Computer Sciences Commons^™

Computational Methods For Single-Cell And Multi-Omic Data Integration And Regulatory Network Inference, Jianlan Ren

Dissertations

Single-cell and multi-omic technologies have transformed the dissection of cellular heterogeneity and regulatory dynamics in health and disease. However, the high dimensionality, technical variability, and biological complexity of these datasets present significant challenges for integration, annotation, and interpretation. In this dissertation, a suite of computational approaches is introduced to address key problems in single-cell and multi-omic data analysis through model-based innovations and applied statistical frameworks.

First, a constrained deep learning framework for single-cell data integration, label transfer, and clustering is proposed. By incorporating biologically motivated constraints into the training process, robust performance is achieved across simulated and benchmark datasets spanning …

Patterns Of Llm Weaponization: A Comparative Analysis Of Exploitation Incidents Across Commercial Ai Systems, George Antoniou

Faculty and Staff Publications & Presentations

This comparative study examines patterns of Large Language Model (LLM) weaponization through systematic analysis of four major exploitation incidents spanning from 2023-2025. While existing research focuses on isolated incidents or theoretical vulnerabilities, this study provides one of the first comprehensive comparative frameworks analyzing exploitation patterns across state-sponsored cyber-espionage (Anthropic Claude incident), academic security research (GPT- 4 autonomous privilege escalation), social engineering platforms (SpearBot phishing framework), and underground criminal commoditization (WormGPT/FraudGPT ecosystem). Through comparative analysis across eight dimensions: Adversary sophistication, target selection, exploitation techniques, autonomy levels, detection evasion, attribution challenges, defensive gaps, and capability democratization, this research identifies critical cross-case patterns …

Quantum Readiness In Cybersecurity Education: A Framework For Preparing The Next Generation In The Post-Quantum Era, George Antoniou

Faculty and Staff Publications & Presentations

This framework addresses the critical gap between post-quantum standards and workforce readiness. Shor's algorithm demonstrates that sufficiently powerful quantum computers can break the cryptographic foundations of internet security. While the cryptography research community has developed quantum-resistant algorithms, educational institutions have not prepared students to implement these solutions. Recent surveys show fewer than half of organizations have begun planning for post-quantum cryptography (PQC) transitions (Entrust Cybersecurity Institute, 2024; U.S. Government Accountability Office, 2023; (ISC)², 2024). The NICE Framework (Newhouse, Keith, Scribner, & Witte, 2017) outlines the knowledge and skills that cybersecurity professionals should possess. The framework omits post-quantum cryptography entirely. Organizations …

From Enhancement To Substitution: A Strategic Provocation On Simulation-Based Sport, Grant B. Morgan, Andreas Stamatis

Journal of Applied Sport Management

Advances in artificial intelligence, large-scale machine learning, and simulation technologies are rapidly transforming how sport is played, analyzed, and consumed. To date, most scholarly and industry discussions frame these technologies as tools that enhance embodied sport by improving performance, officiating, media production, and fan engagement. This paper extends that conversation by posing a more provocative strategic question: under what conditions might simulation move from enhancement to substitution? Focusing explicitly on sport as a business and entertainment enterprise, we argue that many of sport’s core sources of cultural and economic value—uncertainty of outcome, narrative continuity, legitimacy, and collective meaning—are structurally …

Revisiting Underwater Image Enhancement For Object Detection: A Unified Quality–Detection Evaluation Framework, Ali Awad, Ashraf Saleem, Sidike Paheding, Evan Lucas, Serein Al-Ratrout, Timothy C. Havens

Michigan Tech Publications

Underwater images often suffer from severe color distortion, low contrast, and reduced visibility, motivating the widespread use of image enhancement as a preprocessing step for downstream computer vision tasks. However, recent studies have questioned whether enhancement actually improves object detection performance. In this work, we conduct a comprehensive and rigorous evaluation of nine state-of-the-art enhancement methods and their interactions with modern object detectors. We propose a unified evaluation framework that integrates (1) a distribution-level quality assessment using a composite quality index (Q-index), (2) a fine-grained per-image detection protocol based on COCO-style mAP, and (3) a mixed-set upper-bound analysis that quantifies …

