Software Engineering Commons^™

Anomaly Management In Unmanned Aerial Vehicles: A Systematic Literature Review, Ivan Tan Wei Han, Christopher M. Poskitt, Lingxiao Jiang, Lwin Khin Shar

Research Collection School Of Computing and Information Systems

Unmanned Aerial Vehicles (UAVs) are increasingly deployed in safety-critical applications such as logistics, surveillance, disaster response, and urban air mobility. While their autonomy enables powerful capabilities, it also introduces vulnerabilities due to hardware faults, software defects, communication failures, and adversarial interference. This survey presents a comprehensive review of research studies closely related to UAV anomalies published between 2015 and 2025, covering 111 papers from academic and industrial sources. We introduce a unified five-pillar taxonomy—anomaly generation, prevention, detection, recovery, and analysis—that organizes existing work across the full anomaly management lifecycle. In contrast to prior surveys that focus primarily on detection algorithms, …

Survey On Learning-Based Dynamic Fault Localization: From Traditional Machine Learning To Large Language Models, Chunyan Liu, Yan Lei, Huan Xie, Jinping Wang, Yue Yu, David Lo

Research Collection School Of Computing and Information Systems

Learning-based dynamic fault localization techniques play a crucial role in the field of software engineering. These techniques dynamically execute test cases to meticulously extract useful knowledge from the execution information in the program, with the aim of identifying fault locations by leveraging machine learning, deep learning, and large language models. Currently, there is already a flourishing body of research that is intensely focused on learning-based dynamic fault localization. Research literature can be categorized into two main aspects for learning-based dynamic fault localization: data-based enhancements (i.e., the datasets) and model-based enhancements (i.e., the suspiciousness algorithms). Thus, we conduct an extensive literature …

The Texture Of A Threat: Adversarial Training, Cnns, And Obfuscated Malware Detection, Kaelyn Haynie

Senior Honors Theses

Accurately detecting malicious programs is an expanding field of research for machine learning (ML), with a novel approach incorporating a bytecode-to-image pipeline that produces images representative of software. These images are provided to convolutional neural networks (CNNs) to be examined for malicious pattern indicators. However, CNNs struggle to generalize these patterns effectively while still being robust against adversarial data, an issue which this research addresses with adversarial training. In this paper, three unique CNN architectures (a DBFS-MC-inspired baseline, MIRACLE, and PSP-CNN) are trained for binary classification with 15,000 benign and malicious software samples encoded into images for Android, Windows, and …

Bias Testing And Mitigation In Llm-Based Code Generation, Dong Huang, Jie M. Zhang, Qingwen Bu, Xiaofei Xie, Junjie Chen, Heming Cui

Research Collection School Of Computing and Information Systems

As the adoption of LLMs becomes more widespread in software coding ecosystems, a pressing issue has emerged: does the generated code contain social bias and unfairness, such as those related to age, gender, and race? This issue concerns the integrity, fairness, and ethical foundation of software applications that depend on the code generated by these models but are underexplored in the literature. This paper presents a novel bias testing framework that is specifically designed for code generation tasks. Based on this framework, we conduct an extensive empirical study on the biases in code generated by five widely studied LLMs (i.e., …

Introduction To Machine Learning And Machine Learning Systems, Raffi T. Khatchadourian Ph.D.

Open Educational Resources

Lecture slides introducing machine learning and machine learning systems for an undergraduate software engineering course. Topics include what machine learning is and how it differs from traditional programming, foundation models, the major types of learning (supervised, unsupervised, reinforcement, and others), and applications across domains. Using a food-delivery time-prediction case study, the deck walks through a typical ML pipeline—data collection and cleaning, feature engineering, model training, and evaluation—and covers evaluation methods (precision and recall, confusion matrices, error measures) along with underfitting versus overfitting and the realities of learning and evaluation in production. Based on "Machine Learning in Production/AI Engineering" by Christian …

Freqllm: Frequency-Aware Large Language Models For Time Series Forecasting, Shunan Wang, Min Gao, Zongwei Wang, Yibing Bai, Feng Jiang, Guansong Pang

Research Collection School Of Computing and Information Systems

Large Language Models (LLMs) have recently shown promise in Time Series Forecasting (TSF) by effectively capturing intricate time-domain dependencies. However, our preliminary experiments reveal that standard LLM-based approaches often fail to capture global correlations, limiting predictive performance. We found that embedding frequency-domain signals smooths weight distributions and enhances structured correlations by clearly separating global trends (low-frequency components) from local variations (high-frequency components). Building on these insights, we propose FreqLLM, a novel framework that integrates frequency-domain semantic alignment into LLMs to refine prompts for improved time series analysis. By bridging the gap between frequency signals and textual embeddings, FreqLLM effectively captures …

