Digital Commons Network^™

Multi-Modal Mri Based Segmentation Of Brain Metastases Using Adaptive Self-Attention, Evan Savaria

Computer Science Faculty Publications

Brain metastases (BMs) are the most common adult central nervous system malignancy, affecting 20–40% of cancer patients. Accurate segmentation of metastatic lesions in multi-modal MRI is essential for treatment planning and prognosis however, manual delineation is time consuming and prone to variability. Traditional deep learning models such as U-Net, have improved segmentation accuracy but capture limited long-range dependencies and struggle with variations in metastasis size, shape, and distribution. This study introduces the Adaptive Integrated Multi-modal Segmentation (AIMS) model, an adaptive self-attention framework within a hybrid U-Net and Transformer architecture to enhance BM segmentation by leveraging multi-modal MRI integration. The proposed …

Coldstartcpi: Induced-Fit Theory-Guided Dti Predictive Model With Improved Generalization Performance, Qichang Zhao, Haochen Zhao, Linyuan Gao, Kai Zheng, Yajie Li, Qiao Ling, Jing Tang, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Predicting compound-protein interactions (CPIs) plays a crucial role in drug discovery. Traditional methods, based on the key-lock theory and rigid docking, often fail with novel compounds and proteins due to their inability to account for molecular flexibility and the high sparsity of CPI data. Here, we introduce ColdstartCPI, a framework inspired by induced-fit theory, which leverages unsupervised pre-training features and a Transformer module to learn both compound and protein characteristics. ColdstartCPI treats proteins and compounds as flexible molecules during inference, aligning with biological insights. It outperforms state-of-the-art sequence-based models, particularly for unseen compounds and proteins, and shows strong generalization capability …

Optiselect And Enshap: Integrating Machine Learning And Game Theory For Ischemic Stroke Prediction, Pritam Chakraborty, Anjan Bandyopadhyay, Sricheta Parul, Sujata Swain, Partha Sarathy Banerjee, Tapas Si, Hong Qin, Saurav Mallik

Computer Science Faculty Publications

Stroke analysis using game theory and machine learning techniques. The study investigates the use of the Shapley value in predictive ischemic brain stroke analysis. Initially, preference algorithms identify the most important features in various machine learning models, including logistic regression, K-nearest neighbor, decision tree, support vector machine (linear kernel), support vector machine ( RBF kernel), neural networks, etc. For each sample, the top 3, 4, and 5 features are evaluated and selected to evaluate their performance. The Shapley value method was used to rank the models using their best four features based on their predictive capabilities. As a result, better-performing …

Sting: A Stealthy Backdoor Attack On Gnn-Based Malicious Domain Detection Via Dns Perturbations, Muhammad Anan, Mahmoud Nazzal, Abdallah Khreishah, Issa Khalil, Nhathai Phan, Ahmad Sawalmeh

Computer Science Faculty Publications

Detecting malicious Internet domains is essential for safeguarding against various online threats. The current approach to detecting malicious domains (MDD) employs a graph neural network (GNN) method, which uses DNS logs to construct heterogeneous graphs for determining the maliciousness of unknown domains. Despite its success, this method is vulnerable to data poisoning attacks where an adversary can manipulate specific graph nodes to implant a backdoor into the model during training. To showcase the vulnerability, we propose a stealthy trigger injection attack on node features and graph structure in MDD, dubbed (STING). The attacker carefully manipulates selected features and edges of …

Normalizing Images In Various Weather And Lighting Conditions Using Colorpix2pix Generative Adversarial Network, Sanjida Tasnim, Ashif Mahmud Mostafa, Azmain Morshed, Namreen Shaiyaz, Shakib Mahmud Dipto, Saad Aloteibi, Mohammad Ali Moni, Md. Golam Rabiul Alam, Md. Ashraful Alam