Real-Time Likelihood Map Generation To Localize Short-Duration Gamma-Ray Transients, Jeremy Buhler, Marion Sudvarg

Computer Science Faculty Research & Creative Works

High-energy transient astrophysical phenomena, such as supernovae and binary neutron star mergers, benefit from a multi-wavelength investigation in which a space- or balloon-based omnidirectional telescope detects and localizes early high-energy emissions (such as a gamma-ray burst), then alerts a narrow-field follow-up instrument to observe the source. The high-energy telescope must provide a map that assigns to each sky location a likelihood that the source appears there. To issue prompt alerts despite limits on communication bandwidth and latency, it is desirable to compute this map aboard the high-energy telescope, but doing so requires rapid response while computing under stringent size, weight, …

Fpga-Based Data Processing Using High-Level Synthesis On The Antarctic Demonstrator For The Advanced Particle-Astrophysics Telescope (Adapt), Marion Sudvarg, Marion Sudvarg, Longhao Huang, Boran Yang, Blake Bal, Roger Chamberlain, Jeremy Buhler, Leonardo Di Venere, Leonardo Di Venere, Davide Serini, James Buckley, Matthew Andrew, Blake Bal, Elisabetta E. Bissaldi, Richard G. Bose, Dana Braun, James H. Buckley, Jeremy Buhler

Computer Science Faculty Research & Creative Works

FPGAs are widely deployed on high-energy astrophysics telescopes to read out sensor data from front-end electronics. To support continuous data streams or high trigger rates, FPGA logic may be employed to process raw sensor readout values, reducing the volume of data transmitted, processed, and stored by downstream CPU-based computational platforms. Across instruments, these FPGA-based processing pipelines often have similar semantics and share common stages. However, diverse telescope designs require unique implementations of the constituent algorithms, and the logic is often rewritten from scratch for a new instrument. Writing, simulating, and debugging firmware is difficult and time consuming. However, High-Level Synthesis …

Instrument Response Functions Of The Antarctic Demonstrator For The Advanced Particle-Astrophysics Telescope (Adapt), Wenlei Chen, James H. Buckley, Marion Sudvarg

Computer Science Faculty Research & Creative Works

The Antarctic Demonstrator for the Advanced Particle-astrophysics Telescope (ADAPT) gamma-ray/cosmic-ray instrument serves as a precursor to the proposed APT mission. The APT mission is designed to improve sensitivity in the MeV-TeV gamma-ray range by an order of magnitude compared to current missions and is optimized for dark-matter and multimessenger research. The ADAPT instrument uses scintillating fibers for particle tracking and sodium-doped cesium iodide (CsI:Na) tiles read out with wavelength shifting (WLS) fibers for imaging, with solid-state silicon photomultipliers (SiPMs) for calorimetry. It includes four layers of imaging calorimeter detectors and scintillating-fiber trackers, functioning both as a Compton and Pair telescope …

Performance Modeling And Improvements On The Grb Source Localization Streaming Pipeline Aboard The Antarctic Demonstrator For The Advanced Particle-Astrophysics Telescope (Adapt), Ye Htet, Ye Htet, Marion Sudvarg, Marion Sudvarg, Honghao Yang, Jeremy Buhler, Roger Chamberlain, Wenlei Chen, Wenlei Chen, James Buckley, Matthew Andrew, Blake Bal, Elisabetta E. Bissaldi, Richard G. Bose, Dana Braun, James H. Buckley, Jeremy Buhler, Eric Burns

Computer Science Faculty Research & Creative Works

The Advanced Particle-astrophysics Telescope (APT) is a mission concept for a space-based gamma-ray telescope whose capabilities include prompt localization of gamma-ray bursts (GRBs) to support multi-wavelength and multi-messenger astrophysics. ADAPT — APT's balloon-borne prototype — can localize GRBs in well under a second using on-board computing hardware. ADAPT will partner with ground-based, fast-slewing optical telescopes, rapidly providing alerts that enable the partner to observe a short-duration burst within a few seconds of detection. In this work, we investigate the utility of having ADAPT issue progressively more accurate location estimates for a GRB as detected Compton events from the burst accumulate …

