Digital Commons Network^™

Diffseer: Difference-Based Dynamic Weighted Graph Visualization, Xiaolin Wen, Yong Wang, Meixuan Wu, Fengjie Wang, Xuanwu Yue, Qiaomu Shen, Yuxin Ma, Min Zhu

Research Collection School Of Computing and Information Systems

Existing dynamic weighted graph visualization approaches rely on users’ mental comparison to perceive temporal evolution of dynamic weighted graphs, hindering users from effectively analyzing changes across multiple timeslices. We propose DiffSeer, a novel approach for dynamic weighted graph visualization by explicitly visualizing the differences of graph structures (e.g., edge weight differences) between adjacent timeslices. Specifically, we present a novel nested matrix design that overviews the graph structure differences over a time period as well as shows graph structure details in the timeslices of user interest. By collectively considering the overall temporal evolution and structure details in each timeslice, an optimization-based …

Trustworthy And Synergistic Artificial Intelligence For Software Engineering: Vision And Roadmaps, David Lo

Research Collection School Of Computing and Information Systems

For decades, much software engineering research has been dedicated to devising automated solutions aimed at enhancing developer productivity and elevating software quality. The past two decades have witnessed an unparalleled surge in the development of intelligent solutions tailored for software engineering tasks. This momentum established the Artificial Intelligence for Software Engineering (AI4SE) area, which has swiftly become one of the most active and popular areas within the software engiueering field. This Future of Software Engineering (FoSE) paper navigates through several focal points. It commences with a succinct introduction and history of AI4SE. Thereafter, it underscores the core challenges inherent to …

Ncq: Code Reuse Support For Node.Js Developers, Brittany Reid, Marcelo D'Amorim, Markus Wagner, Christoph Treude

Research Collection School Of Computing and Information Systems

Code reuse is an important part of software development. The adoption of code reuse practices is especially common among Node.js developers. The Node.js package manager, NPM, indexes over 1 Million packages and developers often seek out packages to solve programming tasks. Due to the vast number of packages, selecting the right package is difficult and time consuming. With the goal of improving productivity of developers that heavily reuse code through third-party packages, we present Node Code Query (NCQ), a Read-Eval-Print-Loop environment that allows developers to 1) search for NPM packages using natural language queries, 2) search for code snippets related …

What's Behind Tight Deadlines? Business Causes Of Technical Debt, Rodrigo Rebouças De Almeida, Christoph Treude, Uirá Kulesza

Research Collection School Of Computing and Information Systems

What are the business causes behind tight deadlines? What drives the prioritization of features that pushes quality matters to the back burner? We conducted a survey with 71 experienced practitioners and did a thematic analysis of the openended answers to the question: “Could you give examples of how business may contribute to technical debt?” Business-related causes were organized into two categories: pure-business and business/IT gap, and they were related to ‘tight deadlines’ and ‘features over quality’, the most frequently cited management reasons for technical debt. We contribute a cause-effect model which relates the various business causes of tight deadlines and …

She Elicits Requirements And He Tests: Software Engineering Gender Bias In Large Language Models, Christoph Treude, Hideaki Hata

Research Collection School Of Computing and Information Systems

Implicit gender bias in software development is a well-documented issue, such as the association of technical roles with men. To address this bias, it is important to understand it in more detail. This study uses data mining techniques to investigate the extent to which 56 tasks related to software development, such as assigning GitHub issues and testing, are affected by implicit gender bias embedded in large language models. We systematically translated each task from English into a genderless language and back, and investigated the pronouns associated with each task. Based on translating each task 100 times in different permutations, we …

Towards Understanding The Open Source Interest In Gender-Related Github Projects, Rita Garcia, Christoph Treude, Wendy La

Research Collection School Of Computing and Information Systems

The open-source community uses the GitHub platform to exchange and share software applications and services of interest. This paper aims to identify the open-source community’s interest in gender-related projects on GitHub. Our findings create research opportunities and identify resources by the open-source community that promote diversity, equity, and inclusion. We use data mining to identify GitHub projects that focus on gender-related topics. We apply quantitative and qualitative methodologies to examine the projects’ attributes and to classify them within a gender social structure and a gender bias taxonomy. We aim to understand the open-source community’s efforts and interests in gender topics …

