Physical Sciences and Mathematics Commons^™

Deepssetracer 2.0: Improved Deep Learning Model Performance For Protein Secondary Structure Segmentation From Cryo-Em Maps, Bryan Hawickhorst, Thu Nguyen, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

DeepSSETracer is a method for segmenting protein secondary structure from medium-resolution (5-10Å) cryogenic electron microscopy (cryo-EM) density maps. We conducted experiments and ablation studies to examine the effects of normalization methods, max-pooling, activation functions, and loss calculation region on DeepSSETracer. By combining multiple technical improvements, the performance of the new version, DeepSSETracer 2.0, was significantly enhanced compared to DeepSSETracer 1.1. On a set of 77 test cases, the weighted average per-voxel F1 score increased from 62.1% to 70.3% for helix detection, and from 47.8% to 62.5% for β-sheet detection. While each of the five modifications in the network enhanced the …

Benchmarking And Improving Foundation Model Dietary Estimates From Meal Images, Yongcheng Mu, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Accurate quantifying dietary contents, such as calories, proteins, carbohydrates, and fats, from an image of a meal plate is vital for managing diabetes. Recently, Large Multimodal Models (LMMs) have excelled in complex vision-language tasks due to their use of very large, highly diverse data. This study benchmarked the use of seven LMMs that include full and lightweight models of GPT, Gemini, and Llama for nutrition estimation based on Google's Nutrition5k dataset and our own phone-collected DonateAndLearn dataset. We analyzed the performance of LMMs and the RGB-D fusion model, in which the RGB-D model was specifically trained using Nutrition5k data. On …

Symbol-Temporal Consistency Self-Supervised Learning For Robust Time Series Classification, Kevin Garcia, Cassandra Garza, Brooklyn Berry, Yifeng Gao

Computer Science Faculty Publications

The surge in the significance of time series in digital health domains necessitates advanced methodologies for extracting meaningful patterns and representations. Self-supervised contrastive learning has emerged as a promising approach for learning directly from raw data. However, time series data in digital health is known to be highly noisy, inherently involves concept drifting, and poses a challenge for training a generalizable deep learning model. In this paper, we specifically focus on data distribution shift caused by different human behaviors and propose a self-supervised learning framework that is aware of the bag-of-symbol representation. The bag-of-symbol representation is known for its insensitivity …

Balancing Performance And Efficiency: An Autoencoder Approach To Api-Based Malware Detection, Selma Bouraoui

Graduate Theses/Dissertations

The constant evolution of malware presents a critical challenge to today's interconnected world. It poses an increasing threat on different scales, spanning from individuals, organizations to critical infrastructures such as government’s security. Hackers continuously develop new techniques to evade detection methods. When confronted with the high volume and variety of malware, conventional approaches tend to struggle to perform in robust, accurate and timely manner. This thesis explores the application of deep learning methods to improve malware detection and classification techniques. By analyzing API call sequences, the proposed approach leverages Autoencoders to compress high-dimensional malware data into more optimized representations that …

Predicting Real Estate Prices Using Deep Learning Regression Models On Socio Spatial Data, Gentle Engworo

Graduate Theses/Dissertations

ABSTRACT

Cities keep their own kind of ledger. Every block, bus stop, corner store, and year that slips by leaves a small entry about what homes are worth. That ledger is what we call socio-spatial data: simple facts about what a home is (its age), where it sits (latitude/longitude), how easy it is to get around (distance to the nearest MRT station), what’s nearby (number of convenience stores), and when it sold (transaction date). This thesis asks a practical question in that everyday language: given these common clues, can we predict home prices more accurately and explain why? Using 414 …

Approach For Detecting Face Morphing Attacks Using Convolution Neural Network, Essa M. Namis, Khalid Shaker, Sufyan Al-Janabi

Mesopotamian Journal of Computer Science

The facial morphing method combines at least two images of the face to get a singular altered facial image that exposes the vulnerabilities of face recognition systems (FRS). The extensive implementation of face recognition algorithms, particularly in Automatic Border Control (ABC) systems, has raised apprehensions over potential threats, as modified passports present significant risks to national security. In this paper, a new face morphing attack detection approach has been proposed using two different datasets (StyleGAN and AMSL) for testing and validation. A new model for face morphing attack detection based on a special Convolutional Neural Networks (CNNs) architecture has been …

Deepsecure: A Novel Deep Learning Model For Effective Detection Of Attacks On Big Data In Internet Of Urban Things, Laiba Sabir, Nadeem Javaid, Mariam Akbar, Nabil Alrajeh, Safdar Hussain Bouk, Abdulaziz Aldegheishem

