Physical Sciences and Mathematics Commons^™

Persistent Relative Homology For Topological Data Analysis, Christian J. Lentz

Mathematics, Statistics, and Computer Science Honors Projects

A central problem in data-driven scientific inquiry is how to interpret structure in noisy, high-dimensional data. Topological data analysis (TDA) provides a solution via the language of persistent homology, which encodes features of interest as holes within a filtration of the data. The recently presented U-Match Decomposition places the standard persistence computation in a flexible form, allowing for straight-forward extensions of the algorithm to variations of persistent homology. We describe U-Match Decomposition in the context of persistent homology, and extend it to an algorithm for persistent relative homology, providing proofs for the correctness and stability of the presented algorithm.

The Manifesto For Teaching And Learning In A Time Of Generative Ai: A Critical Collective Stance To Better Navigate The Future, Aras Bozkurt, Junhong Xiao, Robert Farrow, John Y. H. Bai, Chrissi Nerantzi, Stephanie Moore, Jon Dron, Christian M. Stracke, Lenandlar Singh, Helen Crompton, Apostolos Koutropoulos, Evgenii Terentev, Angelica Pazurek, Mark Nichols, Alexander M. Sidorkin, Eamon Costello, Steven Watson, Dónal Mulligan, Sarah Honeychurch, Charles B. Hodges, Mike Sharples, Andrew Swindell, Isak Frumin, Ahmed Tlili, Patricia J. Slagter Van Tryon, Melissa Bond, Maha Bali, Jing Leng, Kai Zhang, Mutlu Cukurnova, Thomas K. F. Chiu, Kyungmee Lee, Stefan Hrastinski, Manuel B. Garcia, Ramesh Chander Sharma, Bryan Alexander, Olaf Zawacki-Richter, Henk Huijser, Petar Jandrić, Chanjin Zheng, Peter Shea, Josep M. Duart, Chryssa Themeli, Anton Vorochkov, Sunagül Sani-Bozkurt, Robert L. Moore, Tutaleni Iita Asino

STEMPS Faculty Publications

This manifesto critically examines the unfolding integration of Generative AI (GenAI), chatbots, and algorithms into higher education, using a collective and thoughtful approach to navigate the future of teaching and learning. GenAI, while celebrated for its potential to personalize learning, enhance efficiency, and expand educational accessibility, is far from a neutral tool. Algorithms now shape human interaction, communication, and content creation, raising profound questions about human agency and biases and values embedded in their designs. As GenAI continues to evolve, we face critical challenges in maintaining human oversight, safeguarding equity, and facilitating meaningful, authentic learning experiences. This manifesto emphasizes that …

A Formalism For Extracting Track Functions From Jet Measurements, Kyle Lee, Ian Moult, Felix Ringer, Wouter J. Waalewijn

Physics Faculty Publications

The continued success of the jet substructure program will require widespread use of tracking information to enable increasingly precise measurements of a broader class of observables. The recent reformulation of jet substructure in terms of energy correlators has simplified the incorporation of universal non-perturbative matrix elements, so called “track functions”, in jet substructure calculations. These advances make it timely to understand how these universal non-perturbative functions can be extracted from hadron collider data, which is complicated by the use jet algorithms. In this paper we introduce a new class of jet functions, which we call (semi-inclusive) track jet functions, which …

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 …

Hite: A Fast And Accurate Dynamic Boundary Adjustment Approach For Full-Length Transposable Element Detection And Annotation, Kang Hu, Peng Ning, Minghua Xu, You Zou, Jianye Chang, Xin Gao, Yaohang Li, Jue Ruan, Bin Hu, Jianxin Wang

Computer Science Faculty Publications

Recent advancements in genome assembly have greatly improved the prospects for comprehensive annotation of Transposable Elements (TEs). However, existing methods for TE annotation using genome assemblies suffer from limited accuracy and robustness, requiring extensive manual editing. In addition, the currently available gold-standard TE databases are not comprehensive, even for extensively studied species, highlighting the critical need for an automated TE detection method to supplement existing repositories. In this study, we introduce HiTE, a fast and accurate dynamic boundary adjustment approach designed to detect full-length TEs. The experimental results demonstrate that HiTE outperforms RepeatModeler2, the state-of-the-art tool, across various species. Furthermore, …

Using Feature Selection Enhancement To Evaluate Attack Detection In The Internet Of Things Environment, Khawlah Harahsheh, Rami Al-Naimat, Chung-Hao Chen