Applying Information Theory To Software Evolution, Adriano Torres, Sebastian Baltes, Christoph Treude, Markus Wagner

Research Collection School Of Computing and Information Systems

Although information theory has found success in disciplines, the literature on its applications to software evolution is limit. We are still missing artifacts that leverage the data and tooling available to measure how the information content of a project can be a proxy for its complexity. In this work, we explore two definitions of entropy, one structural and one textual, and apply it to the historical progression of the commit history of 25 open source projects. We produce evidence that they generally are highly correlated. We also observed that they display weak and unstable correlations with other complexity metrics. Our …

Navigating Complexity In Software Engineering: A Prototype For Comparing Gpt-N Solutions, Christoph Treude

Research Collection School Of Computing and Information Systems

Navigating the diverse solution spaces of non-trivial software engineering tasks requires a combination of technical knowledge, problem-solving skills, and creativity. With multiple possible solutions available, each with its own set of trade-offs, it is essential for programmers to evaluate the various options and select the one that best suits the specific requirements and constraints of a project. Whether it is choosing from a range of libraries, weighing the pros and cons of different architecture and design solutions, or finding unique ways to fulfill user requirements, the ability to think creatively is crucial for making informed decisions that will result in …

Lpt: Long-Tailed Prompt Tuning For Image Classification, Bowen Dong, Pan Zhou, Shuicheng Yan, Wangmeng Zuo

Research Collection School Of Computing and Information Systems

For long-tailed classification tasks, most works often pretrain a big model on a large-scale (unlabeled) dataset, and then fine-tune the whole pretrained model for adapting to long-tailed data. Though promising, fine-tuning the whole pretrained model tends to suffer from high cost in computation and deployment of different models for different tasks, as well as weakened generalization capability for overfitting to certain features of long-tailed data. To alleviate these issues, we propose an effective Long-tailed Prompt Tuning (LPT) method for long-tailed classification tasks. LPT introduces several trainable prompts into a frozen pretrained model to adapt it to long-tailed data. For better …

Towards Understanding Why Mask Reconstruction Pretraining Helps In Downstream Tasks, Jiachun Pan, Pan Zhou, Shuicheng Yan

Research Collection School Of Computing and Information Systems

For unsupervised pretraining, mask-reconstruction pretraining (MRP) approaches, e.g. MAE (He et al., 2021) and data2vec (Baevski et al., 2022), randomly mask input patches and then reconstruct the pixels or semantic features of these masked patches via an auto-encoder. Then for a downstream task, supervised fine-tuning the pretrained encoder remarkably surpasses the conventional “supervised learning" (SL) trained from scratch. However, it is still unclear 1) how MRP performs semantic feature learning in the pretraining phase and 2) why it helps in downstream tasks. To solve these problems, we first theoretically show that on an auto-encoder of a two/one-layered convolution encoder/decoder, MRP …

Win: Weight-Decay-Integrated Nesterov Acceleration For Adaptive Gradient Algorithms, Pan Zhou, Xingyu Xie, Shuicheng Yan

Research Collection School Of Computing and Information Systems

Training deep networks on large-scale datasets is computationally challenging. In this work, we explore the problem of “how to accelerate adaptive gradient algorithms in a general manner”, and aim to provide practical efficiency-boosting insights. To this end, we propose an effective and general Weight-decay-Integrated Nesterov acceleration (Win) to accelerate adaptive algorithms. Taking AdamW and Adam as examples, we minimize a dynamical loss per iteration which combines the vanilla training loss and a dynamic regularizer inspired by proximal point method (PPM) to improve the convexity of the problem. To introduce Nesterov-alike-acceleration into AdamW and Adam, we respectively use the first- and …

Two Sides Of The Same Coin: Exploiting The Impact Of Identifiers In Neural Code Comprehension, Shuzheng Gao, Cuiyun Gao, Chaozheng Wang, Jun Sun, David Lo, Yue Yu

