Physical Sciences and Mathematics Commons^™

Plm-Effector: Unleashing The Potential Of Protein Language Models For Bacterial Secreted Protein Prediction, Dandan Zheng, Lihong Chen, Guansong Pang, Jian Yang

Research Collection School Of Computing and Information Systems

Bacterial secreted proteins, particularly effectors delivered by specialized secretion systems, are key mediators of virulence and host-pathogen interactions. However, accurate computational identification remains challenging, as many existing methods rely heavily on sequence similarity or handcrafted features, and often focus on a single secretion system. Recent studies have reported that some bacterial effectors may be associated with more than one secretion system, highlighting the complexity of secretion system annotation and motivating the development of system-aware computational prediction approaches. Here, we present PLM-Effector, a hybrid deep learning framework that integrates modern protein language models (PLMs) with multiple neural architectures via a two-layer …

Navigation Beyond Wayfinding: Robots Collaborating With Visually Impaired Users For Environmental Interactions, Shaojun Cai, Nuwan Janaka, Ashwin Ram, Janidu Shehan, Yingjia Wan, Kotaro Hara, David Hsu

Research Collection School Of Computing and Information Systems

Robotic guidance systems have shown promise in supporting blind and visually impaired (BVI) individuals with wayfinding and obstacle avoidance. However, most existing systems assume a clear path and do not support a critical aspect of navigation—environmental interactions that require manipulating objects to enable movement. These interactions are challenging for a human–robot pair because they demand (i) precise localization and manipulation of interaction targets (e.g., pressing elevator buttons) and (ii) dynamic coordination between the user’s and robot’s movements (e.g., pulling out a chair to sit). We present a collaborative human–robot approach that combines our robotic guide dog’s precise sensing and localization …

Codeultrafeedback: An Llm-As-A-Judge Dataset For Aligning Large Language Models To Coding Preferences, Martin Weyssow, Aton Kamanda, Xin Zhou, Houari Sahraoui

Research Collection School Of Computing and Information Systems

Evaluating the alignment of large language models (LLMs) with user-defined coding preferences is a challenging endeavor that requires a deep assessment of LLMs' outputs. Existing methods and benchmarks rely primarily on automated metrics and static analysis tools, which often fail to capture the nuances of user instructions and LLM outputs. To address this gap, we introduce the LLM-as-a-Judge evaluation framework and present CodeUltraFeedback, a comprehensive dataset for assessing and improving LLM alignment with coding preferences. CodeUltraFeedback consists of 10,000 coding instructions, each annotated with four responses generated from a diverse pool of 14 LLMs. These responses are annotated using GPT-3.5 …

Comparison Of Analytical Techniques From The Extraction Of Bioactive Compounds From Kratom, Curry, Ginger, And Turmeric, Riley Bruno

Honors Program: Senior Projects (Public)

Plants, herbs, and spices have been used as medicines for thousands of years. Early civilizations often attributed healing properties of plants to magical or divine forces. However, as chemistry and analytical technology advanced between the 16th and 18th centuries, scientists began to understand that bioactive compounds within the plants actually caused these effects. Today, natural products remain extremely important in drug discovery. As the number of newly developed synthetic drugs declines, there has been renewed interest in identifying biologically active molecules from plants. Bioactive molecules are a group of diverse chemical compounds that stimulate a response in living tissues. The …

Identification Of Microplastics And Additives From The Lake Erie Watershed And The Cuyahoga River Via Maldi-Ms And Dart-Ms, Chrys Wesdemiotis, Calum Bochenek, Luciana Rivera Molina, Robert Brand

University Research

Micro(nano)plastics have received increased attention as environmental contaminants due to their harmful effects on ecosystems and human health. Conventional extraction methods for microplastic analysis are often lengthy and complicated, resulting in the loss of important chemical components such as additives. In this study, we provide a complementary approach, utilizing matrix-assisted laser desorption/ionization (MALDI) and direct analysis in real time (DART) mass spectrometry (MS) techniques, with minimal extraction and sample preparation to preserve both polymer and additive information. MALDI-MS was applied to aqueous samples collected along the shores of Lake Erie and the Cuyahoga River, successfully identifying the base polymer(s) in …

Invert Your Prompt: Editing-Aware Diffusion Inversion, Yangyang Xu, Wenqi Shao, Yong Du, Haiming Zhu, Yang Zhou, Jiayuan Xie, Ping Luo, Shengfeng He