Electrical & Computer Engineering Faculty Publications

The rapid evolution of technology has given rise to a connected world where billions of devices interact seamlessly, forming what is known as the Internet of Things (IoT). While the IoT offers incredible convenience and efficiency, it presents a significant challenge to cybersecurity and is characterized by various power, capacity, and computational process limitations. Machine learning techniques, particularly those encompassing supervised classification techniques, offer a systematic approach to training models using labeled datasets. These techniques enable intrusion detection systems (IDSs) to discern patterns indicative of potential attacks amidst the vast amounts of IoT data. Our investigation delves into various aspects …

Scene Classification Of Remote Sensing Image Based On Multi-Path Reconfigurable Neural Network, Wenyi Hu, Chunjie Lan, Tian Chen, Shan Liu, Lirong Yin, Lei Wang

Electrical & Computer Engineering Faculty Publications

Land image recognition and classification and land environment detection are important research fields in remote sensing applications. Because of the diversity and complexity of different tasks of land environment recognition and classification, it is difficult for researchers to use a single model to achieve the best performance in scene classification of multiple remote sensing land images. Therefore, to determine which model is the best for the current recognition classification tasks, it is often necessary to select and experiment with many different models. However, finding the optimal model is accompanied by an increase in trial-and-error costs and is a waste of …

Skipresnet: Crop And Weed Recognition Based On The Improved Resnet, Wenyi Hu, Tian Chen, Chunjie Lan, Shan Liu, Lirong Yin

Electrical & Computer Engineering Faculty Publications

Weeds have a detrimental effect on crop yield. However, the prevailing chemical weed control methods cause pollution of the ecosystem and land. Therefore, it has become a trend to reduce dependence on herbicides; realize a sustainable, intelligent weed control method; and protect the land. In order to realize intelligent weeding, efficient and accurate crop and weed recognition is necessary. Convolutional neural networks (CNNs) are widely applied for weed and crop recognition due to their high speed and efficiency. In this paper, a multi-path input skip-residual network (SkipResNet) was put forward to upgrade the classification function of weeds and crops. It …

Integrative Machine Learning Approaches For Enhanced Classification Of Genomic Sequences: A Next-Generation Sequencing Perspective, Sujatha Alla, Nagesh Bheesetty, Sai Gireesh Komaragiri, Prasanthi Chidipudi, Joshit Mohanty, Sathish Kumar Chintala, Jubin Thomas, Jayapal Vummadi, Hemanth Volikatla, Navin Kamuni

Engineering Management & Systems Engineering Faculty Publications

The advent of Next-Generation Sequencing (NGS) techniques has revolutionized genomic research by enabling the rapid sequencing of DNA and RNA. This data can be used for various applications, including genome sequencing, transcriptome profiling, metagenomics, and epigenetics studies. For this study, DNA classifier dataset was extracted from UCI repository of machine learning databases. This vast amount of genomic data necessitates the development of sophisticated machine learning (ML) models for effective classification and analysis. This study presents a comprehensive comparison of various ML models, including Support Vector Machines (SVM), Random Forests (RF), and Neural Networks (NNs), approaches, in classifying genomic data. We …

Mapping Seagrass Distribution And Abundance: Comparing Areal Cover And Biomass Estimates Between Space-Based And Airborne Imagery, Victoria J. Hill, Richard C. Zimmerman, Dorothy A. Byron, Kenneth L. Heck Jr.

OES Faculty Publications

This study evaluated the effectiveness of Planet satellite imagery in mapping seagrass coverage in Santa Rosa Sound, Florida. We compared very-high-resolution aerial imagery (0.3 m) collected in September 2022 with high-resolution Planet imagery (~3 m) captured during the same period. Using supervised classification techniques, we accurately identified expansive, continuous seagrass meadows in the satellite images, successfully classifying 95.5% of the 11.18 km² of seagrass area delineated manually from the aerial imagery. Our analysis utilized an occurrence frequency (OF) product, which was generated by processing ten clear-sky images collected between 8 and 25 September 2022 to determine the frequency with which …

An Open Natural Language Processing (Nlp) Framework For Ehr-Based Clinical Research: A Case Demonstration Using The National Covid Cohort Collaborative (N3c), Sijia Liu, Andrew Wen, Liwei Wang, Huan He, Sunyang Fu, Robert Miller, Andrew Williams, Daniel Harris, Ramakanth Kavuluru, Mei Liu, Noor Abu-El-Rub, Dalton Schutte, Rui Zhang, Masoud Rouhizadeh, John D Osborne, Yongqun He, Umit Topaloglu, Stephanie S Hong, Joel H Saltz, Thomas Schaffter, Emily Pfaff, Christopher G Chute, Tim Duong, Melissa A Haendel, Rafael Fuentes, Peter Szolovits, Hua Xu, Hongfang Liu