Research Collection School Of Computing and Information Systems

Previous studies have demonstrated that neural code comprehension models are vulnerable to identifier naming. By renaming as few as one identifier in the source code, the models would output completely irrelevant results, indicating that identifiers can be misleading for model prediction. However, identifiers are not completely detrimental to code comprehension, since the semantics of identifier names can be related to the program semantics. Well exploiting the two opposite impacts of identifiers is essential for enhancing the robustness and accuracy of neural code comprehension, and still remains under-explored. In this work, we propose to model the impact of identifiers from a …

Psychosis Brain Subtypes Validated In First-Episode Cohorts And Related To Illness Remission: Results From The Phenom Consortium, Dominic B Dwyer, Ganesh B Chand, Aristeidis Sotiras, Et Al.

2020-Current year OA Pubs

Using machine learning, we recently decomposed the neuroanatomical heterogeneity of established schizophrenia to discover two volumetric subgroups-a 'lower brain volume' subgroup (SG1) and an 'higher striatal volume' subgroup (SG2) with otherwise normal brain structure. In this study, we investigated whether the MRI signatures of these subgroups were also already present at the time of the first-episode of psychosis (FEP) and whether they were related to clinical presentation and clinical remission over 1-, 3-, and 5-years. We included 572 FEP and 424 healthy controls (HC) from 4 sites (Sao Paulo, Santander, London, Melbourne) of the PHENOM consortium. Our prior MRI subgrouping …

Approaching Trans Healthcare Competency: The Implementation Of Trans Health Education For Medical Providers In Appalachia, Rebecca Altschuler

Electronic Theses and Dissertations

Barriers to competent and safe healthcare disproportionately impact people who are marginalized because of their race, ethnicity, gender, or socioeconomic status. It is well documented that transgender patients in particular experience barriers to both accessing care and receiving high quality, non-discriminatory care (Hatzenbuehler & Pachankis, 2016; James et al., 2016; Rahman et al., 2019; Safer et al., 2016). This lack of access to culturally competent healthcare services contributes to health disparities that disproportionately impact the trans community. Literature on barriers to competent care for trans patients indicates that providers experience discomfort related to their ability to provide competent care (Safer …

Distinct Effects Of Two Hearing Loss-Associated Mutations In The Sarcomeric Myosin Myh7b, Lindsey A Lee, Samantha K Barrick, Ada E Buvoli, Jonathan Walklate, W Tom Stump, Michael Geeves, Michael J Greenberg, Leslie A Leinwand

2020-Current year OA Pubs

For decades, sarcomeric myosin heavy chain proteins were assumed to be restricted to striated muscle where they function as molecular motors that contract muscle. However, MYH7b, an evolutionarily ancient member of this myosin family, has been detected in mammalian nonmuscle tissues, and mutations in MYH7b are linked to hereditary hearing loss in compound heterozygous patients. These mutations are the first associated with hearing loss rather than a muscle pathology, and because there are no homologous mutations in other myosin isoforms, their functional effects were unknown. We generated recombinant human MYH7b harboring the D515N or R1651Q hearing loss-associated mutation and studied …

Provisional Practice Recommendation For The Management Of Myopathy In Vcp-Associated Multisystem Proteinopathy, Bhaskar Roy, Conrad Chris Weihl, Et Al.

2020-Current year OA Pubs

Valosin-containing protein (VCP)-associated multisystem proteinopathy (MSP) is a rare genetic disorder with abnormalities in the autophagy pathway leading to various combinations of myopathy, bone diseases, and neurodegeneration. Ninety percent of patients with VCP-associated MSP have myopathy, but there is no consensus-based guideline. The goal of this working group was to develop a best practice set of provisional recommendations for VCP myopathy which can be easily implemented across the globe. As an initiative by Cure VCP Disease Inc., a patient advocacy organization, an online survey was initially conducted to identify the practice gaps in VCP myopathy. All prior published literature on …