School of Cybersecurity Faculty Publications

The Internet of Urban Things (IoUTs) regularly generates large amounts of data, making it a focus of cyberthreats such as denial-of-service attacks and malware bot networks. Traditional intrusion detection systems struggle to detect intricate attack patterns, handle class imbalance, capture temporal dependencies, and exhibit transparency. To address these limitations, we introduce a novel deep machine learning model, DeepSecure, a hybrid model that combines Deep Belief Networks (DBN) for hierarchical feature extraction and Deep Neural Networks for attack classification. DBN is used for feature selection through unsupervised learning to extract hierarchical representations in the IoUTs network data. We assess the random …

Long-Term Traffic Prediction Using Deep Learning Long Short-Term Memory, Ange-Lionel Toba, Sameer Kulkarni, Wael Khallouli, Timothy Pennington

School of Cybersecurity Faculty Publications

Traffic conditions are a key factor in our society, contributing to quality of life and the economy, as well as access to professional, educational, and health resources. This emphasizes the need for a reliable road network to facilitate traffic fluidity across the nation and improve mobility. Reaching these characteristics demands good traffic volume prediction methods, not only in the short term but also in the long term, which helps design transportation strategies and road planning. However, most of the research has focused on short-term prediction, applied mostly to short-trip distances, while effective long-term forecasting, which has become a challenging issue …

An Integrated Machine Learning Approach For Identifying Emergency Rescue Messages On Social Media During Natural Disasters, Wael Khallouli, Jiang Li, Jingwei Huang, Ghaith Rabadi, Samuel Kovacic

School of Cybersecurity Faculty Publications

During large-scale disasters, emergency call centers are often overwhelmed by the large volume of rescue requests and calls for help. Consequently, people are turning to social media platforms to seek assistance. Rescue information posted on these platforms is extremely valuable for first responders to make informed rescue decisions. Therefore, the automatic identification of these requests from the vast amount of data posted on social media during crises is critical yet challenging. This work presents our ongoing research on applying deep learning techniques to extract actionable rescue information from social media during crises. We proposed a novel deep learning model that …

Development Of An Ecg-Based Deep Learning Model For Pediatric Congenital Heart Disease (Chd) Diagnosis, Annbar Mekouar

Selected Full-Text Master Theses 2021-

Congenital heart disease (CHD) stands as the leading congenital anomaly which affects pediatric populations throughout the world. The effectiveness of treatment depends on both early diagnosis and accurate identification but echocardiography requires manual interpretation which proves time-consuming and inconsistent especially when examining pediatric patients with their distinct cardiac systems. The research aims to create a deep learning-based diagnostic framework which uses ECG data to identify coronary artery disease subtypes in pediatric patients. The model uses high-quality datasets from Dr. Ignacio Lugones to extract R-R intervals and QRS durations through convolutional neural networks (CNNs). The system addresses pediatric-specific challenges while enhancing …

Physics-Informed Deep Learning With Kalman Filter Mixture For Traffic State Prediction, Niharika Deshpande, Hyoshin (John) Park

Engineering Management & Systems Engineering Faculty Publications

Accurate traffic forecasting is crucial for understanding and managing congestion for efficient transportation planning. However, conventional approaches often neglect epistemic uncertainty, which arises from incomplete knowledge across different spatiotemporal scales. This study addresses this challenge by introducing a novel methodology to establish dynamic spatiotemporal correlations that captures the unobserved heterogeneity in travel time through distinct peaks in probability density functions, guided by physics-based principles. We propose an innovative approach to modifying both prediction and correction steps of the Kalman Filter (KF) algorithm by leveraging established spatiotemporal correlations. Central to our approach is the development of a novel deep learning model …

Leveraging Transformer-Based Ocr Model With Generative Data Augmentation For Engineering Document Recognition, Wael Khallouli, Mohammad Shahab Uddin, Andres Sousa-Poza, Jiang Li, Samuel Kovacic

Engineering Management & Systems Engineering Faculty Publications

The long-standing practice of document-based engineering has resulted in the accumulation of a large number of engineering documents across various industries. Engineering documents, such as 2D drawings, continue to play a significant role in exchanging information and sharing knowledge across multiple engineering processes. However, these documents are often stored in non-digitized formats, such as paper and portable document format (PDF) files, making automation difficult. As digital engineering transforms processes in many industries, digitizing engineering documents presents a crucial challenge that requires advanced methods. This research addresses the problem of automatically extracting textual content from non-digitized legacy engineering documents. We introduced …