Improving The Reproducibility Of Deep Learning Software: An Initial Investigation Through A Case Study Analysis, Nikita Ravi, Abhinav Goel, James C. Davis, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

The field of deep learning has witnessed significant breakthroughs, spanning various applications, and fundamentally transforming current software capabilities. However, alongside these advancements, there have been increasing concerns about reproducing the results of these deep learning methods. This is significant because reproducibility is the foundation of reliability and validity in software development, particularly in the rapidly evolving domain of deep learning. The difficulty of reproducibility may arise due to several reasons, including having differences from the original execution environment, incompatible software libraries, proprietary data and source code, lack of transparency, and the stochastic nature in some software. A study conducted by …

A Data-Driven Recommendation System For Selecting The Appropriate Mode Of Learning And Instructional Tools Based On Course Characteristics, Ayisha Manzoor

Theses

The rapid transformation of educational delivery methods during the COVID-19 pandemic required institutions to transition between online, hybrid, and offline learning approaches, creating both challenges and opportunities for educators and students. While online and hybrid learning modes ensured continuity, their effectiveness across different course types remained uncertain. This thesis addresses this gap by developing a datadriven recommendation framework that predicts Course Learning Outcome (CLO) achievement scores using regression, and recommends the most appropriate learning mode (online, hybrid, or offline) along with instructional tools based on course characteristics. This study analyzed 100 undergraduate and postgraduate courses from the College of Information …

Neural And Computational Approach To Understanding Environmental Modulation Of Behavioral Identity In Zebrafish, John W. Hageter

Graduate Theses, Dissertations, and Problem Reports (ETD)

Organisms rely on behavior for survival. Animals engage in behaviors that allow for feeding, mating, exploring and navigating their environment among others. Necessary for these behaviors to develop are the environmental factors and underlying circuitry which make behavior possible. Specifically, how the environment guides underlying neural circuitry to develop unique facets or phenotypes of a larger behavior are key to understanding why unique behaviors exist. In this thesis, I build foundational evidence for determining these mechanisms through the use of the zebrafish local search behavior. This is a behavior that zebrafish employ following the loss of environmental illumination where they …

Promise And Peril Of Collaborative Code Generation Models : Balancing Effectiveness And Memorization, Zhi Chen, Lingxiao Jiang

Research Collection School Of Computing and Information Systems

In the rapidly evolving field of machine learning, training models with datasets from various locations and organizations presents significant challenges due to privacy and legal concerns. The exploration of effective collaborative training settings, which are capable of leveraging valuable knowledge from distributed and isolated datasets, is increasingly crucial. This study investigates key factors that impact the effectiveness of collaborative training methods in code next-token prediction, as well as the correctness and utility of the generated code, showing the promise of such methods. Additionally, we evaluate the memorization of different participant training data across various collaborative training settings, including centralized, federated, …

Challenges And Practices Of Deep Learning Model Reengineering: A Case Study On Computer Vision, Wenxin Jiang, Vishnu Banna, Naveen Vivek, Abhinav Goel, Nicholas Synovic, George K. Thiruvathukal, James C. Davis

Computer Science: Faculty Publications and Other Works

Many engineering organizations are reimplementing and extending deep neural networks from the research community. We describe this process as deep learning model reengineering. Deep learning model reengineering — reusing, replicating, adapting, and enhancing state-of-the-art deep learning approaches — is challenging for reasons including under-documented reference models, changing requirements, and the cost of implementation and testing.

Peatmoss: A Dataset And Initial Analysis Of Pre-Trained Models In Open-Source Software, Wenxin Jiang, Jerin Yasmin, Jason Jones, Nicholas Synovic, Jiashen Kuo, Nathaniel Bielanski, Yuan Tian, George K. Thiruvathukal, James C. Davis

Computer Science: Faculty Publications and Other Works

The development and training of deep learning models have become increasingly costly and complex. Consequently, software engineers are adopting pre-trained models (PTMs) for their downstream applications. The dynamics of the PTM supply chain remain largely unexplored, signaling a clear need for structured datasets that document not only the metadata but also the subsequent applications of these models. Without such data, the MSR community cannot comprehensively understand the impact of PTM adoption and reuse. This paper presents the PeaTMOSS dataset, which comprises metadata for 281,638 PTMs and detailed snapshots for all PTMs with over 50 monthly downloads (14,296 PTMs), along with …

