Computer Sciences Commons^™

Sccad: Cluster Decomposition-Based Anomaly Detection For Rare Cell Identification In Single-Cell Expression Data, Yunpei Xu, Shaokai Wang, Qilong Feng, Jiazhi Xia, Yaohang Li, Hong-Dong Li, Jianxin Wang

Computer Science Faculty Publications

Single-cell RNA sequencing (scRNA-seq) technologies have become essential tools for characterizing cellular landscapes within complex tissues. Large-scale single-cell transcriptomics holds great potential for identifying rare cell types critical to the pathogenesis of diseases and biological processes. Existing methods for identifying rare cell types often rely on one-time clustering using partial or global gene expression. However, these rare cell types may be overlooked during the clustering phase, posing challenges for their accurate identification. In this paper, we propose a Cluster decomposition-based Anomaly Detection method (scCAD), which iteratively decomposes clusters based on the most differential signals in each cluster to effectively separate …

Retrogressive Document Manipulation Of Us Federal Environmental Websites, Lesley Frew, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

Changes made to webpages can affect their retrievability. Often this is done with the intention of increasing the page's search engine ranking to improve overall access to information on the page. The Environmental Data and Governance Initiative (EDGI) created a dataset that describes changes on US federal environmental webpages between 2016 and 2020. EDGI noted that many environmental terms were deleted from the pages, but without user data, claims that page retrievability and public information access were lowered are only anecdotal. The Open Resource for Click Analysis in Search (ORCAS) dataset was created during the same time frame, from 2017 …

Dilf: Differentiable Rendering-Based Multi-View Image-Language Fusion For Zero-Shot 3d Shape Understanding, Xin Ning, Zaiyang Yu, Lusi Li, Weijun Li, Prayag Tiwari

Computer Science Faculty Publications

Zero-shot 3D shape understanding aims to recognize “unseen” 3D categories that are not present in training data. Recently, Contrastive Language–Image Pre-training (CLIP) has shown promising open-world performance in zero-shot 3D shape understanding tasks by information fusion among language and 3D modality. It first renders 3D objects into multiple 2D image views and then learns to understand the semantic relationships between the textual descriptions and images, enabling the model to generalize to new and unseen categories. However, existing studies in zero-shot 3D shape understanding rely on predefined rendering parameters, resulting in repetitive, redundant, and low-quality views. This limitation hinders the model’s …

A Survey On Few-Shot Class-Incremental Learning, Songsong Tian, Lusi Li, Weijun Li, Hang Ran, Xin Ning, Prayag Tiwari

Computer Science Faculty Publications

Large deep learning models are impressive, but they struggle when real-time data is not available. Few-shot class-incremental learning (FSCIL) poses a significant challenge for deep neural networks to learn new tasks from just a few labeled samples without forgetting the previously learned ones. This setup can easily leads to catastrophic forgetting and overfitting problems, severely affecting model performance. Studying FSCIL helps overcome deep learning model limitations on data volume and acquisition time, while improving practicality and adaptability of machine learning models. This paper provides a comprehensive survey on FSCIL. Unlike previous surveys, we aim to synthesize few-shot learning and incremental …

A Chinese Power Text Classification Algorithm Based On Deep Active Learning, Song Deng, Qianliang Li, Renjie Dai, Siming Wei, Di Wu, Yi He, Xindong Wu

Computer Science Faculty Publications

The construction of knowledge graph is beneficial for grid production, electrical safety protection, fault diagnosis and traceability in an observable and controllable way. Highly-precision text classification algorithm is crucial to build a professional knowledge graph in power system. Unfortunately, there are a large number of poorly described and specialized texts in the power business system, and the amount of data containing valid labels in these texts is low. This will bring great challenges to improve the precision of text classification models. To offset the gap, we propose a classification algorithm for Chinese text in the power system based on deep …

Building Datasets To Support Information Extraction And Structure Parsing From Electronic Theses And Dissertations, William A. Ingram, Jian Wu, Sampanna Yashwant Kahu, Javaid Akbar Manzoor, Bipasha Banerjee, Aman Ahuja, Muntabir Hasan Choudhury, Lamia Salsabil, Winston Shields, Edward A. Fox

Computer Science Faculty Publications

Despite the millions of electronic theses and dissertations (ETDs) publicly available online, digital library services for ETDs have not evolved past simple search and browse at the metadata level. We need better digital library services that allow users to discover and explore the content buried in these long documents. Recent advances in machine learning have shown promising results for decomposing documents into their constituent parts, but these models and techniques require data for training and evaluation. In this article, we present high-quality datasets to train, evaluate, and compare machine learning methods in tasks that are specifically suited to identify and …