Faculty, Staff and Student Publications

Despite recent methodology advancements in clinical natural language processing (NLP), the adoption of clinical NLP models within the translational research community remains hindered by process heterogeneity and human factor variations. Concurrently, these factors also dramatically increase the difficulty in developing NLP models in multi-site settings, which is necessary for algorithm robustness and generalizability. Here, we reported on our experience developing an NLP solution for Coronavirus Disease 2019 (COVID-19) signs and symptom extraction in an open NLP framework from a subset of sites participating in the National COVID Cohort (N3C). We then empirically highlight the benefits of multi-site data for both …

Hiking Trail Generation In Infinite Landscapes, Matthew Jensen

MS in Computer Science Project Reports

This project procedurally generates an infinite wilderness populated with deterministic hiking trails. Our approach recognizes that hiking trails depend on contextual information beyond the location of the path itself. To address this, we implemented a layered procedural system that orchestrates the generation process. This helps ensure the availability of contextual data at each stage. The first layer handles terrain generation, establishing the foundational landscape upon which trails will traverse. Subsequent layers handle point of interest identification and selection, trail network optimization through proximity graphs, and efficient pathfinding across the terrain. A notable feature of our approach is the deterministic nature …

An Open Guide To Data Structures And Algorithms, Paul W. Bible, Lucas Moser

Computer Science Faculty publications

This textbook serves as a gentle introduction for undergraduates to theoretical concepts in data structures and algorithms in computer science while providing coverage of practical implementation (coding) issues. The field of computer science (CS) supports a multitude of essential technologies in science, engineering, and communication as a social medium. The varied and interconnected nature of computer technology permeates countless career paths making CS a popular and growing major program. Mastery of the science behind computer science relies on an understanding of the theory of algorithms and data structures. These concepts underlie the fundamental tradeoffs that dictate performance in terms of …

Evaluation Of Symmetric Functions And Boolean Functions Over Stochastic Input, Naifeng Liu

Dissertations, Theses, and Capstone Projects

In our daily life, we often face situations where we need to make precise judgments based on initially unknown information, while gathering all the evidence to make informed conclusions can be very costly. In this dissertation, we explore the problem of optimizing the decision-making process under uncertainty, and we focus on problems that can be found in both theoretical computer science and discrete mathematics. The primary goal is to develop approximation algorithms with guaranteed worst-case performance. These algorithms aim to minimize the expected cost of acquiring information necessary for evaluating fundamental functions, such as Boolean and symmetric functions. Furthermore, we …

How I Read An Article That Uses Machine Learning Methods, Aziz Nazha, Olivier Elemento, Shannon Mcweeney, Moses Miles, Torsten Haferlach

Kimmel Cancer Center Faculty Papers

No abstract provided.

Minimal Positional Substring Cover Is A Haplotype Threading Alternative To Li And Stephens Model, Ahsan Sanaullah, Degui Zhi, Shaojie Zhang

Faculty, Staff and Student Publications

The Li and Stephens (LS) hidden Markov model (HMM) models the process of reconstructing a haplotype as a mosaic copy of haplotypes in a reference panel. For small panels, the probabilistic parameterization of LS enables modeling the uncertainties of such mosaics. However, LS becomes inefficient when sample size is large, because of its linear time complexity. Recently the PBWT, an efficient data structure capturing the local haplotype matching among haplotypes, was proposed to offer a fast method for giving some optimal solution (Viterbi) to the LS HMM. Previously, we introduced the minimal positional substring cover (MPSC) problem as an alternative …

Artificial Intelligence Cad Tools In Trauma Imaging: A Scoping Review From The American Society Of Emergency Radiology (Aser) Ai/Ml Expert Panel, David Dreizin, Pedro V Staziaki, Garvit D Khatri, Nicholas M Beckmann, Zhaoyong Feng, Yuanyuan Liang, Zachary S Delproposto, Maximiliano Klug, J Stephen Spann, Nathan Sarkar, Yunting Fu

Faculty, Staff and Student Publications

BACKGROUND: AI/ML CAD tools can potentially improve outcomes in the high-stakes, high-volume model of trauma radiology. No prior scoping review has been undertaken to comprehensively assess tools in this subspecialty.

PURPOSE: To map the evolution and current state of trauma radiology CAD tools along key dimensions of technology readiness.

METHODS: Following a search of databases, abstract screening, and full-text document review, CAD tool maturity was charted using elements of data curation, performance validation, outcomes research, explainability, user acceptance, and funding patterns. Descriptive statistics were used to illustrate key trends.