A Phase 1 First-In-Human Study Of Gs-0189, An Anti-Signal Regulatory Protein Alpha (Sirpα) Monoclonal Antibody, In Patients With Relapsed/Refractory (R/R) Non-Hodgkin Lymphoma (Nhl), Mayur Narkhede, Nancy L Bartlett, Sami Ibrahimi, Leslie Popplewell, Anna Seto, Jamie Bates, Yeonju Lee, Vaishnavi Ganti, Ling Han, Tianling Chen, Manish R Patel

2020-Current year OA Pubs

Signal regulatory protein alpha (SIRPα) is the receptor for cluster of differentiation (CD)47, a potent "don't eat me" signal for macrophages. Disruption of CD47-SIRPα signaling in the presence of prophagocytic signals can lead to enhanced phagocytosis of tumor cells, resulting in a direct antitumor effect; agents targeting this pathway have shown efficacy in non-Hodgkin lymphoma (NHL) and other tumor types. GS-0189 is a novel anti-SIRPα humanized monoclonal antibody. Here we report: (1) clinical safety, preliminary activity, and pharmacokinetics of GS-0189 as monotherapy and in combination with rituximab from a phase 1 clinical trial in patients with relapsed/refractory NHL (NCT04502706, SRP001); …

Genetic Associations Between Modifiable Risk Factors And Alzheimer Disease, Benjamin Grenier-Boley, Itziar De Rojas, Atahualpa Castillo, Kayenat Parveen, Fahri Küçükali, Aude Nicolas, Oliver Peters, Anja Schneider, Martin Dichgans, Dan Rujescu, Norbert Scherbaum, Deckert Jürgen, Steffi Riedel-Heller, Lucrezia Hausner, Laura Molina Porcel, Emrah Düzel, Timo Grimmer, Jens Wiltfang, Stefanie Heilmann-Heimbach, Susanne Moebus, Thomas Tegos, Nikolaos Scarmeas, Jordi Clarimon, Fermin Moreno, Jordi Pérez-Tur, María J Bullido, Pau Pastor, Raquel Sánchez-Valle, Victoria Álvarez, Mercè Boada, Pablo García-González, Raquel Puerta, Pablo Mir, Luis M Real, Gerard Piñol-Ripoll, Jose María García-Alberca, Jose Luís Royo, Eloy Rodriguez-Rodriguez, Hilkka Soininen, Teemu Kuulasmaa, Alexandre De Mendonça, Shima Mehrabian, Jakub Hort, Martin Vyhnalek, Sven Van Der Lee, Caroline Graff, Goran Papenberg, Vilmantas Giedraitis, Anne Boland, Delphine Bacq-Daian, Jean-François Deleuze, Gael Nicolas, Carole Dufouil, Florence Pasquier, Olivier Hanon, Stéphanie Debette, Edna Grünblatt, Julius Popp, Luisa Benussi, Daniela Galimberti, Beatrice Arosio, Patrizia Mecocci, Vincenzo Solfrizzi, Lucilla Parnetti, Alessio Squassina, Lucio Tremolizzo, Barbara Borroni, Benedetta Nacmias, Sandro Sorbi, Paolo Caffarra, Davide Seripa, Innocenzo Rainero, Antonio Daniele, Carlo Masullo, Gianfranco Spalletta, Julie Williams, Philippe Amouyel, Frank Jessen, Patrick Kehoe, Magda Tsolaki, Giacomina Rossi, Pascual Sánchez-Juan, Kristel Sleegers, Martin Ingelsson, Ole A Andreassen, Mikko Hiltunen, Cornelia Van Duijn, Rebecca Sims, Wiesje Van Der Flier, Agustín Ruiz, Alfredo Ramirez, Jean-Charles Lambert, Ruth Frikke-Schmidt

Faculty, Staff and Students Publications

IMPORTANCE: An estimated 40% of dementia is potentially preventable by modifying 12 risk factors throughout the life course. However, robust evidence for most of these risk factors is lacking. Effective interventions should target risk factors in the causal pathway to dementia.

OBJECTIVE: To comprehensively disentangle potentially causal aspects of modifiable risk factors for Alzheimer disease (AD) to inspire new drug targeting and improved prevention.