Don’T Complete It! Preventing Unhelpful Code Completion For Productive And Sustainable Neural Code Completion Systems, Zhensu Sun, Xiaoning Du, Fu Song, Shangwen Wang, Mingze Ni, Li Li, David Lo

Research Collection School Of Computing and Information Systems

Currently, large pre-trained language models are widely applied in neural code completion systems. Though large code models significantly outperform their smaller counterparts, around 70% of displayed code completions from Github Copilot are not accepted by developers. Being reviewed but not accepted, their help to developer productivity is considerably limited and may conversely aggravate the workload of developers, as the code completions are automatically and actively generated in state-of-the-art code completion systems as developers type out once the service is enabled. Even worse, considering the high cost of the large code models, it is a huge waste of computing resources and …

Deep Learning-Based Model For Automated Prediction Of Coastal Changes: A Robust Approach To Environmental Forecasting, Tsair-Fwu Lee, Chu-Ho Chang, Chin-Shiuh Shieh, Chih-Hsien Wu, Jen-Chung Shao, Chien-Liang Chiu

Journal of Marine Science and Technology–Taiwan

The coastline stands as a critical domain encompassing industry and the environment. The escalating global warming, leading to elevated sea levels and intensified wave-current interactions, has given rise to substantial coastal erosion. This predicament, in conjunction with excessive human development and Taiwan's coastal areas' extreme climatic impact, accentuates the perceptibility of coastal beach alterations. As a result, coastal erosion has emerged as a pressing issue necessitating resolution. Traditional methodologies for assessing coastline changes have conventionally relied on manual measurements. However, owing to the fluctuating distance of coastlines, influenced by tidal patterns, extended measurement processes over several months are susceptible to …

Predicting Human Steering From Optic Flow Using Deep Convolutional Neural Networks, Katie E. Bernard

Honors Theses

Human driving is a complex visuomotor task and the specific visual clues that guide it remain under investigation. While prior research has emphasized gaze-based strategies such as the Tangent Point and Future Path hypotheses, recent evidence highlights the potential role of optic flow, the visual motion pattern perceived during self-movement, as critical to steering ability. This thesis explores whether raw optic flow alone can support accurate predictions of human steering behavior. We trained a convolutional neural network to map optic flow vector fields to steering angles in a virtual reality driving simulation. The dataset, collected by Giguere et al., included …

Leveraging Sentiment Analysis Of Food Delivery Services Reviews Using Deep Learning And Word Embedding, Dheya Mustafa, Safaa M. Khabour, Mousa Al-Kfairy, Ahmed Shatnawi

All Works

Companies that deliver food (food delivery services, or FDS) try to use customer feedback to identify aspects where the customer experience could be improved. Consumer feedback on purchasing and receiving goods via online platforms is a crucial tool for learning about a company’s performance. Many English-language studies have been conducted on sentiment analysis (SA). Arabic is becoming one of the most extensively written languages on the World Wide Web, but because of its morphological and grammatical difficulty as well as the lack of openly accessible resources for Arabic SA, like as dictionaries and datasets, there has not been much research …

Ai Innovations In Rppg Systems For Driver Monitoring: Comprehensive Systematic Review And Future Prospects, Soha G. Ahmed, Katrien Verbert, Nazar Zaki, Ashraf Khalil, Hamad Aljassmi, Fady Alnajjar

All Works

Advanced technologies, notably camera-based systems using remote photoplethysmography (rPPG), are increasingly used in automotive safety to non-invasively monitor driver well-being and fatigue by measuring physiological metrics like heart and respiration rates. This review examines recent advancements in machine learning algorithms and signal processing for rPPG in driver monitoring. A literature search up to April 2, 2024, across major databases, identified 344 studies; 29 were analyzed in depth, focusing on: 1) rPPG signal extraction and heart rate estimation, where deep learning improved accuracy; 2) fatigue detection, showing benefits of multimodal data fusion; 3) mental state monitoring, with machine learning classifying cognitive …

Deep Learning Approaches For Eeg-Based Biometrics: A Systematic Review, Ali E. Albaiati, Muhammad Firdaus Akbar, Murtadha D. Hssayeni, Ashraf Khalil, Mohd Nadhir Ab Wahab, Sundus Sulaiman Weli, Enas A. Raheema

All Works

Biometics such as fingerprint, face, and iris are vulnerable to spoof attacks. The unique characteristics of Electroencephalography (EEG) make it a promising biometric modality especially because of its resistance to spoofing attacks. Many deep learning methods have been proposed for EEG-based biometric systems. This systematic review examines these methods in terms of their feature extraction ability and authentication performance. We follow the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines to search IEEE Xplore, PubMed, Web of Science, ScienceDirect, and Springer databases. Initially, we identified 285 relevant articles published between 2018 and 2024. After removing duplicates and applying …