Computer Science Faculty Publications

Autonomous vehicles (AVs) are widely regarded as the future of transportation due to their tremendous benefits and user comfort. However, the AVs have been struggling with very crucial challenges, such as achieving reliable accuracy in object detection as well as faster computation required for quick decision-making. In recent years, perception systems in driverless cars have been significantly enhanced, mainly due to advances in deep-learning-based object detection systems. However, these perception systems are still heavily affected by environmental variables, such as changes in illumination, refractive interference, and adverse weather conditions, which may compromise their reliability and safety. This research proposes an …

A Survey On Deep Learning For Drug-Target Binding Prediction: Models, Benchmarks, Evaluation, And Case Studies, Kusal Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Conventional drug discovery is expensive, time-consuming, and prone to failure. Artificial intelligence has become a potent substitute over the last decade, providing strong answers to challenging biological issues in this field. Among these difficulties, drug-target binding (DTB) is a key component of drug discovery techniques. In this context, drug-target affinity and drug–target interaction are complementary and essential frameworks that work together to improve our comprehension of DTB dynamics. In this work, we thoroughly analyze the most recent deep learning models, popular benchmark datasets, and assessment metrics for DTB prediction. We look at the paradigm shift in the development of drug …

Can Llms Beat Humans On Discerning Human-Written And Llm-Generated Science News, Dominik Soós, Meng Jiang, Jian Wu

Computer Science Faculty Publications

Science news is increasingly important in connecting scientists and the public by sharing discoveries and innovations. With the rise of large language models (LLMs), there is potential to automate science news creation, but concerns exist about the quality of LLM-generated news versus human-written news. This paper explores whether LLMs can outperform humans in distinguishing between human-written and LLM-generated news. Inspired by the Chain-of-Thought prompting method, we designed a simple yet effective variant called Guided Few-shot (GFS), which encodes the characteristics of news of two types with examples. Our experiments indicated that GFS with just a single example effectively boosted the …

Geometric Gnns For Charged Particle Tracking At Gluex, Ahmed Hossam Mohammed, Kishansingh Rajput, Simon Taylor, Denis Furletov, Sergey Furletov, Malachi Schram

Computer Science Faculty Publications

Nuclear physics experiments are aimed at uncovering the fundamental building blocks of matter. The experiments involve high-energy collisions that produce complex events with many particle trajectories. Tracking charged particles resulting from collisions in the presence of a strong magnetic field is critical to enable the reconstruction of particle trajectories and precise determination of interactions. It is traditionally achieved through combinatorial approaches that scale worse than linearly as the number of hits grows. Since particle hit data naturally form a point cloud and can be structured as graphs, graph neural networks (GNNs) emerge as an intuitive and effective choice for this …

Adapting Online Customer Reviews For Blind Users: A Case Study Of Restaurant Reviews, Mohan Sunkara, Akshay Kolgar Nayak, Sandeep Kalari, Yash Prakash, Sampath Jayarathna, Hae-Na Lee, Vikas Ashok

Computer Science Faculty Publications

Online reviews have become an integral aspect of consumer decision-making on e-commerce websites, especially in the restaurant industry. Unlike sighted users who can visually skim through the reviews, perusing reviews remains challenging for blind users, who rely on screen reader assistive technology that supports predominantly one-dimensional narration of content via keyboard shortcuts. In an interview study, we uncovered numerous pain points of blind screen reader users with online restaurant reviews, notably, the listening fatigue and frustration after going through only the first few reviews. To address these issues, we developed QuickCue assistive tool that performs aspect-focused sentiment-driven summarization to reorganize …

From Philosophy To Nlu: Evolving Definitions Of Research Hypotheses, Jian Wu, Sarah Rajtmajer

Computer Science Faculty Publications

Over the past decades, alongside advancements in natural language processing, significant attention has been paid to training models to automatically extract, understand, test, and generate hypotheses in open and scientific domains. However, interpretations of the term hypothesis for various natural language understanding (NLU) tasks have migrated from traditional definitions in the natural, social, and formal sciences. Even within NLU, we observe differences defining hypotheses across literature. In this paper, we overview and delineate various definitions of hypothesis. Especially, we discern the nuances of definitions across recently published NLU tasks. We highlight the importance of well-structured and well-defined hypotheses, particularly as …