Semantic Segmentation Of Point Cloud Sequences Using Point Transformer V3, Marion Sisk

Master's Theses

Semantic segmentation of point clouds is a basic step for many autonomous systems including automobiles. In autonomous driving systems, LiDAR sensors are frequently used to produce point cloud sequences that allow the system to perceive the environment and navigate safely. Modern machine learning techniques for segmentation have predominately focused on single-scan segmentation, however sequence segmentation has often proven to perform better on common segmentation metrics. Using the popular Semantic KITTI dataset, we show that by providing point cloud sequences to a segmentation pipeline based on Point Transformer v3, we increase the segmentation performance between seven and fifteen percent when compared …

Cm-Ii Meditation As An Intervention To Reduce Stress And Improve Attention: A Study Of Ml Detection, Spectral Analysis, And Hrv Metrics, Sreekanth Gopi

Master of Science in Computer Science Theses

Students frequently face heightened stress due to academic and social pressures, particularly in de- manding fields like computer science and engineering. These challenges are often associated with serious mental health issues, including ADHD (Attention Deficit Hyperactivity Disorder), depression, and an increased risk of suicide. The average student attention span has notably decreased from 21⁄2 minutes to just 47 seconds, and now it typically takes about 25 minutes to switch attention to a new task (Mark, 2023). Research findings suggest that over 95% of individuals who die by suicide have been diagnosed with depression (Shahtahmasebi, 2013), and almost 20% of students …

Constructing Cyber-Physical System Testing Suites Using Active Sensor Fuzzing, Fan. Zhang, Qianmei. Wu, Bohan. Xuan, Yuqi. Chen, Wei. Lin, Christopher M. Poskitt, Jun Sun, Binbin. Chen

Research Collection School Of Computing and Information Systems

Cyber-physical systems (CPSs) automating critical public infrastructure face a pervasive threat of attack, motivating research into different types of countermeasures. Assessing the effectiveness of these countermeasures is challenging, however, as benchmarks are difficult to construct manually, existing automated testing solutions often make unrealistic assumptions, and blindly fuzzing is ineffective at finding attacks due to the enormous search spaces and resource requirements. In this work, we propose active sensor fuzzing , a fully automated approach for building test suites without requiring any a prior knowledge about a CPS. Our approach employs active learning techniques. Applied to a real-world water treatment system, …

Experimental Comparison Of Features, Analyses, And Classifiers For Android Malware Detection, Lwin Khin Shar, Biniam Fisseha Demissie, Mariano Ceccato, Naing Tun Yan, David Lo, Lingxiao Jiang, Christoph Bienert

Research Collection School Of Computing and Information Systems

Android malware detection has been an active area of research. In the past decade, several machine learning-based approaches based on different types of features that may characterize Android malware behaviors have been proposed. The usually-analyzed features include API usages and sequences at various abstraction levels (e.g., class and package), extracted using static or dynamic analysis. Additionally, features that characterize permission uses, native API calls and reflection have also been analyzed. Initial works used conventional classifiers such as Random Forest to learn on those features. In recent years, deep learning-based classifiers such as Recurrent Neural Network have been explored. Considering various …

Characterization And Estimation Of Musculoskeletal Pain Using Machine Learning, Boluwatife Faremi

Master's Theses

Traditional scales utilized for recording pain are known to be highly subjective and biased due to inaccuracies in recollecting actual pain intensities. As a result, machine learning (ML) models that are trained using these scores as ground truth are reported to have low performance for objective pain classification because of the huge disparity between what was felt in moments of pain and the scores recorded afterward.

In the present study, two devices were designed for gathering real-time, continuous in-session subjective pain scores and the recording of the autonomic nervous system (ANS) altered endodermal (EDA) activity. 24 participants were recruited to …

Ptmtorrent: A Dataset For Mining Open-Source Pre-Trained Model Packages, Wenxin Jiang, Nicholas Synovic, Purvish Jajal, Taylor R. Schorlemmer, Arav Tewari, Bhavesh Pareek, George K. Thiruvathukal, James C. Davis

Computer Science: Faculty Publications and Other Works

Due to the cost of developing and training deep learning models from scratch, machine learning engineers have begun to reuse pre-trained models (PTMs) and fine-tune them for downstream tasks. PTM registries known as “model hubs” support engineers in distributing and reusing deep learning models. PTM packages include pre-trained weights, documentation, model architectures, datasets, and metadata. Mining the information in PTM packages will enable the discovery of engineering phenomena and tools to support software engineers. However, accessing this information is difficult — there are many PTM registries, and both the registries and the individual packages may have rate limiting for accessing …