Panda-Plus: Improved Dataset Of Prostate Whole Slide Images From Panda Challenge With Pixel-Level Expert Annotations, Spencer Hopson, Carson Mildon, Corbyn Kubalek, Joshua L. Ebbert, Ryan Vance, Lauren Laverty, Paul Urie, Dennis Della Corte

Faculty Publications

Artificial intelligence (AI)-based prostate cancer detection through whole slide images (WSIs) offers promising potential to address the global pathologist shortage while improving clinical consistency. Digital slides and improving image analysis methods encourage the creation of tools to aid in WSI classification. Despite promising advances, these tools are still limited by available training data. Current publicly available datasets, such as Kaggle's PANDA Challenge, while large in scale, rely on slide-level labels that may introduce noise and limit model reliability. Others contain detailed annotations, but are smaller in size due to manual processing efforts. In this work, we introduce PANDA-PLUS, a 546-image …

Supply Chain Network Based On Blockchain And Intelligent Agent, Hiba Hamdi Hassan, Rana Fareed Ghani

Journal of Soft Computing and Computer Applications

In agricultural supply chains, the complexity and indeterminacy pose serious challenges to traceability, reliability and confidence today. This challenge is especially acute in the olive oil industry where adulteration, wrong labeling, and uneven chemical quality threaten the actual well-being of producers and consumers. The project aims to design a blockchain-based hybrid architecture with intelligent agents (FNNs) to enhance transparency, reliability and responsiveness in the olive oil supply chain. The Blockchain component enables a completely open, tamper-proof ledger to be built in a very decentralized way and preserved as an archive of every account of its transactions. The intelligent agents contribute …

Intelligent Extensible Markup Language Encryption Using Type-2 Fuzzy Logic, Faiez Musa Lahmood Alrufaye, Seham Ahmed Hashem

Journal of Soft Computing and Computer Applications

Financial and commercial institutions increasingly rely on Extensible Markup Language (XML) files as a standard means of exchanging data. However, this extensive use has created serious security challenges due to the fact that these files contain sensitive information such as bank card numbers and expiration dates. Relying on traditional full file encryption methods achieves a high degree of security, but it causes problems related to the large file sizes that consume memory and the long encryption and decryption times, which reduces the efficiency of systems when dealing with a large number of daily transactions. Methods based on Type-1 Fuzzy Logic …

Enhanced Generative Convolutional Networks: A Hybrid Algorithm For Refinement Video Classification, Dalal Thair Mahjoub, Hala Bahjat Abdulwahab, Kesra Nermend

Journal of Soft Computing and Computer Applications

Video classification is a vital area of research due to the growing volume of video content in various applications. Accurate category across various resolutions poses challenges, which include adapting to scaling, resizing, and compression. Therefore, this paper introduces an innovative Generative Convolutional Network (GCN) set of rules tailored for multi-resolution video classes. The proposed GCN model utilizes Convolutional Neural Networks (CNNs) combined with generative modeling to enhance the extraction of functions across varying video resolutions, which is crucial for maintaining class robustness in the face of common video adjustments, such as scaling, resizing, and compression. In contrast, traditional fashions frequently …

Review Of Video Steganography By Using Deep Learning Methods: Datasets, Techniques, And Evaluations, Noor Fahem Sahib, Soukaena Hassan Hashem, Ekhlas Falih Naser

Journal of Soft Computing and Computer Applications

The growing prevalence of cyber threats, including fraud and attacks, has intensified the demand for secure methods of safeguarding confidential information exchanged between users. As telecommunications increasingly rely on multimedia data, video steganography has become a prominent technique to address these concerns. By embedding sensitive data within video files, this approach enhances protection against unauthorized access and common internet-based attacks, offering a robust layer of security in an era of escalating digital risks. With the introduction of Deep Learning (DL) steganography methods recently, video steganography can be defined as a rapidly developing subject within information security. This study provides a …