Decode The Workload: Training Deep Learning Models For Efficient Compute Cluster Representation, Ahmed Hossam Mohammed, Mark Jones, Diana Mcspadden, Malachi Schram, Bryan Hess, Kishansingh Rajput

Computer Science Faculty Publications

In this study, we address the mounting challenge of monitoring high throughput computing clusters running computationally intensive jobs, which increasingly strains system administrators. We develop autoencoders that analyze traces of Linux kernel CPU metrics to capture salient system features by producing robust compressed embeddings for various downstream tasks. In addition, we employ graph neural networks to incorporate contextual information from surrounding CPUs and assess their performance. We also demonstrate the enhanced job differentiation achieved by increasing the sampling rate of these traces. Our models are evaluated based on their ability to generate meaningful latent representations, detect anomalies, and distinguish between …

Neural Topic Modeling Via Contextual And Graph Information Fusion, Jiyuan Liu, Jiaxing Yan, Chunjiang Zhu, Xingyu Liu, Qing Li, Yanghui Rao

Computer Science Faculty Publications

Topic modeling is a powerful unsupervised tool for knowledge discovery. However, existing work struggles with generating limited-quality topics that are uninformative and incoherent, which hindering interpretable insights from managing textual data. In this paper, we improve the original variational autoencoder framework by incorporating contextual and graph information to address the above issues. First, the encoder utilizes topic fusion techniques to combine contextual and bag-of-words information well, and meanwhile exploits the constraints of topic alignment and topic sharpening to generate informative topics. Second, we develop a simple word co-occurrence graph information fusion strategy that efficiently increases topic coherence. On three benchmark …

Adversarially Attacking Graph Properties And Sparsification In Graph Learning, Chunjiang Zhu, Blake Gaines, Jing Deng, Jinbo Bi

Computer Science Faculty Publications

Graph neural networks and graph transformers explicitly or implicitly rely on fundamental properties of the underlying graph, such as spectral properties and shortest-path distances. However, it is still not clear how these graph properties are vulnerable to adversarial attacks and what impacts this has on the downstream graph learning. Moreover, while graph sparsification has been used to improve computational cost of learning over graphs, its susceptibility to adversarial attacks has not been studied. In this paper, we study adversarial attacks on graph properties and graph sparsification and their impacts on downstream graph learning, paving the way for how to protect …

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 …

S²Il: Structurally Stable Incremental Learning, S. Balasubramanian, P. Yedu Krishna, Talasu Sai Sriram, M. Sai Subramaniam, Manepalli Pranav Phanindra Sai, Ravi Mukkamala

Computer Science Faculty Publications

Feature Distillation (FD) strategies are proven to be effective in mitigating Catastrophic Forgetting (CF) seen in Class Incremental Learning (CIL). However, current FD approaches enforce strict alignment of feature magnitudes and directions across incremental steps, limiting the model’s ability to adapt to new knowledge. In this paper, we propose Structurally Stable Incremental Learning (S²IL), a FD method for CIL that mitigates forgetting by focusing on preserving the overall spatial patterns of features which promote flexible (plasticity) yet stable representations that preserve old knowledge (stability). We also demonstrate that our proposed method S²IL achieves strong incremental accuracy and outperforms other FD …

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 …

Delivery Of Medical Supplies To Remote Locations Via Unmanned Aerial Vehicles: Approaches, Challenges, And Solutions, Meshari Aljohani, Ravi Mukkamala, Stephanie Olariu

Computer Science Faculty Publications

Unmanned Aerial Vehicles (UAVs) are becoming more important in improving healthcare logistics, in particular due to their cost effectiveness, minimized risk, and versatile operational capabilities. This study explores the deployment of autonomous UAVs to deliver medical supplies to remote areas. Advances in ledger technology, smart contracts, and machine learning have transformed tasks previously managed by human teams or manually controlled UAVs into fully autonomous missions. We present a comprehensive analysis of the challenges and initial solutions vital for the effective use of autonomous UAVs in the delivery of medical supplies. In addition, we propose a machine-learning model to optimize UAV …