An Analysis Of Text-Based Machine Learning Models For Vulnerability Detection, Kollin Ryne Napier

Theses and Dissertations

With an increase in complexity of software, developers rely more on reuse and dependencies in their source code via code snippets. As a result, it is becoming harder to identify and mitigate vulnerabilities. Although traditional analysis tools are still utilized, machine learning models are being adopted to expand efforts and combat such threats. Given the possibilities towards usage of such models, research in this area has introduced various approaches which vary in usability and prediction. In generalizing models to a more natural language approach, researchers have opted to train models on source code to identify existing and potential vulnerabilities. Exploratory …

Lidar Buoy Detection For Autonomous Marine Vessel Using Pointnet Classification, Christopher Adolphi, Dorothy Dorie Parry, Yaohang Li, Masha Sosonkina, Ahmet Saglam, Yiannis E. Papelis

Modeling, Simulation and Visualization Student Capstone Conference

Maritime autonomy, specifically the use of autonomous and semi-autonomous maritime vessels, is a key enabling technology supporting a set of diverse and critical research areas, including coastal and environmental resilience, assessment of waterway health, ecosystem/asset monitoring and maritime port security. Critical to the safe, efficient and reliable operation of an autonomous maritime vessel is its ability to perceive on-the-fly the external environment through onboard sensors. In this paper, buoy detection for LiDAR images is explored by using several tools and techniques: machine learning methods, Unity Game Engine (herein referred to as Unity) simulation, and traditional image processing. The Unity Game …

Defining Safe Training Datasets For Machine Learning Models Using Ontologies, Lynn C. Vonder Haar

Doctoral Dissertations and Master's Theses

Machine Learning (ML) models have been gaining popularity in recent years in a wide variety of domains, including safety-critical domains. While ML models have shown high accuracy in their predictions, they are still considered black boxes, meaning that developers and users do not know how the models make their decisions. While this is simply a nuisance in some domains, in safetycritical domains, this makes ML models difficult to trust. To fully utilize ML models in safetycritical domains, there needs to be a method to improve trust in their safety and accuracy without human experts checking each decision. This research proposes …

An Empirical Study Of Pre-Trained Model Reuse In The Hugging Face Deep Learning Model Registry, Wenxin Jiang, Nicholas Synovic, Matt Hyatt, Taylor R. Schorlemmer, Rohan Sethi, Yung-Hsiang Lu, George K. Thiruvathukal, James C. Davis

Department of Electrical and Computer Engineering Faculty Publications

Deep Neural Networks (DNNs) are being adopted as components in software systems. Creating and specializing DNNs from scratch has grown increasingly difficult as state-of-the-art architectures grow more complex. Following the path of traditional software engineering, machine learning engineers have begun to reuse large-scale pre-trained models (PTMs) and fine-tune these models for downstream tasks. Prior works have studied reuse practices for traditional software packages to guide software engineers towards better package maintenance and dependency management. We lack a similar foundation of knowledge to guide behaviors in pre-trained model ecosystems.

In this work, we present the first empirical investigation of PTM reuse. …

An Empirical Study Of Artifacts And Security Risks In The Pre-Trained Model Supply Chain, Wenxin Jiang, Nicholas Synovic, Rohan Sethi, Aryan Indarapu, Matt Hyattt, Taylor R. Schorlemmer, George K. Thiruvathukal, James C. Davis

Computer Science: Faculty Publications and Other Works

Deep neural networks achieve state-of-the-art performance on many tasks, but require increasingly complex architectures and costly training procedures. Engineers can reduce costs by reusing a pre-trained model (PTM) and fine-tuning it for their own tasks. To facilitate software reuse, engineers collaborate around model hubs, collections of PTMs and datasets organized by problem domain. Although model hubs are now comparable in popularity and size to other software ecosystems, the associated PTM supply chain has not yet been examined from a software engineering perspective.

