Computer Sciences Commons^™

Religious Bias In Llms Is Significantly Understudied, Sheryl Carty, Nancy Fulda, Walter Reade

Faculty Publications

In the earlier years of development of LLMs, it was relatively easy to prompt an LLM to respond with toxic or biased statements about religion. Subsequent improvements in frontier models addressed many of the issues of bias and toxicity in general, including against religion. At the same time, the adoption and usage of these models has grown exponentially. Small and implicit biases, therefore, have a magnified overall impact. In this paper, we (1) briefly review previous efforts to measure religious bias in LLMs, (2) show, by reviewing over 12,000 papers dealing with bias in LLMs, that religious bias has been …

Panda-Plus-Bench: A Clinical Benchmark For Evaluating The Robustness Of Ai Foundation Models In Prostate Cancer Diagnosis, Joshua L. Ebbert, Dennis Della Corte

Faculty Publications

Artificial intelligence foundation models are increasingly deployed for prostate cancer Gleason grading, where GP3/GP4 distinction directly impacts treatment decisions (active surveillance vs. intervention). However, these models may achieve high validation accuracy by learning specimen-specific artifacts rather than generalizable biological features, limiting real-world clinical utility. We introduce PANDA-PLUS-Bench, a curated benchmark dataset derived from expertly annotated prostate biopsies designed specifically to quantify this failure mode. The benchmark comprises nine carefully selected whole slide images from nine unique patients containing diverse Gleason patterns, with non-overlapping tissue patches extracted at both 512 × 512 and 224 × 224-pixel resolutions across eight augmentation conditions. …

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

Faculty Publications

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

Chronosort: Revealing Hidden Dynamics In Alphafold3 Structure Predictions, Matthew J. Argyle, William P. Heaps, Corbyn Kubalek, Spencer Gardiner, Bradley C. Bundy, Dennis Della Corte

Faculty Publications

Protein function emerges from dynamic conformational changes, yet structure prediction methods provide only static snapshots. While AlphaFold3 (AF3) predicts protein structures, the potential for extracting dynamic information from its ensemble predictions has remained underexplored. Here, we demonstrate that AF3 structural ensembles contain substantial dynamic information that correlates remarkably well with molecular dynamics simulations (MD). We developed ChronoSort, a novel algorithm that organizes static structure predictions into temporally coherent trajectories by minimizing structural differences between neighboring frames. Through systematic analysis of four diverse protein targets, we show that root-mean-square fluctuations derived from AF3 ensembles can correlate strongly with those from MD …

Using Linear Programming And Game Theory To Optimize The Relation Between Us And China, Junhao Su

Student Works

This paper develops an optimization model to analyze U.S.–China bilateral trade dynamics and competition in artificial intelligence (AI). First, grounded in WTO tariff limits, we formulate a linear programming model to maximize the combined trade volume and conduct a comprehensive sensitivity analysis on tariff parameters. Second, we integrate zero‑sum and non‑zero‑sum game‑theoretic frameworks to identify the Nash equilibria governing both trade negotiations and technological rivalry. The model is implemented in Python using PuLP and is empirically validated with real‑world tariff data to highlight the policy relevance of the optimal solutions. Our results reveal a high concordance between the zero‑sum game …

Equipping Future Physicians With Artificial Intelligence Competencies Through Student Associations, Spencer Hopson, Carson Mildon, Kyle Hassard, Paul Urie, Dennis Della Corte

Faculty Publications

Advances in artificial intelligence (AI) in the medical sector necessitate the development of AI literacy among future physicians. This article explores the pioneering efforts of the AI in Medicine Association (AIM) at Brigham Young University, which offers a framework for undergraduate pre-medical students to gain hands-on experience, receive principled education, explore ethical considerations, and learn appraisal of AI models. By supplementing formal, university-organized pre-medical education with a student-led, faculty-supported introduction to AI through an extracurricular academic association, AIM alleviates apprehensions regarding AI in medicine early and empowers students preparing for medical school to navigate the evolving landscape of AI in …

Addressing Social Inequalities Using Ai, Big Data, And Machine Learning, Erica L. Jensen, Lakell Archer, Sumaya Ali

Journal of Nonprofit Innovation

No abstract provided.