Research Collection School Of Computing and Information Systems

Recent advancements in text-guided diffusion models have enabled powerful image manipulation capabilities. However, balancing reconstruction fidelity and editability for real images remains a significant challenge. In this work, we introduce Editing Inversion (EditInv), a novel framework that inverts and edits real images for specific editing tasks by optimizing specific prompt embeddings within the extended  space. By leveraging distinct embeddings across different U-Net layers and time steps, EditInv seamlessly integrates inversion and editing through reciprocal optimization, ensuring both high fidelity and precise editability. This hierarchical editing mechanism classifies tasks into structure, appearance, and global edits, optimizing only those embeddings that are …

Learning To Search For Vehicle Routing With Multiple Time Windows, Kuan Xu, Zhiguang Cao, Chenlong Zheng, Lindong Liu

Research Collection School Of Computing and Information Systems

In this study, we propose a reinforcement learning-based adaptive variable neighborhood search (RL-AVNS) method designed for effectively solving the Vehicle Routing Problem with Multiple Time Windows (VRPMTW). Unlike traditional adaptive approaches that rely solely on historical operator performance, our method integrates a reinforcement learning framework to dynamically select neighborhood operators based on real-time solution states and learned experience. We introduce a fitness metric that quantifies customers’ temporal flexibility to improve the shaking phase, and employ a transformer-based neural policy network to intelligently guide operator selection during the local search. Extensive computational experiments are conducted on realistic scenarios derived from the …

Cylindformer: Image-To-Point Cloud Registration With Cylindrical Transformer, Jingtao Wang, Hao Tang, Yanpeng Sun, Shengfeng He, Zechao Li

Research Collection School Of Computing and Information Systems

Accurate correspondence extraction between distinctive pixel-wise and point-wise features is critical for image-to-point cloud (I2P) registration. Recent efforts leveraging Transformers for I2P feature representation have demonstrated potential, primarily by first capturing intra-modality global contextual dependencies via self-attention, and then learning cross-modality correlations via cross-attention. The strength of vanilla Transformers lies in modeling cross-modality global feature correlations. However, such mechanisms often struggle with the structural disparity between dense image pixels and sparse 3D points, hindering the establishment of fine-grained correspondences. Moreover, global attention may introduce ambiguity, as interactions with many inconsistent regions of intra-modality may degrade feature distinctiveness. To address these …

Draft Final Quarterly Operations And Maintenance Report: Butte Treatment Lagoon System – Fourth Quarter 2025, Pioneer Technical Services, Inc.

Silver Bow Creek/Butte Area Superfund Site

No abstract provided.

Time-Dependent Amplification Of Growth Rates In A Plankton-Oxygen Model, Rapha Coutin

Master's Theses

Near-bottom hypoxia occurs when dissolved oxygen levels drop to a level that is harmful to marine biology, creating biological dead zones along the ocean floor. Recent years have seen a dramatic increase in the percentage of coastal, near-bottom, hypoxic water, with the average in 2021 nearly double that of the average from 2009 to 2018 and about twenty-eight times the average from 1950 to 1980. Recent literature has linked this increase in oceanic hypoxia to the increase in upwelling-favorable winds caused by climate change. Upwelling brings low-oxygen, nutrient-rich water up to the surface, leading to plankton blooms and mass consumption …

Improving Public Transport Through Machine Learning Influence Flow Analysis (Mifa): Southern England Bus Case Study, Benjamin Lee, Wolfgang Garn, Masoud Fakhimi, Nick F. Ryman-Tubb

Research Collection School Of Accountancy

Public transport (PT) is crucial for enhancing the quality of life and enabling sustainable urban development. As part of the UK Transport Investment Strategy, increasing PT usage is critical to achieving efficient and sustainable mobility. This paper introduces Machine Learning Influence Flow Analysis (MIFA), a novel framework for identifying the key influencers of PT usage. Using survey data from bus passengers in Southern England, we evaluate machine learning models. Subsequently, MIFA uncovers that easy payments, e-ticketing, and mobile applications can substantially improve the PT service. MIFA’s implementation demonstrates that strength and importance lead to specific insights into how service characteristics …

Video Generation Techniques For Novel View Synthesis With Flow-Matching Transformers, Xiuyuan Qiu