DESIGN, SETTING, AND PARTICIPANTS: This genetic association study was conducted using 2-sample univariable and multivariable mendelian randomization. Independent genetic variants associated with modifiable risk factors were selected as instrumental variables from genomic consortia. Outcome data for …

Factors Associated With No-Show To Ambulatory Tele-Video Neurology Visits., Aashrai Sai Venkat Gudlavalleti, John O Elliott, Rafah Asadi

Neuroscience Articles

Introduction Telehealth visits (TH) have become an important pillar of healthcare delivery during the COVID pandemic. No-shows (NS) may result in delays in clinical care and in lost revenue. Understanding the factors associated with NS may help providers take measures to decrease the frequency and impact of NS in their clinics. We aim to study the demographic and clinical diagnoses associated with NS to ambulatory telehealth neurology visits. Methods We conducted a retrospective chart review of all telehealth video visits (THV) in our healthcare system from 1/1/2021 to 5/1/2021 (cross-sectional study). All patients at or above 18 years of age …

Dual Credit: The Relationship Between Grade Point Average, Hours Earned, And Semesters To Degree Attainment, Amanda R. Ritchie

Electronic Theses and Dissertations

Despite the reported benefits of dual credit programs, questions remain regarding the long-term influence of dual credit courses on long-term student achievement and time to degree attainment. A lack of consistent policies regarding dual credit results in students taking college courses without knowing what courses they may need for their anticipated major. Dual credit programs are continuing to expand, and if dual credit courses are to contribute to college success, policymakers, educators, high schools, and institutions must understand how the combination of dual credit courses taken impacts student success and academic progress towards degree completion. The purpose of this non-experimental, …

Healthcare Workers’ Perceptions, Practices, And Knowledge Of Trauma-Informed Care In The Hospital Setting, Emily Gayle Tippens

Electronic Theses and Dissertations

Psychological trauma has become a pervasive term throughout the mental health field but has been slow to gain momentum in the healthcare field. Hospitals have always been a place where people with mental health concerns or psychosis seek help, but hospitals have historically not implemented a trauma-informed care (TIC) approach. As the mental health crisis continues to become more detrimental, trauma-informed care skills will become more valuable. This study measured the knowledge, opinions, perceptions healthcare professionals in West Texas have regarding trauma-informed care. This study hypothesized that healthcare workers in West Texas would benefit from TIC training. This study hypothesized …

Impostor Phenomenon, College-Going Knowledge, And Staff Expectations: Ramifications On First Time In College Students Enrollment, Julia A. Vickery

Electronic Theses and Dissertations

A lack of technically trained, skilled, and educated workforce has become a critical issue in Texas. Furthermore, an educated workforce improves communities and individuals with economic, health, and personal benefits. Community colleges not only provide open-access admissions and low-cost tuition but are specifically aligned with educating the technical and industrial skilled workforce. Although a post-high school education has never been more accessible or necessary for obtaining high-earning jobs, post-high school college enrollment is declining, and conventional reform strategies do not appear to be effecting change. Graduating high school students aspire to attend postsecondary training by applying and being accepted but …

Argentine Women’S Narratives Of Leadership, Ileana Andrea Mocciola

Electronic Theses and Dissertations

The present study investigated and examined the narratives of Argentine women leaders while obtaining and exercising leadership positions. This research was based on narrative theory and the feminist standpoint theory. Argentine female participants (N = 10) were subject to interviews that overall lasted 600 minutes and were conducted through the Zoom platform. Fifty-five pages of single-spaced transcripts were analyzed and studied. The results of this study revealed that Argentine women face major challenges when it comes to tokenism, exclusion, mentorship, and stereotypes that prevent and limit them from reaching and succeeding in leadership positions.