Reducing Food Scarcity: The Benefits Of Urban Farming, S.A. Claudell, Emilio Mejia

Journal of Nonprofit Innovation

Urban farming can enhance the lives of communities and help reduce food scarcity. This paper presents a conceptual prototype of an efficient urban farming community that can be scaled for a single apartment building or an entire community across all global geoeconomics regions, including densely populated cities and rural, developing towns and communities. When deployed in coordination with smart crop choices, local farm support, and efficient transportation then the result isn’t just sustainability, but also increasing fresh produce accessibility, optimizing nutritional value, eliminating the use of ‘forever chemicals’, reducing transportation costs, and fostering global environmental benefits.

Imagine Doris, who is …

Evaluating A Large Language Model’S Ability To Solve Programming Exercises From An Introductory Bioinformatics Course, Stephen R. Piccolo, Paul Denny, Andrew Luxton-Reilly, Samuel H. Payne, Perry G. Ridge

Faculty Publications

Life scientists frequently write computer code when doing research. Computer programming can aid researchers in performing tasks that are not supported by existing tools. Programming can also help researchers to implement analytical logic in a way that documents their steps and thus enables others to repeat those steps. Many educational resources are available to teach computer programming, but this skill remains challenging for many researchers and students to master. Artificial-intelligence tools like OpenAI’s ChatGPT are able to interpret human-language requests to generate code. Accordingly, we evaluated the extent to which this technology might be used to perform programming tasks described …

Don't Fear The Artificial Intelligence: A Systematic Review Of Machine Learning For Prostate Cancer Detection In Pathology, Aaryn Frewing, Alexander B. Gibson, Richard Robertson, Paul Urie, Dennis Della Corte

Faculty Publications

The adoption of whole slide image (WSI) scanners in clinical practice was accelerated by US Food and Drug Administration approval in 2017, which allowed primary pathologic diagnoses to be made on scanned images. Images in the digital domain allow the application of pathology artificial intelligence (AI), including clinical decision support with algorithms performing specific diagnoses.1,2 These algorithms, if trained properly, could go beyond the ability of human observation to detect and quantify features that are not recognizable by human perception.1,3,4

Confronting Barriers To Human-Robot Cooperation: Balancing Efficiency And Risk In Machine Behavior, Tim Whiting

Theses and Dissertations

In strategically rich settings in which machines and people do not fully share the same preferences, machines must learn to cooperate and compromise with people to establish mutually successful relationships. However, designing machines that effectively cooperate with people in these settings is difficult due to a variety of technical and psychological challenges. To better understand these challenges, we conducted a series of user studies in which we investigated human-human, robot-robot, and human-robot cooperation in a simple, yet strategically rich, resource-sharing scenario called the Block Dilemma, a game in which players must balance fairness, efficiency, and risk. While both human-human and …

Symbolic Semantic Memory In Transformer Language Models, Robert Kenneth Morain

Theses and Dissertations

This paper demonstrates how transformer language models can be improved by giving them access to relevant structured data extracted from a knowledge base. The knowledge base preparation process and modifications to transformer models are explained. We evaluate these methods on language modeling and question answering tasks. These results show that even simple additional knowledge augmentation leads to a reduction in validation loss by 73%. These methods also significantly outperform common ways of improving language models such as increasing the model size or adding more data.

Outvoice: Bringing Transparency To Healthcare, Autumn Clark

Undergraduate Honors Theses

Industries are not incentivized to price reasonably and spend responsibly if consumers do not have the ability to shop around within that industry, and shopping around is not possible without pricing transparency (knowing how much a good or service costs before purchasing it). But in the healthcare industry, we typically default to whichever clinic or hospital is closest, with no prior knowledge of what costs we can expect to incur at that particular institution. According to a poll published by Harvard University, nine out of ten Americans feel the healthcare industry is too opaque and greater transparency is needed.

We …

Evaluation Of Deep Neural Network Prospr For Accurate Protein Distance Predictions On Casp14 Targets, Jacob A. Stern, Bryce Eric Hedelius, Olivia Fisher, Wendy M. Billings, Dennis Della Corte

Faculty Publications

The field of protein structure prediction has recently been revolutionized through the introduction of deep learning. The current state-of-the-art tool AlphaFold2 can predict highly accurate structures; however, it has a prohibitively long inference time for applications that require the folding of hundreds of sequences. The prediction of protein structure annotations, such as amino acid distances, can be achieved at a higher speed with existing tools, such as the ProSPr network. Here, we report on important updates to the ProSPr network, its performance in the recent Critical Assessment of Techniques for Protein Structure Prediction (CASP14) competition, and an evaluation of its …

Beware Of Ips In Sheep's Clothing: Measurement And Disclosure Of Ip Spoofing Vulnerabilities, Alden Douglas Hilton