Identifying Patterns For Neurological Disabilities By Integrating Discrete Wavelet Transform And Visualization, Soo Yeon Ji, Sampath Jayarathna, Anne M. Perrotti, Katrina Kardiasmenos, Dong Hyun Jeong

Computer Science Faculty Publications

Neurological disabilities cause diverse health and mental challenges, impacting quality of life and imposing financial burdens on both the individuals diagnosed with these conditions and their caregivers. Abnormal brain activity, stemming from malfunctions in the human nervous system, characterizes neurological disorders. Therefore, the early identification of these abnormalities is crucial for devising suitable treatments and interventions aimed at promoting and sustaining quality of life. Electroencephalogram (EEG), a non-invasive method for monitoring brain activity, is frequently employed to detect abnormal brain activity in neurological and mental disorders. This study introduces an approach that extends the understanding and identification of neurological disabilities …

Triphlapan: Predicting Hla Molecules Binding Peptides Based On Triple Coding Matrix And Transfer Learning, Meng Wang, Chuqi Lei, Jianxin Wang, Yaohang Li, Min Li

Computer Science Faculty Publications

Human leukocyte antigen (HLA) recognizes foreign threats and triggers immune responses by presenting peptides to T cells. Computationally modeling the binding patterns between peptide and HLA is very important for the development of tumor vaccines. However, it is still a big challenge to accurately predict HLA molecules binding peptides. In this paper, we develop a new model TripHLApan for predicting HLA molecules binding peptides by integrating triple coding matrix, BiGRU + Attention models, and transfer learning strategy. We have found the main interaction site regions between HLA molecules and peptides, as well as the correlation between HLA encoding and binding …

Learning Optimal Inter-Class Margin Adaptively For Few-Shot Class-Incremental Learning Via Neural Collapse-Based Meta-Learning, Hang Ran, Weijun Li, Lusi Li, Songsong Tian, Xin Ning, Prayag Tiwari

Computer Science Faculty Publications

Few-Shot Class-Incremental Learning (FSCIL) aims to learn new classes incrementally with a limited number of samples per class. It faces issues of forgetting previously learned classes and overfitting on few-shot classes. An efficient strategy is to learn features that are discriminative in both base and incremental sessions. Current methods improve discriminability by manually designing inter-class margins based on empirical observations, which can be suboptimal. The emerging Neural Collapse (NC) theory provides a theoretically optimal inter-class margin for classification, serving as a basis for adaptively computing the margin. Yet, it is designed for closed, balanced data, not for sequential or few-shot …

Robots Still Outnumber Humans In Web Archives In 2019, But Less Than In 2015 And 2012, Himarsha R. Jayanetti, Kritika Garg, Sawood Alam, Michael L. Nelson, Michele C. Weigle

Computer Science Faculty Publications

The significance of the web and the crucial role of web archives in its preservation highlight the necessity of understanding how users, both human and robot, access web archive content, and how best to satisfy this disparate needs of both types of users. To identify robots and humans in web archives and analyze their respective access patterns, we used the Internet Archive’s (IA) Wayback Machine access logs from 2012, 2015, and 2019, as well as Arquivo.pt’s (Portuguese Web Archive) access logs from 2019. We identified user sessions in the access logs and classified those sessions as human or robot based …

Osfs-Vague: Online Streaming Feature Selection Algorithm Based On A Vague Set, Jie Yang, Zhijun Wang, Guoyin Wang, Yanmin Liu, Yi He, Di Wu

Computer Science Faculty Publications

Online streaming feature selection (OSFS), as an online learning manner to handle streaming features, is critical in addressing high-dimensional data. In real big data-related applications, the patterns and distributions of streaming features constantly change over time due to dynamic data generation environments. However, existing OSFS methods rely on presented and fixed hyperparameters, which undoubtedly lead to poor selection performance when encountering dynamic features. To make up for the existing shortcomings, the authors propose a novel OSFS algorithm based on vague set, named OSFS-Vague. Its main idea is to combine uncertainty and three-way decision theories to improve feature selection from the …

A-Disetrac Advanced Analytic Dashboard For Distributed Eye Tracking, Yasasi Abeysinghe, Bhanuka Mahanama, Gavindya Jayawardena, Yasith Jayawardena, Mohan Sunkara, Andrew T. Duchowski, Vikas Ashok, Sampath Jayarathna