Master's Theses

Novel view synthesis (NVS) aims to generate images of a scene from unseen camera viewpoints. Recent work, such as Stable Virtual Camera, shows that large-scale image diffusion models like Stable Diffusion can be adapted for pose-conditioned view synthesis by incorporating video-generation techniques with camera conditioning. In this thesis, we introduce MVFlow, a new NVS model that extends this approach to a different image generation architecture: a flow-matching diffusion transformer, specifically FLUX.1, which has demonstrated strong performance in image synthesis. We evaluate MVFlow under varying input view counts and pose distance settings. Our results show that this architectural transfer is feasible; …

Demystifying Hardware Formal Verification For Undergraduate Education: A Risc-V Processor Case Study With Coursework Implementation, Riley A. Peters

Master's Theses

Hardware verification engineers apply formal methods to prove that a digital device always behaves according to its specification. This differs from traditional functional verification, in which engineers establish correctness by repeatedly sending test inputs to the device and comparing the outputs against a reference model. With the growing complexity of integrated circuits, the demand for digital verification engineers with formal methods experience has continued to increase. However, California Polytechnic State University: San Luis Obispo's current curriculum lacks dedicated material to prepare students for these roles.

This thesis seeks to address the lack of formal methods material through two efforts. First, …

A Critical Review Of Statistical, Signal Processing And Machine Learning Methods For Continuous And High-Frequency Water Quality Data Improvement, A.T. Badrudeen, D. Sahoo, Calvin Sawyer, Jeremy Pike, R.D. Haramel

Publications

In the digital water world, high-frequency water quality monitoring from sensors is crucial for capturing rapid changes, especially during storm events or discharge fluctuations, in which important signals can occur at sub-hourly intervals. These signals are represented in a time series and can sometimes be irregular, noisy, and prone to missing values or errors due to buried conditions, sediment interference, and signal loss. The fine resolution of reporting also increases the risk of sensor errors and data loss, necessitating effective correction methods to ensure the accuracy and usability of the data. This literature review investigates the current state of time …

Does Genetic Testing Influence Outcomes: Early Experience In Melanoma Case Series, Ryan Reyes, George Skenteris, Stella Coker Watson Self Ph.D., Ms, Christine Marie-Gilligan Schammel, Steven D. Trocha

Faculty Publications

Background:

The treatment and prognosis of melanoma have historically been based on histologic stage and Breslow depth; however, due to the increase in surveillance, melanomas are being identified at an earlier stage and lower Breslow depth. Advances in genetic testing, such as Decision Dx®, mean that melanoma diagnostic decisions and prognosis can now be directed by genetics. The purpose of this project was to assess the influence of a Decision Dx® high-grade (Class 2A/B) classification on the treatment of melanoma patients at a regional medical center, particularly those not deemed high risk by conventional classification methods, including Breslow depth and …

Wayne E. Sabbe Arkansas Soil Fertility Studies 2025, Nathan A. Slaton

Arkansas Agricultural Experiment Station Research Series

Rapid technological changes in crop management and production require that the research efforts be presented in an expeditious manner. The contributions of soil fertility and fertilizers are major production factors in all Arkansas crops. The studies described within will allow producers to compare their practices with the university’s research efforts. Additionally, soil-test data and fertilizer sales are presented to allow comparisons among years, crops, and other areas within Arkansas.

How Agile Became The Design Philosophy Of Ai Fishbowl Under Real-World Constraints, Jad Saad

University Honors Theses

This capstone review examines the development of AI Fishbowl, a public-facing, interactive artificial intelligence system, as a case study in how Agile methods evolve from a project management tool into a design philosophy under real-world constraints. Although the project adopted an Agile workflow early on through a Kanban-style task management approach, the initial system design and architecture were still shaped by a largely plan-first mindset. This created a mismatch between flexible process and rigid design assumptions, which became increasingly apparent as the team moved from high-level architecture into implementation.

A critical turning point occurred when early architectural plans proved difficult …

A Unified Methodological Framework For Generating Digital Twins Of Multi Class Uncrewed Systems (Uxs), Sai Raghava Pathuri

Shelby Hall Graduate Research Forum Presentations

No abstract provided.

Detecting Bitstream-Level Fpga Trojans With An Snn, Kylie Arnett

Shelby Hall Graduate Research Forum Presentations

Limited research has been conducted on SNNs for FPGA Trojan detection. FPGA design is often handled by manufacturers outside the U.S. FPGA manufactures outsource production to third-party foundries. This multi-step process introduces security vulnerabilities and increases risk of Hardware Trojan insertion.

Key Questions: To what extent can an FPGA be manipulated at the bitstream level to enable or disable encryption algorithms?