Theses and Dissertations

Networks not employing destination-side source address validation (DSAV) expose themselves to a class of pernicious attacks which could be prevented by filtering inbound traffic purporting to originate from within the network. In this work, we survey the pervasiveness of networks vulnerable to infiltration using spoofed addresses internal to the network. We issue recursive Domain Name System (DNS) queries to a large set of known DNS servers world-wide using various spoofed-source addresses. In late 2019, we found that 49% of the autonomous systems we tested lacked DSAV. After a large-scale notification campaign run in late 2020, we repeated our measurements in …

Simplifying The Development Of Portable, Scalable, And Reproducible Workflows, Stephen Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang, Andrea H. Bild

Faculty Publications

Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution details. CWL documents can include instructions for executing tools inside software containers. Accordingly, CWL tools are portable—they can be executed on diverse computers—including personal workstations, high-performance clusters, or the cloud. CWL also supports workflows, which describe dependencies among tools and using outputs from one tool as inputs to others. To date, CWL has been used …

Who Uses Multi-Factor Authentication?, Leah Roberts

Undergraduate Honors Theses

A sample of 47 BYU students were recruited to participate in this study to determine who was using Multi-factor Authentication (MFA) on their online accounts. This study determined that there were many different factors that separated those who used MFA and those who did not. Some of those factors included: time spent on the internet each day, gender, the website itself, and personal privacy behaviors.

The Whole Is Greater Than Its Parts: Ensembling Improves Protein Contact Prediction, Wendy M. Billings, Connor J. Morris, Dennis Della Corte

Faculty Publications

The prediction of amino acid contacts from protein sequence is an important problem, as protein contacts are a vital step towards the prediction of folded protein structures. We propose that a powerful concept from deep learning, called ensembling, can increase the accuracy of protein contact predictions by combining the outputs of different neural network models. We show that ensembling the predictions made by different groups at the recent Critical Assessment of Protein Structure Prediction (CASP13) outperforms all individual groups. Further, we show that contacts derived from the distance predictions of three additional deep neural networks—AlphaFold, trRosetta, and ProSPr—can be substantially …

Realium: Building The Future Of Real Estate On The Blockchain, Demitri Haddad

Undergraduate Honors Theses

This paper discusses the prospective challenges, limitations and opportunities in the real estate sector for blockchain. It outlines the idea of Realium, a financial technology application that aims to assist in the purchase, sale, and legal compliance of real estate assets. For more information see docs.realium.io

The Communicative Effects Of Anonymity Online: A Natural Language Analysis Of The Faceless, Caleb Johnson

Undergraduate Honors Theses

An ever-increasing number of Americans have an active social media

presence online. As of March 2020, an estimated 79% of Americans were active

monthly users of some sort. Many of these online platforms allow users to

operate anonymously which could potentially lead to shifts in communicative

behavior. I first discuss my compilation process of the Twitter Anonymity

Dataset (TAD), a human-classified dataset of 100,000 Twitter accounts that are

categorized by their level of identifiability to their real-world agent. Next, I

investigate some of the structural differences between the classification levels

and employ a variety of Natural Language Processing models and …

Metalearning By Exploiting Granular Machine Learning Pipeline Metadata, Brandon J. Schoenfeld

Theses and Dissertations

Automatic machine learning (AutoML) systems have been shown to perform better when they use metamodels trained offline. Existing offline metalearning approaches treat ML models as black boxes. However, modern ML models often compose multiple ML algorithms into ML pipelines. We expand previous metalearning work on estimating the performance and ranking of ML models by exploiting the metadata about which ML algorithms are used in a given pipeline. We propose a dynamically assembled neural network with the potential to model arbitrary DAG structures. We compare our proposed metamodel against reasonable baselines that exploit varying amounts of pipeline metadata, including metamodels used …

Trace: A Differentiable Approach To Line-Level Stroke Recovery For Offline Handwritten Text, Taylor Neil Archibald

Theses and Dissertations

Stroke order and velocity are helpful features in the fields of signature verification, handwriting recognition, and handwriting synthesis. Recovering these features from offline handwritten text is a challenging and well-studied problem. We propose a new model called TRACE (Trajectory Recovery by an Adaptively-trained Convolutional Encoder). TRACE is a differentiable approach using a convolutional recurrent neural network (CRNN) to infer temporal stroke information from long lines of offline handwritten text with many characters. TRACE is perhaps the first system to be trained end-to-end on entire lines of text of arbitrary width and does not require the use of dynamic exemplars. Moreover, …