Computer Science Faculty Publications

Understanding how individuals focus and perform visual searches during collaborative tasks can help improve user engagement. Eye tracking measures provide informative cues for such understanding. This article presents A-DisETrac, an advanced analytic dashboard for distributed eye tracking. It uses off-the-shelf eye trackers to monitor multiple users in parallel, compute both traditional and advanced gaze measures in real-time, and display them on an interactive dashboard. Using two pilot studies, the system was evaluated in terms of user experience and utility, and compared with existing work. Moreover, the system was used to study how advanced gaze measures such as ambient-focal coefficient K …

Autonomous Strike Uavs In Support Of Homeland Security Missions: Challenges And Preliminary Solutions, Meshari Aljohani, Ravi Mukkamala, Stephan Olariu

Computer Science Faculty Publications

Unmanned Aerial Vehicles (UAVs) are becoming crucial tools in modern homeland security applications, primarily because of their cost-effectiveness, risk reduction, and ability to perform a wider range of activities. This study focuses on the use of autonomous UAVs to conduct, as part of homeland security applications, strike missions against high-value terrorist targets. Owing to developments in ledger technology, smart contracts, and machine learning, activities formerly carried out by professionals or remotely flown UAVs are now feasible. Our study provides the first in-depth analysis of the challenges and preliminary solutions for the successful implementation of an autonomous UAV mission. Specifically, we …

Mosaic: A Prune-And-Assemble Approach For Efficient Model Pruning In Privacy-Preserving Deep Learning, Yifei Cai, Qiao Zhang, Rui Ning, Chunsheng Xin, Hongyi Wu

Computer Science Faculty Publications

To enable common users to capitalize on the power of deep learning, Machine Learning as a Service (MLaaS) has been proposed in the literature, which opens powerful deep learning models of service providers to the public. To protect the data privacy of end users, as well as the model privacy of the server, several state-of-the-art privacy-preserving MLaaS frameworks have also been proposed. Nevertheless, despite the exquisite design of these frameworks to enhance computation efficiency, the computational cost remains expensive for practical applications. To improve the computation efficiency of deep learning (DL) models, model pruning has been adopted as a strategic …

Speculative Anisotropic Mesh Adaptation On Shared Memory For Cfd Applications, Christos Tsolakis, Nikos Chrisochoides

Computer Science Faculty Publications

Efficient and robust anisotropic mesh adaptation is crucial for Computational Fluid Dynamics (CFD) simulations. The CFD Vision 2030 Study highlights the pressing need for this technology, particularly for simulations targeting supercomputers. This work applies a fine-grained speculative approach to anisotropic mesh operations. Our implementation exhibits more than 90% parallel efficiency on a multi-core node. Additionally, we evaluate our method within an adaptive pipeline for a spectrum of publicly available test-cases that includes both analytically derived and error-based fields. For all test-cases, our results are in accordance with published results in the literature. Support for CAD-based data is introduced, and its …

Charged Track Reconstruction With Artificial Intelligence For Clas12, Gagik Gavalian, Polykarpos Thomadakis, Angelos Angelopoulos, Nikos Chrisochoides

Computer Science Faculty Publications

In this paper, we present the results of charged particle track reconstruction in CLAS12 using artificial intelligence. In our approach, we use neural networks working together to identify tracks based on the raw signals in the Drift Chambers. A Convolutional Auto-Encoder is used to de-noise raw data by removing the hits that do not satisfy the patterns for tracks, and second Multi-Layer Perceptron is used to identify tracks from combinations of clusters in the drift chambers. Our method increases the tracking efficiency by 50% for multi-particle final states already conducted experiments. The de-noising results indicate that future experiments can run …

Multi-Activity Student Knowledge And Behavior Modeling Via Transfer Learning, Siqian Zhao

Electronic Theses & Dissertations (2024 - present)

Online education systems have grown in popularity over the past few years, providing abundant opportunities for students to learn. As the number of students using these systems grows, it promotes the development of the Educational Data Mining (EDM) field, which leverages statistical, machine learning, and data mining technologies to explore large-scale educational data and develop methods to better understand student learning.