We present an empirical study of artifacts and security features in 8 model hubs. We indicate the potential …

Right To Know, Right To Refuse: Towards Ui Perception-Based Automated Fine-Grained Permission Controls For Android Apps, Vikas Kumar Malviya, Chee Wei Leow, Ashok Kasthuri, Naing Tun Yan, Lwin Khin Shar, Lingxiao Jiang

Research Collection School Of Computing and Information Systems

It is the basic right of a user to know how the permissions are used within the Android app’s scope and to refuse the app if granted permissions are used for the activities other than specified use which can amount to malicious behavior. This paper proposes an approach and a vision to automatically model the permissions necessary for Android apps from users’ perspective and enable fine-grained permission controls by users, thus facilitating users in making more well-informed and flexible permission decisions for different app functionalities, which in turn improve the security and data privacy of the App and enforce apps …

Real Time Call-Flagging System To Respond To Suicidal Ideation In Call Centers, Vishnu Menon, Joseph Carrigan, Charles Floeder, Thomas Walton, Devin Mcguire

Honors Program: Senior Projects (Public)

The 2021-2022 Signature Performance Design Studio team developed a live audio call-flagging system that enables faster responses and new response pathways to veteran crises by call service representatives and their management team. Using a custom made deep learning model, live audio streaming server, and Teams broadcasting add-on, the system empowers Signature Performance call service representatives to make quicker and more well informed decisions to provide veteran’s the best care possible.

Performance Of Sentiment Classification On Tweets Of Clothing Brands, Muhammad Shafiq Jalani, Hu Ng, Timothy Tzen Vun Yap, Vik Tor Goh

Journal of Informatics and Web Engineering

Social media such as Facebook, Instagram, LinkedIn, and Twitter ease the sharing of ideas, thoughts, videos, and photos and information through the building of virtual networks and communities. This has allowed companies and products to reach a wider audience in terms of marketing and advertising, and to gauge feedback from the public. This research investigates clothing brand mentions on Twitter to perform sentiment analysis on users’ thoughts on three clothing brands, namely Asos, Uniqlo and Topshop. The data is collected by applying python libraries, Tweepy to access data from the Twitter streaming API. Following that, data pre-processing such as tokenization, …

Automated Reverse Engineering Of Role-Based Access Control Policies Of Web Applications, Ha Thanh Le, Lwin Khin Shar, Domenico Bianculli, Lionel C. Briand, Cu Duy Nguyen

Research Collection School Of Computing and Information Systems

Access control (AC) is an important security mechanism used in software systems to restrict access to sensitive resources. Therefore, it is essential to validate the correctness of AC implementations with respect to policy specifications or intended access rights. However, in practice, AC policy specifications are often missing or poorly documented; in some cases, AC policies are hard-coded in business logic implementations. This leads to difficulties in validating the correctness of policy implementations and detecting AC defects.In this paper, we present a semi-automated framework for reverse-engineering of AC policies from Web applications. Our goal is to learn and recover role-based access …

Predictive Models In Software Engineering: Challenges And Opportunities, Yanming Yang, Xin Xia, David Lo, Tingting Bi, John C. Grundy, Xiaohu Yang

Research Collection School Of Computing and Information Systems

Predictive models are one of the most important techniques that are widely applied in many areas of software engineering. There have been a large number of primary studies that apply predictive models and that present well-performed studies in various research domains, including software requirements, software design and development, testing and debugging, and software maintenance. This article is a first attempt to systematically organize knowledge in this area by surveying a body of 421 papers on predictive models published between 2009 and 2020. We describe the key models and approaches used, classify the different models, summarize the range of key application …

A Survey On Deep Learning For Software Engineering, Yanming Yang, Xin Xia, David Lo

Research Collection School Of Computing and Information Systems

In 2006, Geoffrey Hinton proposed the concept of training "Deep Neural Networks (DNNs)" and an improved model training method to break the bottleneck of neural network development. More recently, the introduction of AlphaGo in 2016 demonstrated the powerful learning ability of deep learning and its enormous potential. Deep learning has been increasingly used to develop state-of-the-art software engineering (SE) research tools due to its ability to boost performance for various SE tasks. There are many factors, e.g., deep learning model selection, internal structure differences, and model optimization techniques, that may have an impact on the performance of DNNs applied in …

Taming The Data In The Internet Of Vehicles, Shahab Tayeb

Mineta Transportation Institute

As an emerging field, the Internet of Vehicles (IoV) has a myriad of security vulnerabilities that must be addressed to protect system integrity. To stay ahead of novel attacks, cybersecurity professionals are developing new software and systems using machine learning techniques. Neural network architectures improve such systems, including Intrusion Detection System (IDSs), by implementing anomaly detection, which differentiates benign data packets from malicious ones. For an IDS to best predict anomalies, the model is trained on data that is typically pre-processed through normalization and feature selection/reduction. These pre-processing techniques play an important role in training a neural network to optimize …