RESULTS: A total of 4052 records were screened, and 233 full-text …

Rapid-Query For Fast Identity By Descent Search And Genealogical Analysis, Yuan Wei, Ardalan Naseri, Degui Zhi, Shaojie Zhang

Faculty, Staff and Student Publications

MOTIVATION: Due to the rapid growth of the genetic database size, genealogical search, a process of inferring familial relatedness by identifying DNA matches, has become a viable approach to help individuals finding missing family members or law enforcement agencies locating suspects. A fast and accurate method is needed to search an out-of-database individual against millions of individuals. Most existing approaches only offer all-versus-all within panel match. Some prototype algorithms offer one-versus-all query from out-of-panel individual, but they do not tolerate errors.

RESULTS: A new method, random projection-based identity-by-descent (IBD) detection (RaPID) query, is introduced to make fast genealogical search possible. …

Algorithmic Bias: Causes And Effects On Marginalized Communities, Katrina M. Baha

Undergraduate Honors Theses

Individuals from marginalized backgrounds face different healthcare outcomes due to algorithmic bias in the technological healthcare industry. Algorithmic biases, which are the biases that arise from the set of steps used to solve or analyze a problem, are evident when people from marginalized communities use healthcare technology. For example, many pulse oximeters, which are the medical devices used to measure oxygen saturation in the blood, are not able to accurately read people who have darker skin tones. Thus, people with darker skin tones are not able to receive proper health care due to their pulse oximetry data being inaccurate. This …

Procedural Level Generation For A Top-Down Roguelike Game, Kieran Ahn, Tyler Edmiston

Honors Thesis

In this file, I present a sequence of algorithms that handle procedural level generation for the game Fragment, a game designed for CMSI 4071 and CMSI 4071 in collaboration with students from the LMU Animation department. I use algorithms inspired by graph theory and implementing best practices to the best of my ability. The full level generation sequence is comprised of four algorithms: the terrain generation, boss room placement, player spawn point selection, and enemy population. The terrain generation algorithm takes advantage of tree traversal methods to create a connected graph of walkable tiles. The boss room placement algorithm randomly …

Algorithms, Leadership, And Morality: Why A Mere Human Effect Drives The Preference For Human Over Algorithmic Leadership, Jack Mcguire, David De Cremer

Research Collection Lee Kong Chian School Of Business

Algorithms are increasingly making decisions in organizations that carry moral consequences and such decisions are considered to be ordinarily made by leaders. An important consideration to be made by organizations is therefore whether adopting algorithms in this domain will be accepted by employees and whether this practice will harm their reputation. Considering this emergent phenomenon, we set out to examine employees’ perceptions about (a) algorithmic decision-making systems employed to occupy leadership roles and make moral decisions in organizations, and (b) the reputation of organizations that employ such systems. Furthermore, we examine the extent to which the decision agent needs to …

Why Is Biomedical Informatics Hard? A Fundamental Framework, Todd R Johnson, Elmer V Bernstam

Faculty, Staff and Student Publications

Building on previous work to define the scientific discipline of biomedical informatics, we present a framework that categorizes fundamental challenges into groups based on data, information, and knowledge, along with the transitions between these levels. We define each level and argue that the framework provides a basis for separating informatics problems from non-informatics problems, identifying fundamental challenges in biomedical informatics, and provides guidance regarding the search for general, reusable solutions to informatics problems. We distinguish between processing data (symbols) and processing meaning. Computational systems, that are the basis for modern information technology (IT), process data. In contrast, many important challenges …

Automated Contouring And Planning In Radiation Therapy: What Is 'Clinically Acceptable'?, Hana Baroudi, Kristy K Brock, Wenhua Cao, Xinru Chen, Caroline Chung, Laurence E Court, Mohammad D El Basha, Maguy Farhat, Skylar Gay, Mary P Gronberg, Aashish Chandra Gupta, Soleil Hernandez, Kai Huang, David A Jaffray, Rebecca Lim, Barbara Marquez, Kelly Nealon, Tucker J Netherton, Callistus M Nguyen, Brandon Reber, Dong Joo Rhee, Ramon M Salazar, Mihir D Shanker, Carlos Sjogreen, Mckell Woodland, Jinzhong Yang, Cenji Yu, Yao Zhao

Faculty, Staff and Student Publications

Developers and users of artificial-intelligence-based tools for automatic contouring and treatment planning in radiotherapy are expected to assess clinical acceptability of these tools. However, what is 'clinical acceptability'? Quantitative and qualitative approaches have been used to assess this ill-defined concept, all of which have advantages and disadvantages or limitations. The approach chosen may depend on the goal of the study as well as on available resources. In this paper, we discuss various aspects of 'clinical acceptability' and how they can move us toward a standard for defining clinical acceptability of new autocontouring and planning tools.