Real-Time Hand Gesture Recognition System For Abductees Rescue Using Deep Learning Techniques, Aws Saood Mohamed, Nidaa Flaih Hassan, Abeer Salim Jamil

Journal of Soft Computing and Computer Applications

Hand gesture recognition is a challenging problem in computer vision, particularly in terms of security surveillance applications. This study presents the first efficient system for abduction-related hand gesture real-time detection based on deep learning. The most critical problem is to detect and recognize hand gestures in real surveillance conditions and to be computationally effective for real-time multi-hand tracking in various lighting situations while allowing reliable surveillance beyond the 1–4 meters limitation. The proposed system consists of three main parts: The adaptive hand tracking algorithm, which has been used to create the Abductees-Rescue dataset. Introduced pose estimation You Only Look Once …

Hate Speech Detection Using Optimized Feature Representation Via Spiral-Grey Wolf Optimizer-Based Machine Learning Approaches, Noor S. Farhan, Matheel E. Abdulmunim, Hasanen S. Abdullah

Journal of Soft Computing and Computer Applications

Hate speech detection is crucial as social media diversifies. This research present a lightweight, scalable system using traditional machine learning methods along with a new approach called Spiral-Grey Wolf Optimizer (S-GWO).

S-GWO effectively selects key features that consider both meaning and content from the Term Frequency Inverse Document Frequency (TF-IDF) space, leading to high-quality representation without excessive computing power.

The propoused system was tested on Arabic and another English datasets using six machine learning methods: SVM, RF, LR, KNN, NB, and SGD. It achieved 92% accuracy and F1 score on the Arabic dataset, while reaching 100% accuracy on the English …

(R2141) Analysis Of Map^I_1 , Ph^(Oa)_2 / Ph^I_1 , Ph^O_2 / 1 Retrial Inventory Queue With Two Way Communication, (S, S) Replenishment Policy, Feedback, Bernoulli Vacation And Impatient Customers, G. Ayyappan, V. Ganesan

Applications and Applied Mathematics: An International Journal (AAM)

This work discusses about the topic as the two-way communication retrial inventory queue model, the (s, S) replenishment policy, immediate feedback, Bernoulli vacations, and impatient customers. The assumption we make is that arrivals follow a Markovian arrival process, and the server provides phase type services. When the server is idle and there is a positive inventory, an arriving customer immediately receives service. If not, arriving customers goes to orbit with infinite capacity. Only in the account of positive inventory the server renders rapid feedback for incoming call arrivals, otherwise customer departs. Outgoing calls will only be made by the server …

Measurement Of Luminous Intensity Distribution For Film And Television Led Light Sources And Its Simulation Research In Game Engines, Jingyi Suo, Baihong Lu, Che Qu

Journal of System Simulation

Abstract: To address the issues of mismatched photometric characteristics between light sources in virtual environments and real-world lighting during film and television lighting design and lighting preview using game engines, a testing solution for measuring the luminous intensity distribution for film and television LED light sources was proposed, building upon existing luminaire light intensity distribution testing systems. Based on the obtained data, a light source calibration process was constructed in the UE5 to correctly simulate the photometric characteristics of light sources in the virtual environment. Simulation results have shown that the calibration process can accurately and efficiently reproduce the …

Improved Pid Search Algorithm For Uav Path Planning In Mountainous Environments, Yi Peng, Yunkui Lei, Qingqing Yang, Hui Li, Jianming Wang

Journal of System Simulation

Abstract: To address the challenges of UAV path planning in mountainous environments, including high computational complexity and suboptimal optimization performance, and the disadvantages of the PIDbased search algorithm, such as low optimization accuracy and slow convergence rate, this paper proposed an improved PID search algorithm (IPSA). The method introduced a good point set to ensure a more uniform population distribution, thereby enhancing population diversity and global search capability. The Q-learning algorithm was employed to adapt PID parameter adjustments, incorporating an exploration rate factor to further improve the algorithm's exploration and computational capabilities. A lens imaging opposition-based learning mechanism was also …

Dynamic Characteristic Simulation And Optimization Of Ground Test System For Airborne Launch Rack, Yuguang Bai, Sheng Zhang, Yushun Cao, Xiaoshi Zhang, Hu Huang