Can SNNs accurately detect the presence of Trojans within an FPGA?

Designing For Trust In Chat-Based Question Answering Systems: An Exchange-Based Retrieval Approach, Nathan Mccutchen

Master's Theses

Community chat platforms such as Discord and Slack support spontaneous, collaborative communication but make it difficult to retrieve previously discussed information. As conversations accumulate, valuable exchanges become buried, leading to repeated questions and sustained burden on experienced community members.

This work contributes a set of design requirements for question-answering systems operating over unstructured chat data, a Discord bot prototype implementing those requirements named Echo, and an empirical evaluation of how such a system affects user trust. Rather than encoding discrete question-answer pairs or generating synthetic responses with a language model, Echo indexes conversation topics for semantic retrieval and presents results …

A Scalable Iteration Of The Horizon Simulation Framework Using Multithreading Techniques, Jason E. Beals

Master's Theses

The Horizon Simulation Framework (HSF) occupies a unique space in the modern aerospace modeling landscape, enabling flexible, modular modeling of mission-level agent behavior through an object-oriented, hierarchical design. HSF's hallmark breadth-first search scheduling algorithm explores a "multiverse" of possible mission execution pathways, enabling exhaustive evaluation of schedule combinations against user-defined heuristics.

As aerospace systems become increasingly complex, HSF faces critical challenges in establishing verifiable, deterministic behavior. The framework's core scheduling algorithm had not undergone systematic validation, leaving questions about temporal consistency, state management correctness, and reproducibility across different program executions. Furthermore, the exponential growth of schedule combinations creates computational bottlenecks …

Vaccination Games Of Boundedly Rational Parents Toward New Childhood Immunization, Wei Yin, Martial L. Ndeffo-Mbah, Tamer Oraby

School of Mathematical & Statistical Sciences Faculty Publications

Infectious diseases harm societies through disease-induced morbidity, mortality, loss of productivity, and inequality. Thus, controlling and preventing them is critical for public health and societal well-being. However, societies can hinder efforts to control the spread of diseases by failing to adhere to public health recommendations, such as through vaccine hesitancy. Various disease-transmission models have been utilized to help policymakers respond to (re)emerging outbreaks. The usefulness of such models in assessing the effectiveness of public health policies is significantly dependent on human behavior. This paper introduces a new model of parental behavior toward a new childhood immunization. The model incorporates societal …

Opencil: Benchmarking Out-Of-Distribution Detection In Class Incremental Learning, Wenjun Miao, Guansong Pang, Trong-Tung Nguyen, Ruohuan Fang, Jin Zheng, Xiao Bai

Research Collection School Of Computing and Information Systems

Class incremental learning (CIL) aims to learn a model that can not only incrementally accommodate new classes, but also maintain the learned knowledge of old classes. Out-of-distribution (OOD) detection in CIL is to retain this incremental learning ability, while being able to reject unknown samples that are drawn from different distributions of the learned classes. This capability is crucial to the safety of deploying CIL models in open worlds. However, despite remarkable advancements in the respective CIL and OOD detection, there lacks a systematic and large-scale benchmark to assess the capability of advanced CIL models in detecting OOD samples. To …

Comprehensively Evaluating The Perception Systems Of Autonomous Vehicles Against Hazards, Xiaodong Zhang, Jie Bao, Jianlei Chi, Jun Sun, Zijiang Yang

Research Collection School Of Computing and Information Systems

Perception systems are vital for the safety of autonomous driving. In complex autonomous driving scenarios, autonomous vehicles must overcome various natural hazards, such as heavy rain or raindrops on the camera lens. Therefore, it is essential to conduct comprehensive testing of the perception systems in autonomous vehicles against these hazards, as demanded by the regulatory agencies of many countries for human drivers. Since there are many hazard scenarios, each of which has multiple configurable parameters, the challenges are (1) how do we systematically and adequately test an autonomous vehicle against these hazard scenarios, with measurable outcome; and (2) how do …

Interpretable Machine Learning For Personalized Profiling Of Mild Cognitive Impairment From Daily Activities, Budhitama Subagdja, Ah-Hwee Tan, Kenneth Kwok, Iris Rawtaer