Machine Learning Algorithms Improve Modis Gpp Estimates In United States Croplands, D. Menefee, T. O. Lee, K. C. Flynn, J. Chen, M. Abraha, J. Baker, A. Suyker

School of Natural Resources: Faculty Publications

No abstract provided.

Visualization Teaching Tool For Computational Geometry Algorithms, Seth Spire

Honors Projects

Computational geometry is a branch of computer science dedicated to the study and development of algorithms that solve geometric problems. These algorithms are often complex, so this project involves the development of a teaching tool for various computational geometry algorithms. A Node app was developed which allows a user to create their own inputs for an algorithm and watch a visualization of how an algorithm solves one of the various problems. There is highlighted pseudocode matching the steps of the visualization along with more in-depth writeups of the inner workings of the algorithm. 4 algorithms have been implemented in the …

Patch-Wise Training With Convolutional Neural Networks To Synthetically Upscale Cfd Simulations, John P. Romano, Alec C. Brodeur, Oktay Baysal

Mechanical & Aerospace Engineering Faculty Publications

This paper expands the authors’ prior work[1], which focuses on developing a convolutional neural network (CNN) model capable of mapping time-averaged, unsteady Reynold’s-averaged Navier-Stokes (URANS) simulations to higher resolution results informed by time-averaged detached eddy simulations (DES). The authors present improvements over the prior CNN autoencoder model that result from hyperparameter optimization, increased data set augmentation through the adoption of a patch-wise training approach, and the predictions of primitive variables rather than vorticity magnitude. The training of the CNN model developed in this study uses the same URANS and DES simulations of a transonic flow around several NACA 4-digit airfoils …

Machine-Learning-Based Vulnerability Detection And Classification In Internet Of Things Device Security, Sarah Bin Hulayyil, Shancang Li, Li Da Xu

Information Technology & Decision Sciences Faculty Publications

Detecting cyber security vulnerabilities in the Internet of Things (IoT) devices before they are exploited is increasingly challenging and is one of the key technologies to protect IoT devices from cyber attacks. This work conducts a comprehensive survey to investigate the methods and tools used in vulnerability detection in IoT environments utilizing machine learning techniques on various datasets, i.e., IoT23. During this study, the common potential vulnerabilities of IoT architectures are analyzed on each layer and the machine learning workflow is described for detecting IoT vulnerabilities. A vulnerability detection and mitigation framework was proposed for machine learning-based vulnerability detection in …

An Empirical Analysis Of Algorithms For Simple Stochastic Games, Cody William Klingler

Graduate Theses, Dissertations, and Problem Reports (ETD)

This thesis presents the findings of a computational study on algorithms for Simple Stochastic Games (SSG). Simple Stochastic Games are a restriction of the Shapley stochastic model motivated by their applications in AI planning, logic synthesis, and theoretical computer science. This thesis seeks to empirically assess the performance of these algorithms to compensate for their lack of strong complexity results. Where applicable, we include both variations of algorithms where stable strategies are computed by a linear-programming and naive approach. These algorithms are evaluated on random inputs, in addition to specific difficult cases that were identified experimentally. We are interested in …

Relation Preserving Triplet Mining For Stabilising The Triplet Loss In Re-Identification Systems, Adhiraj Ghosh, Kuruparan Shanmugalingam, Wen-Yan Lin

Research Collection School Of Computing and Information Systems

Object appearances change dramatically with pose variations. This creates a challenge for embedding schemes that seek to map instances with the same object ID to locations that are as close as possible. This issue becomes significantly heightened in complex computer vision tasks such as re-identification(reID). In this paper, we suggest that these dramatic appearance changes are indications that an object ID is composed of multiple natural groups, and it is counterproductive to forcefully map instances from different groups to a common location. This leads us to introduce Relation Preserving Triplet Mining (RPTM), a feature matching guided triplet mining scheme, that …

Comparative Analysis Of Fullstack Development Technologies: Frontend, Backend And Database, Qozeem Odeniran

College of Graduate Studies: Theses & Dissertations

Accessing websites with various devices has brought changes in the field of application development. The choice of cross-platform, reusable frameworks is very crucial in this era. This thesis embarks in the evaluation of front-end, back-end, and database technologies to address the status quo. Study-a explores front-end development, focusing on angular.js and react.js. Using these frameworks, comparative web applications were created and evaluated locally. Important insights were obtained through benchmark tests, lighthouse metrics, and architectural evaluations. React.js proves to be a performance leader in spite of the possible influence of a virtual machine, opening the door for additional research. Study b …