Journal of System Simulation

Abstract: To solve the ground equivalent test problem of the airborne launch system, an optimization method for the dynamic characteristics of the ground launch rack test system based on a multi-variable optimization approach was proposed. Through the discussion on the boundary conditions of the foundation, an effective dynamic simulation model of the ground launch test system was established. By comparing the dynamic characteristics of the launch rack structure in the airborne state and the ground test state, the objectives and constraints of the optimization design were determined. The dynamic characteristics of the ground test system were optimized and designed. …

Optimization Of Dynamic Weapon Target Assignment Considering Random Disturbances, Zhenzu Bai, Yizhi Hou, Zhangming He, Juhui Wei, Haiyin Zhou, Jiongqi Wang

Journal of System Simulation

Abstract: The impact of various random disturbances in the actual command and control environment of unmanned systems on problem modeling and solving of weapon target assignment was considered, and three types of uncertainty disturbance constraints were investigated. A multi-objective dynamic sensor weapon target assignment model was established. By considering the issues of model property changes caused by disturbances and insufficient robustness of the traditional single-operator solving algorithm, a multi-operator constrained multi-objective evolutionary framework based on the deep Q-network was proposed. The algorithm described the convergence, diversity, and feasibility of the population in both the objective and decision spaces. It established …

Fault Diagnosis Method For Photovoltaic Systems Based On Multi-Strategy Fusion, Bin Li, Yuchuo Wang

Journal of System Simulation

Abstract: To address the problem of frequent PV system faults, a multimodal fusion fault diagnosis model based on the optimization of the improved lemming algorithm was proposed. The one-dimensional time series signals of PV currents and voltages were converted into two-dimensional images by Markov transformation field, and the spatial features of the original waveforms were mined by using multiscale CNN (MCCNN); BiGRU was used to extract the temporal dynamic features of the original waveforms, and complementary enhancement of the temporal and spatial features was realized by the feature fusion layer. The improved lemming algorithm was innovatively introduced to adaptively optimize …

Survey Of Cooperative Multi-Agent Path Finding, Jun Xiong, Wenbo Zhang, Zhi Xiong, Feng Zhou, Bo Yang

Journal of System Simulation

Abstract: Cooperative multi-agent path finding (Co-MAPF) has been widely applied in fields such as UAV formation and multi-agent systems, which enhances the overall system efficiency through task collaboration, path planning, and task execution among multiple agents. This paper introduced three main system architectures, namely centralized, distributed, and hybrid, along with their advantages and disadvantages based on the definition of the Co-MAPF problem, categorized, and reviewed mainstream Co-MAPF algorithms, including those based on sampling, search, intelligent optimization, and learning. Furthermore, this paper analyzed the main current challenges faced by Co-MAPF algorithms on the basis of summarizing existing research and outlined the …

Numerical Simulations Of Ship Liquid Tank Sloshing Based On Graph Neural Networks, Wenkang Zhang, Xiaofeng Sun, Yiping Zhong, Yong Yin

Journal of System Simulation

Abstract: To address the high consumption of computational resources in simulating ship liquid tank sloshing using computational fluid dynamics simulation methods, a data-driven numerical simulation model was proposed based on graph neural networks. An encoder-processor-decoder framework was employed in the proposed model. The encoder extracted features of fluid particles from the first five time steps. The processor learnt latent motion patterns of fluid and updated features, and the decoder predicted features of particles at subsequent time steps. The processor incorporated a self-attention mechanism to enable dynamic adjacency weight allocation and emphasize the influence of irregular tank wall regions. Training …

Optimization Of Order Picking And Sorting Coordintion In “Goods-To-Person” System, Liang Ren, Zerong Zhou, Yunfeng Ma

Journal of System Simulation

Abstract: To improve the order picking and sorting collaboration with time windows in the "goods-to-person" system, a mathematical model aiming to minimize the number of sorting batches was established. With the characteristics of this issue considered, a hybrid variable neighborhood search (HVNS) algorithm based on the "classified loading" strategy was proposed for solutions. The numerical experimental results show that the HVNS algorithm can obtain high-quality solutions while shortening the solution time; different order structures have varying effects on the utilization of the loading capacity of sorting automated guided vehicles (AGVs); under the tested experimental conditions, the collaborative operation mode …