Research Collection School Of Computing and Information Systems

Continuous monitoring of individual daily activities is essential to detect mild cognitive impairment (MCI) wherein timely intervention can still be applied to prevent more severe mental decline. Recent approaches in predicting MCI are mostly considering digital biomarkers across individuals but often neglecting specific indicators from a single person over a long period of time. Making this personalized, dynamic, and highly noisy prediction model with irregular distribution of missing information to be explainable and actionable for clinical use, remains a challenge. This paper presents a study on a personalized MCI prediction and profiling from an in-home and mobile cognitive health monitoring …

Improving Credit Card Transaction Fraud Detection Using Cvqboosting, Bethel Hui Ting Loke, Nirvik Sahoo, Bingyan Guan, Minrui Xu, Dev Verma, Paul R. Griffin

Research Collection School Of Computing and Information Systems

This paper introduces a novel hybrid quantum-classical approach to credit card fraud detection using CVQBoost, a hybrid quantum-classical boosting algorithm executed on the photonic Dirac-3 processor from Quantum Computing Inc. (QCi). By integrating a diverse set of weak classifiers, which includes K-nearest neighbours (KNN), linear discriminant analysis, logistic regression, and XGBoost, within a hybrid quantum-classical ensemble, the proposed method demonstrates significant improvements over the latest published classical benchmarks. Experiments on a Kaggle credit card fraud dataset show that the quantum-enhanced model achieves a mean AUC-PR score of over 0.8, corresponding to an approximately 9% relative improvement over the best published …

Deep Learning Approaches For Anti-Money Laundering On Mobile Transactions: Review, Framework, And Directions, Jiani Fan, Lwin Khin Shar, Ruichen Zhang, Ziyao Liu, Wenzhuo Yang, Dusit Niyato, Kwok-Yan Lam

Research Collection School Of Computing and Information Systems

Money laundering is a financial crime that obscures the origin of illicit funds, necessitating the development and enforcement of anti-money laundering (AML) policies by governments and organizations. The proliferation of mobile payment platforms and smart IoT devices has significantly complicated AML investigations. As payment networks become more interconnected, there is an increasing need for efficient real-time detection to process large volumes of transaction data on heterogeneous payment systems by different operators such as digital currencies, cryptocurrencies, and account-based payments. Most of these mobile payment networks are supported by connected devices, many of which are considered loT devices in the FinTech …

Exploring Neural Network Structure Code Reuse In The Open-Source Community For Improving Maintenance, Xiaoning Ren, Yuekun Wang, Chongyang Liu, Yueming Wu, Qiang Hu, Lijun Zhang, Yinxing Xue

Research Collection School Of Computing and Information Systems

Neural networks (NNs) have rapidly advanced, demonstrating exceptional performance across various fields, leading to a surge in open-source NN projects. The complexity and rapid growth of these projects pose significant challenges for maintenance within the open-source community. Given that NN architecture code is the core asset of NN projects, understanding its reuse in the open-source community is essential for effective maintenance, such as reducing redundancy and identifying potential intellectual property violations. While prior studies have examined code reuse in open-source projects, they have two key limitations: They do not specifically address NN structure code, and they rely on manually selected …

Compositions Of Variant Experts For Integrating Short-Term And Long-Term Preferences, Dinh Hieu Do, Hady Wirawan Lauw

Research Collection School Of Computing and Information Systems

In the online digital realm, recommendation systems are ubiquitous and play a crucial role in enhancing user experience. These systems leverage user preferences to provide personalized recommendations, thereby helping users navigate through the paradox of choice. This work focuses on personalized sequential recommendation, where the system considers not only a user’s immediate, evolving session context, but also their cumulative historical behavior to provide highly relevant and timely recommendations. Through an empirical study conducted on diverse real-world datasets, we have observed and quantified the existence and impact of both short-term (immediate and transient) and long-term (enduring and stable) preferences on users’ …

A Novel Privacy-Preserving User Information Queries Scheme With Functional Policy, Yuhang Lei, Rui Shi, Yang Yang, Chunjie Cao, Huamin Feng

Research Collection School Of Computing and Information Systems

Privacy-preserving information queries enable a requester to obtain only the value f(x) computed over sensitive data x, while preventing disclosure of the underlying records. Existing approaches typically reveal full data, incur high on-chain overhead, or lack fair and verifiable delivery of function outputs. We propose a general-purpose, blockchain-compatible framework that ensures the requester learns only f(x) with no extra leakage and that the provider receives fair payment. The design integrates Adaptor Signatures (AS) for fair exchange and Inner-Product Functional Encryption (IPFE) for fine-grained function extraction. The framework is domain-agnostic and applicable to privacy-sensitive applications such as medical insurance and financial …