An Analytical Review Of Preprocessing Techniques In Bengali Natural Language Processing, Sovon Chakraborty, Protiva Das, Shakib Mahmud Dipto, Md Aktaruzzaman Pramanik, Jannatun Noor

Computer Science Faculty Publications

Research in Bengali Natural Language Processing (BNLP) is rapidly expanding. Despite being one of the most widely spoken languages in the world, BNLP research remains insufficient, particularly in Bengali speech recognition. The languages rich morphology, agglutinative structure, and diverse dialects make text and speech processing especially challenging. However, these challenges can be addressed with effective preprocessing techniques. Various organizations in Bangladesh and West Bengal are integrating Natural Language Processing (NLP) into their services, but without a thorough understanding of preprocessing, these implementations remain incomplete. Applying proper preprocessing techniques to the Bengali language will serve as a foundation for developing robust …

Point Cloud-Based Diffusion Models For The Electron-Ion Collider, Jack Y. Araz, Vinicius Mikuni, Felix Ringer, Nobuo Sato, Fernando Torales Acosta, Richard Whitehill

Physics Faculty Publications

At high-energy collider experiments, generative models can be used for a wide range of tasks, including fast detector simulations, unfolding, searches of physics beyond the Standard Model, and inference tasks. In particular, it has been demonstrated that score-based diffusion models can generate high-fidelity and accurate samples of jets or collider events. This work expands on previous generative models in three distinct ways. First, our model is trained to generate entire collider events, including all particle species with complete kinematic information. We quantify how well the model learns event-wide constraints such as the conservation of momentum and discrete quantum numbers. We …

Predictive Maintenance In Naval Vessel Propulsion Systems For Enhanced Marine Operations Using A Bigmm-Hmm Framework With Divergence-Based Clustering, Farshid Javadnejad, Hyoshin John Park, Samuel Kovacic, Andres Sousa-Poza

Engineering Management & Systems Engineering Faculty Publications

This study introduces a BiGMM-HMM Integration Framework designed to improve predictive maintenance strategies for naval vessel propulsion systems, addressing the need for efficient and reliable operation in marine engineering applications. The framework effectively manages multimodal sensor data by leveraging a unique combination of Gaussian Mixture Models (GMMs) and Hidden Markov Models (HMMs) in a bidirectional architecture. It analyses the dynamic interactions between sensors and subsystems. Two preprocessing methods are evaluated: Method 1 focuses on subsystem interactions, employing divergence-based root cause analysis to identify key sensor variables by clustering of sensors and subsystems. In contrast, Method 2 processes the entire dataset …

Maritime Industry Cybersecurity Threats In 2025: Advanced Persistent Threats (Apts), Hacktivism And Vulnerabilities, Minodora Badea, Olga Bucovetchi, Adrian V. Gheorghe, Mihaela Hnatiuc, Gabriel Raicu

Engineering Management & Systems Engineering Faculty Publications

Background: The maritime industry, vital for global trade, faces escalating cyber threats in 2025. Critical port infrastructures are increasingly vulnerable due to rapid digitalization and the integration of IT and operational technology (OT) systems. Methods: Using 112 incidents from the Maritime Cyber Attack Database (MCAD, 2020-2025), we developed a novel quantitative risk assessment model based on a Threat-Vulnerability-Impact (T-V-I) framework, calibrated with MITRE ATT&CK techniques and validated against historical incidents. Results: Our analysis reveals a 150% rise in incidents, with OT compromise identified as the paramount threat (98/100 risk score). Ports in Poland and Taiwan face the …

Optimizing Port Logistics Through Generative Ai: Revolutionizing Efficiency And Resilience In The Maritime Industry, Minodora Badea, Olga Bucovetchi, Adrian V. Gheorghe, Gabriel Raicu