Lightweight Assembly Workpiece Detection Algorithm Based On Improved Yolov8, Shuheng Wu, Yongkui Liu, Lin Zhang, Yingying Xiao, Lihui Wang

Journal of System Simulation

Abstract: To address the issues of low recognition accuracy and slow detection speed with existing deep learning-based object detection algorithms for robotic automatic assembly tasks, a lightweight assembly workpiece object detection algorithm based on YOLOv8 was proposed. The PConv was introduced to improve the C2f module, and a new Faster_C2f module was designed to enhance the detection speed of the model. The SIoU loss function was employed to optimize the location prediction accuracy of the CIoU loss function and improve the localization accuracy of small targets. The high-level screening-feature fusion pyramid networks (HS-FPN) structure was used to improve the Neck …

Interoperability Model And Application Of Military Training System For Combination Of Virtuality And Reality, Jianxing Gong, Hai Hu, Haihui Ren, Ruixiang Wu

Journal of System Simulation

Abstract: With the development of AI technology, VR technology, and combat simulation technology, in order to achieve the practical training effect of "how to fight and how to train soldiers", virtual and real training has become a widely popular military training mode. It has become a trend to integrate digital systems, virtual equipment, semi-physical models, physical models, and other heterogeneous systems to carry out training in the same training environment. Therefore, it is necessary to study the interoperability model and application of training systems for the combination of virtuality and reality. This paper proposed the definition of interoperability between virtuality …

Research On Infrared And Visible Light Fusion Method Based On Resnet-50 And Laplacian Filtering, Xiao Wang, Xiangyang Li, Feng Liang, Zhili Zhang

Journal of System Simulation

Abstract: In order to solve the problem that existing infrared and visible light image fusion techniques often suffer from artifacts caused by insufficient contrast, spectral distortion, and high computational complexity, a fusion framework based on ResNet-50 and Laplacian filtering was proposed. ResNet-50 was used to extract shallow and deep features, followed by multi-scale feature fusion. Laplacian filtering was applied to optimize feature information, and an automatic discriminator was introduced to further improve the fusion effect. Simulation results show that, compared with comparison algorithms, the proposed method achieves an average increase of 2.71% and 2.16% in information entropy, 5.98% and …

Analysis Of Optimal Spectral Bands For Thermal Infrared Hyperspectral Image Reconstruction Driven By Physical Simulation Model, Yonghao Yang, Xiaoyu He

Journal of System Simulation

Abstract: To achieve accurate reconstruction of thermal infrared hyperspectral images under limited spectral bands, this paper proposed a reconstruction method based on physical modeling and simulation. Semi-global decomposition algorithm was adopted to invert the thermophysical properties of the scenario based on the physical model of thermal radiation, simulating and generating full-band hyperspectral data. An optimal spectral band selection strategy driven by a physical model was proposed, which integrated the sensitivity of temperature inversion and the separability of material spectra. Experiments were conducted on both simulated and measured datasets to evaluate the performance of material identification, temperature inversion, and spectral …

Research On Pac-Bayes-Based A2c Algorithm For Multi-Objective Reinforcement Learning, Xiang Liu, Qiankun Jin

Journal of System Simulation

Abstract: To address the theoretical challenges of exploration and exploitation trade-offs and uncertainty modeling in multi-objective reinforcement learning (MORL), this study developed a learning framework, MO-PAC, based on PAC-Bayes theory. By introducing a multi-objective stochastic Critic network and a dynamic preference mechanism, the framework extended the conventional A2C architecture, enabling adaptive and efficient approximation of complex Pareto fronts. Experimental results demonstrate that in multi-objective MuJoCo environments, MO-PAC outperforms baseline algorithms, achieving approximately 20% improvement in hypervolume and 60% increase in expected utility, while exhibiting superior convergence efficiency and robustness. It verifies both theoretical value and practical performance advantages in …