paper, we propose a novel image downscaling approach that combines the strengths of both …

An Intelligent Prediction Method And Interpretability For Drag And Torque Of Drill String, Liu Muchen, Song Xianzhi, Li Dayu, Zhu Shuo, Fu Li, Zhu Zhaopeng, Zhang Chengkai, Pan Tao

Coal Geology & Exploration

The accurate characterization and dynamic analysis of drilling string mechanics are essential to ensure the safe and efficient drilling. In the classical soft/rigid string model for drag & torque of drilling string, the friction coefficient of the drilling string is determined by empirical estimation or post-drilling inversion, of which the accuracy and timeliness needs to be improved. Based on the effectiveness of artificial intelligence technology applied in complex nonlinear mapping, a drag and torque prediction method of drill string with mechanism-data fusion was proposed by predicting the friction coefficient. Firstly, the friction coefficient was inversed using the drilled and logged …