In this dissertation, we investigate two essential topics in EDM: Student Knowledge Tracing (KT) and Behavior Modeling (BM). KT aims to quantify and model student knowledge gained from learning activities, while BM focuses on tasks such as modeling student …

Sparse Representation Learning For Temporal Networks, Maxwell Mcneil

Electronic Theses & Dissertations (2024 - present)

Temporal networks arise in many domains including activity of social network users, sensor network readings over time, and time course gene expression within the interaction network of a model organism. Data of this type contains a wealth of prior information such as the connectivity among nodes (e.g., a friendship graph), and prior knowledge of expected temporal patterns (e.g., periodicity). Modeling these temporal and network patterns jointly is essential for state-of-the-art performance in temporal network data analysis and mining. Sparse dictionary encoding is one modeling approach for such underlying patterns. However, most classical approaches consider only one dimension of the data …

Bias-Aware Gaze Uniformity Assessment In Group Images, Omkar Kulkarni

Electronic Theses & Dissertations (2024 - present)

Today, more than 5 billion photos are captured every day, with smartphones generating over 94\% of these images. However, despite advancements in technology, achieving aesthetically pleasing group photos remains challenging, especially when it comes to aligning the direction of everyone’s gaze. While current methods focus on facial features, they often fail to ensure consistent gaze direction. The introduction of the iPhone's Live mode, which captures a 1.5-second video snippet along with still images, complicates the selection of the best key photo due to its subjective nature and a lack of publicly available data, especially during the pandemic.

To address these …

The Effectiveness Of Cybersecurity Training, Courtney Knight

Electronic Theses & Dissertations (2024 - present)

This study seeks to answer the question of what kinds of cybersecurity training are effective by reviewing the existing literature, analyzing for gaps, and bridging the connection with known learning techniques. The research is exploratory in nature, and is inductive – intending to develop a theory. Additionally, this study seeks to offer a taxonomy of cybersecurity training methods to be evaluated.

This study did not include security operation center (SOC), cyber incident response teams (CIRTs), or other types of advanced cybersecurity professional training. This research specifically focuses on training to improve the average employee and population’s tactical cybersecurity skills.

Several …

Disentangling Cyclic Causality: An Instance-Based Framework For Causal Discovery, Chase A. Yakaboski

Dartmouth College Ph.D Dissertations

Correlation does not imply causation" is one of the fundamental principles taught in science, emphasizing that associations between variables do not necessarily indicate causality. Yet, over the past three decades, extensive research has begun to challenge this perspective by developing sophisticated methods to differentiate causal from correlative relationships. This research suggests that correlations often involve a blend of confounded and causal interactions, which, given certain assumptions, can be disentangled to uncover actionable insights and deepen our understanding of physical, biological, and societal systems.

Accurately discovering causal relationships from data amidst cyclic dynamics remains a challenging open problem in causality research. …

Consistent Monte Carlo Methods For Non-Linear Applications In Light Transport, Zackary T. Misso

Dartmouth College Ph.D Dissertations

The study of light transport focuses on describing the propagation of light from emitters to sensors through accurately describing the interactions light can undergo with everything in between. Physically-based rendering is the process of applying the laws of light transport to formulate practical algorithms which simulate the flow of light for the purpose of synthesizing images of virtual environments.

Unfortunately, there are very few interesting scene configurations which can be computed analytically. Instead, modern solutions predominantly rely on Monte Carlo integration to stochastically estimate the transfer of light since the process is both unbiased and consistent. Meaning, it is expected …

Mitigating Safety Issues In Pre-Trained Language Models: A Model-Centric Approach Leveraging Interpretation Methods, Weicheng Ma

Dartmouth College Ph.D Dissertations

Pre-trained language models (PLMs), like GPT-4, which powers ChatGPT, face various safety issues, including biased responses and a lack of alignment with users' backgrounds and expectations. These problems threaten their sociability and public application. Present strategies for addressing these safety concerns primarily involve data-driven approaches, requiring extensive human effort in data annotation and substantial training resources. Research indicates that the nature of these safety issues evolves over time, necessitating continual updates to data and model re-training—an approach that is both resource-intensive and time-consuming. This thesis introduces a novel, model-centric strategy for understanding and mitigating the safety issues of PLMs by …

Scalable Methods For Resource-Constrained Adaptive Sampling, Kizito Masaba

Dartmouth College Ph.D Dissertations

As the global community confronts the pressing issues of climate change, the importance of environment monitoring cannot be overstated. This process is essential in identifying and tracking critical environmental trends to facilitate efficient and effective conservation efforts. Traditionally, scientists perform this task using hand-held, in-situ instruments. With the recent robot advancements, this task can be fully automated by applying multi-robot systems to a task referred to as multi-robot adaptive sampling. However, the cost of purchasing and operating robot systems for this application are still prohibitive due to various environmental, technological, and logistical constraints. Some of the outstanding constraints to the …

Random Walk Methods For Geometry Representation Agnostic Transport, Dario R. Seyb

Dartmouth College Ph.D Dissertations

In computer graphics, we use geometry representations to model a wide range of virtual scenes—from the fantastical worlds shown in animated movies to intricate mechanical parts.
These representations provide the context for transport problems—light transport is used to produce images of virtual scenes and diffusive transport to simulate distributions of quantities like heat.