Positive Psychology For Mdd And Ptsd: A Systematic Review Of Treatment Benefits And Efficacy, Jackson Taylor

Electronic Theses and Dissertations

Positive psychology was founded by Martin Seligman and Mihaly Csikszentmihalyi in 2000 as a psychological school of thought that focused more on identifying and building up a client’s positive strengths instead of just focusing on their mental health deficits. The question asked in this systematic review is as follows, “Is there a unique benefit to treating MDD or PTSD with positive psychotherapeutic interventions and does it result in lower rates of suicide/relief from severe MDD/PTSD?” Objective: The objective of this literature review and meta-analysis was to examine the evidence and determine if positive psychology-based interventions such as PsyCap, IPPI, and …

Forming And Maintaining Intimate Friendships As A Twentysomething, Molly S. Burke

Electronic Theses and Dissertations

Emerging adulthood is a life stage of great change, and often instability in relationships and attachment (Demir et al., 2015; Lane et al., 2017; Shulman & Connolly, 2013). Intimate friendships can be a moderating factor and assistance in gaining stability and increasing life satisfaction (Demir, 2021; Demir et al., 2015; Sanchez et al., 2020). This study used grounded theory methodology (Creswell & Poth, 2018) to develop a model of the process which Twentysomethings undergo while forming and maintaining intimate, or best, friendships. Through interviews with best friend pairs, this study found three main phases of the best friend process: forming …

Attitudes Towards Mental Health, Spiritual Seeking, And Well-Being, David Mitchell

Electronic Theses and Dissertations

Religion plays a crucial role in many peoples’ lives, shaping the way they interact with the world and react to stressors. The Relational Spirituality Model (Sandage & Shults, 2007) posits that individuals’ relationship with God resembles humans’ relationships with one another. That is, relationships consist of intimacy and closeness as well as independence and time away from each other, otherwise known as dwelling and seeking. Previous literature has analyzed the relationship between spiritual coping and well-being, yet none have analyzed the relationship between spiritual seeking and overall well-being using attitudes towards mental health as a moderator. Participants were 84 undergraduate …

Crossing Over: A Description Of Dual Status Youth In Taylor County, Texas, Kimberly S. Putnam

Electronic Theses and Dissertations

This study explores and describes the experiences of ten dual status youth in Taylor County, Texas by examining the factors of race, sex, child welfare allegation, and juvenile justice offense. A review of the literature suggests that this population has unique challenges in and outside the courtroom, including being at increased risk for disparate outcomes in later adolescence and adulthood. This study compared single-system child welfare and juvenile justice data from Texas DFPS Region 2 and Taylor County to raw data provided on a sample of ten dual status youth identified in Taylor County from 2017–2021. Findings included a disproportionately …

The Impact Of Covid-19 On The Mental Health Of College Students, Jack Marcelain

Electronic Theses and Dissertations

COVID-19 changed the world in the span of a few months. Schools and other businesses had to close and move to an online format to decrease physical interaction and stop the spread of the virus. Many people went without seeing close friends and loved ones due to the quarantine or lost someone close to them due to the virus. Students enrolled in college were sent home abruptly and could not return in person to school for the remainder of the year. Even when they were allowed to return to school, new guidelines and how classroom content was delivered were put …

TíNh ThốNg NhấT Trong Sự Đa DạNg: Hanoi International Fellowship Ethnography, Ariel Marie Bloomer

Electronic Theses and Dissertations

Hanoi International Fellowship (HIF) is a multinational, multiethnic International Church (IC) in Hanoi, Vietnam. This thesis investigates how HIF constitutes unity among such lived diversity in its congregation. Chapter one reviews existing literature and provides the methodology of the study. Chapter two investigates where unity and diversity are present in HIF, focusing specifically on its mission and values, ministries, and leadership. Chapter three provides a theological basis for unity in diversity. Chapter four presents the research findings from this study. Lastly, Chapter five expresses the study’s limitations, summarizes the findings, offers suggestions to HIF and other Christian communities, recommends future …

Goal Setting And Student Retention, Hugh Castillo

Electronic Theses and Dissertations

Student retention has been a problem with which higher education institutions must face. Institutions have employed numerous different programs and services to improve student retention. This study sought to open up a new way to improve student retention by utilizing a goal-setting intervention that focused on creating SMART goals for student areas of weaknesses. This study employed the use of a quasi-experimental interrupted time series to better understand how goal-setting interventions could impact the participant attitudes correlated to retention. It was shown that goal-setting interventions had no significant impact on likelihood of retention but did exhibit improvement in client engagement …