Securing The Internet Of Wetland Things (Iowt) Using Machine And Deep Learning Methods: A Survey, Guma Ali, Wamusi Robert, Maad M. Mijwil, Malik Sallam, Jenan Ayad

Mesopotamian Journal of Computer Science

Wetlands are essential ecosystems that provide ecological, hydrological, and economic benefits. However, human activities and climate change are degrading their health and jeopardizing their long-term sustainability. To address these challenges, the Internet of Wetland Things (IoWT) has emerged as an innovative framework integrating advanced sensing, data collection, and communication technologies to monitor and manage wetland ecosystems. Despite its potential, the IoWT faces substantial security and privacy risks, compromising its effectiveness and hindering adoption. This survey explores integrating machine learning (ML) and deep learning (DL) techniques as solutions to address the security threats, vulnerabilities, and challenges inherent in IoWT ecosystems. The …

Pushing The Boundaries Of Large Language Models: Innovations And Limitations In Nlp, Finance, And Mathematics, A M Muntasir Rahman

Dissertations

Large Language Models (LLMs) have emerged as transformative tools across a spectrum of domains, yet their practical deployment reveals a blend of remarkable potential and notable limitations. This research explores innovative methodologies to extend the capabilities of LLMs while addressing critical challenges in their evaluation and application. By leveraging rule-based approaches, the in-context learning capabilities of LLMs, and human-in-the-loop validation across three focused studies, this research introduces robust strategies for dataset synthesis, model enhancement, and model assessment in three distinct domains: natural language processing, financial sentiment analysis, and mathematical reasoning

The first study proposes an efficient data augmentation framework, EASE, …

Machine Learning Methods For Pattern Recognition Analysis Of Genomic And Molecular Data, Kuang Du

Dissertations

While immune therapies achieve remarkable success in treating various cancers, only a subset of patients achieves a durable clinical response, and many exhibit innate or acquired resistance. Precision medicine aims to tailor treatments to individual patients based on specific biological markers, ensuring that each patient receives the therapy most likely to be effective. Predictive biomarkers and gene signatures offer potential for more personalized treatment strategies by identifying patients likely to benefit. Recent studies suggest that gene signatures, comprising sets of genes, hold predictive value for certain clinical variables. Typically derived from biological expert knowledge, these signatures demonstrate substantial predictive potential, …

Automated Segmentation Of The Ulnar Nerve In Mri Using Deep Learning Techniques, Akhil Nagulapalli

Theses

Cubital Tunnel Syndrome (CuTS), a condition caused by compression of the ulnar nerve, results in numbness, tingling, pain, and even muscle atrophy, affecting fine motor skills and diminishing patient quality of life. Accurate diagnosis of CuTS is challenging, as current diagnostic methods—including clinical exams, nerve conduction studies, and unaided MRI—often lack the precision to reliably identify the nerve and detect compression in its early stages. Deep learning-based segmentation offers a promising solution, enabling precise and automated identification of nerve structures in MRI images, which could significantly improve diagnostic accuracy and support timely intervention.

A novel deep learning model for segmenting …

Artificial Intelligence In Fetal And Pediatric Echocardiography, Alan Wang, Tam T Doan, Charitha Reddy, Pei-Ni Jone

Faculty, Staff and Students Publications

Echocardiography is the main modality in diagnosing acquired and congenital heart disease (CHD) in fetal and pediatric patients. However, operator variability, complex image interpretation, and lack of experienced sonographers and cardiologists in certain regions are the main limitations existing in fetal and pediatric echocardiography. Advances in artificial intelligence (AI), including machine learning (ML) and deep learning (DL), offer significant potential to overcome these challenges by automating image acquisition, image segmentation, CHD detection, and measurements. Despite these promising advancements, challenges such as small number of datasets, algorithm transparency, physician comfort with AI, and accessibility must be addressed to fully integrate AI …

Predicted Water Yield Of Open-Pit Metal Mines Based On A Bi-Rnn And Gms Coupling Model, Zhao Yuxing, Li Xiangwen

Coal Geology & Exploration

Objective Accurately predicting water yield of mine before mining can provide directive guidance for preventing potential water hazards and ensuring safe production. Methods To enhance the prediction accuracy and stability of water yield of open-pit metal mines, for which atmospheric precipitation acts as the primary recharge source of water, this study developed a prediction model that coupled a bidirectional recurrent neural network (Bi-RNN) and the Groundwater Modeling System (GMS) software. Specifically, based on historical forecasted precipitation data provided by the Global Forecast System (GFS), the fluctuation pattern of differences between predicted forecasted and actual precipitation was analyzed. After being corrected …