There are many types of representations each with their own advantages.
For example, explicit ones make it easy to directly manipulate surfaces, while implicit representations allow for intuitive modeling by non-technical users and straightforward integration into machine learning systems.
Unfortunately, many algorithms that work on these digital …

Gnss Software Defined Radio: History, Current Developments, And Standardization Efforts, Thomas Pany, Dennis Akos, Javier Arribas, M. Zahidul H. Bhuiyan, Pau Closas, Fabio Dovis, Ignacio Fernandez-Hernandez, Carles Fernandez-Prades, Sanjeev Gunawardena, Todd Humphreys, Zaher M. Kassas, Jose A. Lopez Salcedo, Mario Nicola, Mario L. Psiaki, Alexander Rugamer, Yong-Jin Song, Jong-Hoon Won

Faculty Publications

Taking the work conducted by the global navigation satellite system (GNSS) software-defined radio (SDR) working group during the last decade as a seed, this contribution summarizes, for the first time, the history of GNSS SDR development. This report highlights selected SDR implementations and achievements that are available to the public or that influenced the general development of SDR. Aspects related to the standardization process of intermediate-frequency sample data and metadata are discussed, and an update of the Institute of Navigation SDR Standard is proposed. This work focuses on GNSS SDR implementations in general-purpose processors and leaves aside developments conducted on …

Garbage In ≠ Garbage Out: Exploring Gan Resilience To Image Training Set Degradations, Nicholas Crino, Bruce A. Cox, Nathan B. Gaw

Faculty Publications

Generative Adversarial Networks (GANs) have received immense attention in recent years due to their ability to capture complex, high-dimensional data distributions without the need for extensive labeling. Since their conception in 2014, a wide array of GAN variants have been proposed featuring alternative architectures, optimizers, and loss functions with the goal of improving performance and training stability. This manuscript focuses on quantifying the resilience of a GAN architecture to specific modes of image degradation. We conduct systematic experimentation to empirically determine the effects of 10 fundamental image degradation modes, applied to the training image dataset, on the Fréchet inception distance …

Understanding And Augmenting Scientific Software Testing Practices, Kris Roker

UNF Graduate Theses and Dissertations

Scientific software can be broadly defined as software written to aid in conducting scientific research activities. As this software is often written by the scientists themselves, who often learned programming to build that software, some important aspects of software development may get less attention than they would have gotten on enterprise software developed by programmers. One area of development that often gets overlooked in this regard is testing. Thus, in this study, we seek to better understand the testing processes and propose methods to improve the effectiveness of those tests. We begin with examining the software's Continuous Integration/Delivery practices. This …

Advancing Machine Learning Interpretability: Lime Applications To Temporal Data And A Novel Method Of Counterfactual Generation, Shou Nakano, Yang Liu

Theses and Dissertations (Comprehensive)

As machine learning has advanced significantly over the past decade, predictive models have achieved substantial success across various domains. However, they often lack transparency in their decision-making processes. This opacity presents risks, particularly in sectors like healthcare and finance, where transparency is crucial. To address these challenges, explainable artificial intelligence (XAI) has risen in importance. Techniques such as LIME (Local Interpretable Model-agnostic Explanations) have been developed, utilizing simpler alternative models like linear regression or tree-based models to explain decisions for specific instances.

This thesis initially concentrates on the application of LIME to three global annual datasets, specifically within the relatively …

A Memory Efficient Deep Recurrent Q-Learning Approach For Autonomous Wildfire Surveillance, Jeremy A. Cantor

UNF Graduate Theses and Dissertations

Previous literature demonstrates that autonomous UAVs (unmanned aerial vehicles) have the po- tential to be utilized for wildfire surveillance. This advanced technology empowers firefighters by providing them with critical information, thereby facilitating more informed decision-making processes. This thesis applies deep Q-learning techniques to the problem of control policy design under the objective that the UAVs collectively identify the maximum number of locations that are under fire, assuming the UAVs can share their observations. The prohibitively large state space underlying the control policy motivates a neural network approximation, but prior work used only convolutional layers to extract spatial fire information from …