Engineering Management & Systems Engineering Faculty Publications

The maritime industry faces growing challenges in optimizing port logistics due to increasing trade volumes, environmental regulations, and supply chain disruptions. This comprehensive literature review examines the transformative role of artificial intelligence (AI), with particular focus on generative AI, in enhancing efficiency and resilience in port operations. Through systematic analysis of 23 peer-reviewed studies published between 2021-2025, this review synthesizes advancements in real-time data integration, machine learning, digital twins, IoT, and autonomous systems that collectively improve operational decision-making, risk management, and environmental sustainability. Key findings reveal that machine learning applications achieve 90% effectiveness ratings in operational optimization, while predictive analytics …

Empirical Assessment Of Cybersecurity Competencies Through Human-Generative Artificial Intelligence (Genai) Teaming, Dariusz Witko

CCAC Theses and Dissertations

The critical shortage of skilled cybersecurity professionals, with over 750,000 unfilled positions in the United States (U.S.), combined with rising practitioner burnout and the complexity of modern cyber threats, poses significant risks to national security. As Generative Artificial Intelligence (GenAI) emerges as a potential tool to support cybersecurity operations, its role in assisting human analysts with high-demand tasks offers both opportunities and challenges. While GenAI can improve efficiency, it also introduces adversarial risks if manipulated by malicious actors. This study investigated how human-GenAI collaboration can address these challenges, focusing on the fundamental cybersecurity knowledge, skills, and task completion required for …

Uso De Herramientas De Inteligencia Artificial Generativa Por Parte De Docentes En Una Escuela Del Suroeste De Puerto Rico, Glorimar N. Rodríguez Guiliani

Theses and Dissertations

Esta disertación aplicada fue diseñada para investigar el nivel de conocimiento, uso y dificultades que enfrentan los docentes de quinto a duodécimo grado en una escuela privada del suroeste de Puerto Rico respecto a tecnologías emergentes las cuales presentan desafíos significativos para los docentes y los estudiantes. Se exploró la utilización de herramientas de inteligencia artificial generativa (GenAI) como ChatGPT dentro y fuera del aula para actividades pedagógicas y administrativas.

Los hallazgos revelaron una notable carencia en el conocimiento docente sobre el uso y habilidades de la inteligencia artificial. Se identificó, también, una deficiencia en la capacidad de los docentes …

Predicting Mental Health Disparities Using Machine Learning For African Americans In Southeastern Virginia, Ismail El Moudden, Michael C. Bittner, Matvey V. Karpov, Isaac O. Osunmakinde, Akosua Acheamponmaa, Breshell J. Nevels, Mamadou T. Mbaye, Tonya L. Fields, Karthiga Jordan, Messaoud Bahoura

Department of Obstetrics & Gynecology Faculty Publications

This study examined mental health disparities among African Americans using AI and machine learning for outcome prediction. Analyzing data from African American adults (18–85) in Southeastern Virginia (2016–2020), we found Mood Affective Disorders were most prevalent (41.66%), followed by Schizophrenia Spectrum and Other Psychotic Disorders. Females predominantly experienced mood disorders, with patient ages typically ranging from late thirties to mid-forties. Medicare coverage was notably high among schizophrenia patients, while emergency admissions and comorbidities significantly impacted total healthcare charges. Machine learning models, including gradient boosting, random forest, neural networks, logistic regression, and Naive Bayes, were validated through 100 repeated 5-fold cross-validations. …

Symp25s: A Multi-View Feature Construction And Multi-Encoder-Decoder Transformer Architecture For Time Series Classification, Zihan Li, Wei Ding, Inal Mashukov, Ping Chen, Scott Crouter

Paul English Applied Artificial Intelligence (AI) Institute Publications

Time series data plays a significant role in many research fields since it can record and disclose the dynamic trends of a phenomenon with a sequence of ordered data points. Time series data is dynamic, of variable length, and often contains complex patterns, which makes its analysis challenging especially when the amount of data is limited. In this paper, we propose a multi-view feature construction approach that can generate multiple feature sets of different resolutions from a single dataset and produce a fixed-length representation of variable-length time series data. Furthermore, we propose a multi- encoder-decoder Transformer (MEDT) architecture to effectively …