Not All Samples Are Created Equal: Task-Aware Informative Sampling And Adaptive Inference For Efficient Edge Ai, Rebati Gaire

School of Computing: Dissertations, Theses, and Student Research

The rapid proliferation of Internet of Things (IoT) devices has resulted in an unprecedented influx of data generated at the edge by billions of sensors. Traditional approaches relying on cloud-based processing are increasingly inadequate due to constraints in bandwidth, latency, and privacy. Edge computing has emerged as a transformative paradigm, enabling real-time data processing and decision-making by decentralizing computation to the edge. While the integration of deep learning into edge environments—termed edge intelligence—promises autonomous and personalized operations, it is hindered by challenges such as limited computational resources, energy constraints, and data redundancies.

This thesis addresses these challenges by presenting three …

Adan: Adaptive Nesterov Momentum Algorithm For Faster Optimizing Deep Models, Xingyu Xie, Pan Zhou, Huan Li, Zhouchen Lin, Shuicheng Yan

Research Collection School Of Computing and Information Systems

In deep learning, different kinds of deep networks typically need different optimizers, which have to be chosen after multiple trials, making the training process inefficient. To relieve this issue and consistently improve the model training speed across deep networks, we propose the ADAptive Nesterov momentum algorithm, Adan for short. Adan first reformulates the vanilla Nesterov acceleration to develop a new Nesterov momentum estimation (NME) method, which avoids the extra overhead of computing gradient at the extrapolation point. Then Adan adopts NME to estimate the gradient's first- and second-order moments in adaptive gradient algorithms for convergence acceleration. Besides, we prove that …

Domain-Specific Machine Learning Approaches For Geospatial Problems, Shine Bedi

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

This dissertation explores novel algorithms for complex geospatial problems at the intersection of environmental, social, and computational sciences. Emphasizing the unique challenges of the geospatial domain, particularly the deviation from the independent and identical distribution (IID) assumption, the research spans various methodologies across different domains, demonstrating the benefits of specialized approaches in spatial analysis.

First, we show that machine learning techniques can be effectively used in environmental modeling, which often has severe class imbalance challenges. Using artificial neural networks (ANN), support vector machines (SVM), and extreme gradient boosting (XGB) and techniques to address class imbalance provides insights into groundwater quality …

Variable Selection In Distance Metric Learning And Triplet Constraints For Deep Learning Based Ordinal Classification, James D. Clothier

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The purpose of this research is to augment linear and kernelized ordinal distance metric learning (L/KODML) techniques with a proposed variable selection methodology that integrates the Sequential Multi-Response Feature Selection (SMuRFS) algorithm. Additionally, we aim to embed ordinal triplet constraints into a deep learning architecture, and to propose a general framework for deep learning-based ordinal classification. A variety of simulation studies and real data experiments were conducted to evaluate the various methodologies. For the distance metric learning and variable selection, results showed that the integration of SMuRFS performed effective variable selection and improved prediction accuracy. For the triplet constraints, incorporating …

Decoding Neural Networks: An Information-Theoretic Guide To Interpretability, Error Analysis And Efficiency, Mackenzie J. Meni

Theses and Dissertations

This dissertation addresses critical challenges in neural network design by leveraging entropy-based techniques to improve model efficiency, interpretability, and bias reduction. Focusing on the unique demands of computer vision applications, particularly object detection and classification for real-time systems, this work introduces a series of innovative methods centered on information theory. At the core of these methods is the Probabilistic Explanations of Entropic Knowledge (PEEK) framework, a tool developed to analyze and visualize entropy distributions across feature maps. PEEK offers insights into information flow within neural networks, making it possible to pinpoint layers that contribute meaningfully to decision-making or identify those …

Sustainable Energysense: A Predictive Machine Learning Framework For Optimizing Residential Electricity Consumption, Murad Al-Rajab, Samia Loucif

All Works

In a world where electricity is often taken for granted, the surge in consumption poses significant challenges, including elevated CO2 emissions and rising prices. These issues not only impact consumers but also have broader implications for the global environment. This paper endeavors to propose a smart application dedicated to optimizing the electricity consumption of household appliances. It employs Augmented Reality (AR) technology along with YOLO to detect electrical appliances and provide detailed electricity consumption insights, such as displaying the appliance consumption rate and computing the total electricity consumption based on the number of hours the appliance was used. The application …