Ansible: Select-To-Edit For Physical Widgets, Benjamin M. Crowder

Theses and Dissertations

Ansible brings select-to-edit functionality to physical widgets. When programming sets of physical widgets, it can be bothersome for a programmer to remember the name of the software object that corresponds to a specific widget. Click-to-edit functionality in GUI programming provides a physical action--moving the mouse to a widget and clicking a button on the mouse--to select a virtual widget. In a similar vein, when programming physical widgets, it is natural to point at a widget and think, "I want to program that one." Ansible allows physical user interface programmers to "click" on a physical widget by making a physical action: …

Specialization: Do Your Job Well Helping Students Who Are Considering A Career In Programming Know How To Invest Their Time., Scott Pulley

Marriott Student Review

The article examines the effects of specialization on the hiring process for undergraduates studying programming whether in information systems or computer science.

Using Logical Specifications For Multi-Objective Reinforcement Learning, Kolby Nottingham

Undergraduate Honors Theses

In the multi-objective reinforcement learning (MORL) paradigm, the relative importance of environment objectives is often unknown prior to training, so agents must learn to specialize their behavior to optimize different combinations of environment objectives that are specified post-training. These are typically linear combinations, so the agent is effectively parameterized by a weight vector that describes how to balance competing environment objectives. However, we show that behaviors can be successfully specified and learned by much more expressive non-linear logical specifications. We test our agent in several environments with various objectives and show that it can generalize to many never-before-seen specifications.

Machine Learning For Effective Parkinson's Disease Diagnosis, Brennon Brimhall

Undergraduate Honors Theses

Parkinson’s Disease is a degenerative neurological condition that affects approximately 10 million people globally. Because there is currently no cure, there is a strong motivation for research into improved and automated diagnostic procedures. Using Random Forests, a computer can effectively learn to diagnose Parkinson’s disease in a patient with high accuracy (94%), precision (95%), and recall (91%) across the data of over 2800 patients. Using similar techniques, I further determine that the most predictive medical tests relate to tremors observed in patients.

Analysis Of Identification Method For Bacterial Species And Antibiotic Resistance Genes Using Optical Data From Dna Oligomers, Ryan L. Wood, Tanner Jensen, Cindi Wadsworth, Mark Clement, Prashant Nagpal, William G. Pitt

Faculty Publications

Bacterial antibiotic resistance is becoming a significant health threat, and rapid identification of antibiotic-resistant bacteria is essential to save lives and reduce the spread of antibiotic resistance. This paper analyzes the ability of machine learning algorithms (MLAs) to process data from a novel spectroscopic diagnostic device to identify antibiotic-resistant genes and bacterial species by comparison to available bacterial DNA sequences. Simulation results show that the algorithms attain from 92% accuracy (for genes) up to 99% accuracy (for species). This novel approach identifies genes and species by optically reading the percentage of A, C, G, T bases in 1000s of short …

Data For The Review Of Gamified Fitness Tracker Apps, Aatish Neupane, Derek Hansen, Anud Sharma, Jerry Alan Fails

ScholarsArchive Data

This is a supplemental dataset to a paper that reviews 103 gamified fitness tracker apps and analyzes the presence and usage of various game elements. This dataset contains the list of those apps that were reviewed. It also contains the coding that represents the presence of difference game elements.

Light-Field Style Transfer, David Marvin Hart

Theses and Dissertations

For many years, light fields have been a unique way of capturing a scene. By using a particular set of optics, a light field camera is able to, in a single moment, take images of the same scene from multiple perspectives. These perspectives can be used to calculate the scene geometry and allow for effects not possible with standard photographs, such as refocus and the creation of novel views.Neural style transfer is the process of training a neural network to render photographs in the style of a particular painting or piece of art. This is a simple process for a …

Cybersecurity Education In Utah High Schools: An Analysis And Strategy For Teacher Adoption, Cariana June Cornel

Theses and Dissertations

The IT Education Specialist for the USBE, Brandon Jacobson, stated:I feel there is a deficiency of and therefore a need to teach Cybersecurity.Cybersecurity is the “activity or process, ability or capability, or state whereby information and communications systems and the information contained therein are protected from and/or defended against damage, unauthorized use or modification, or exploitation” (NICE, 2018). Practicing cybersecurity can increase awareness of cybersecurity issues, such as theft of sensitive information. Current efforts, including but not limited to, cybersecurity camps, competitions, college courses, and conferences, have been created to better prepare cyber citizens nationwide for such cybersecurity occurrences. In …