Symp25s: Can Llm Detect Dementia?, Rishank Singh, Youxiang Zhu, Xiaohui Liang, John A. Batsis, Caroline Summerour

Paul English Applied Artificial Intelligence (AI) Institute Publications

High Cost of Traditional Screening: Formal cognitive assessments for dementia are resource-intensive and not easily accessible for large-scale screening. Speech-Based Alternatives: Existing speech-based methods (e.g., picture description, telephone interviews) aim to address this but have limitations. Lack of Natural Dialogue: These conventional approaches often use rigid, repetitive prompts and do not simulate real conversations. Engagement Issues: Repetition and lack of conversational depth can reduce engagement and affect the accuracy of responses over time. Untapped Potential of LLMs: Large language models (LLMs) are capable of generating natural, coherent, and adaptive dialogue. Research Gap: The application of LLMs for dementia detection through …

Flexible Hybrid Self-Powered Piezo-Triboelectric Nanogenerator Based On Bto-Pvdf/Pdms Nanocomposites For Human Machine Interaction, Wentao Dong, Mengyun Li, Chang Chen, Kun Xie, Jinhua Hong, Lin Yang

Civil & Environmental Engineering Faculty Publications

As flexible and wearable electronics play more and more important role in smart watches, smart glass and virtual reality, and the power supply to the wearable electronics have been revealed more attentions for long-term usage and continuous healthy monitoring. To overcome the challenge, flexible self-powered BTO-PVDF/PDMS piezoelectric-triboelectric electric hybrid generators (BPP-HNG) are developed to human gesture monitoring and human machine interaction (HMI) application without external power supply. BPP-HNG based on BTO-PVDF and PDMS films are prepared by sol-gel and spin-coating method. When the BTO content is 20 wt.%, BPP-HNG exhibits better electrical performance with an output voltage of 20.51 V. …

Optimizing Ai Language Models: A Study Of Chatgpt-4 Vs. Chatgpt-4o, Md Nurul Absar Siddiky, Muhammad Enayetur Rahman, Md Fayaz Bin Hossen, Muhammad Rezaur Rahman, Md. Shahadat Jaman

Electrical & Computer Engineering Faculty Publications

This paper presents a comparative analysis of OpenAI's GPT-4 and its optimized variant, GPT-4o, focusing on their architectural differences, performance, and real-world applications. GPT-4, built upon the Transformer architecture, has set new standards in natural language processing (NLP) with its capacity to generate coherent and contextually relevant text across a wide range of tasks. However, its computational demands, requiring substantial hardware resources, make it less accessible for smaller organizations and real-time applications. In contrast, GPT-4o addresses these challenges by incorporating optimizations such as model compression, parameter pruning, and memory-efficient computation, allowing it to deliver similar performance with significantly lower computational …

T3-Ciders: Fostering A Community Of Practice In Ci-And Data Enabled Cybersecurity Research Through A Train-The-Trainer Program, Wirawan Purwanto, Mohan Yang, Peng Jiang, Masha Sosonkina

Electrical & Computer Engineering Faculty Publications

We present a training program named T³-CIDERS, the Train- The-Trainer approach to fostering cyberinfrastructure (CI)- and Data-Enabled Research in CyberSecurity. T³-CIDERS is a train-the-trainer program for advanced cyberinfrastructure (CI) skills that is designed to be synergistic with research, teaching, and learning activities in cybersecurity and cyber-related disciplines. The participants, termed 'future trainers' (FTs), are trained in effective instructional design and CI hands-on materials from DeapSECURE, developed in a previous CyberTraining program. T³-CIDERS aims to enhance cybersecurity research and education through broader adoption of advanced CI techniques such as artificial intelligence, big data, parallel programming, and platforms like high-performance computing (HPC) …