Digital Commons Network^™

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 …

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 …

Quantification Of Landside Congestion In Ports: An Analysis Based On Gps Data, Kumushini Thennakoon, Namal Bandaranayake, Senevi Kiridena, Asela K. Kulatunga

Computer Science Faculty Publications

Hinterland transport is a critical segment in maritime cross-border logistics, which links the end-users of global supply chains to the maritime segment. Truck-based hinterland transport is known to cause congestion in and around ports. This study aimed to quantify the congestion caused by trucks at the Port of Colombo, which has not been a subject of a systematic study. To this end, the study makes use of GPS data. In addition to revealing heavy congestion within the port, the study also reveals significant variations in congestion during different times of the day with the duration of journeys peaking from 1200hrs …

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 …

Identifying New Cancer Genes Based On The Integration Of Annotated Gene Sets Via Hypergraph Neural Networks, Chao Deng, Hong-Dong Li, Li-Shen Zhang, Yiwei Liu, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation

Identifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations among multiple genes, and cancer genes have been shown to cluster in hallmark signaling pathways and biological processes. The knowledge of annotated gene sets is critical for discovering cancer genes but remains to be fully exploited.

Results

Here, we present the DIsease-Specific Hypergraph neural network (DISHyper), a hypergraph-based computational method that integrates the knowledge from multiple types of annotated gene sets to predict cancer genes. First, our benchmark results demonstrate that DISHyper outperforms the existing state-of-the-art methods and highlight the advantages of …

Can Large Language Models Discern Evidence For Scientific Hypotheses? Case Studies In The Social Sciences, Sai Koneru, Jian Wu, Sarah Rajtmajer

Computer Science Faculty Publications

Hypothesis formulation and testing are central to empirical research. A strong hypothesis is a best guess based on existing evidence and informed by a comprehensive view of relevant literature. However, with exponential increase in the number of scientific articles published annually, manual aggregation and synthesis of evidence related to a given hypothesis is a challenge. Our work explores the ability of current large language models (LLMs) to discern evidence in support or refute of specific hypotheses based on the text of scientific abstracts. We share a novel dataset for the task of scientific hypothesis evidencing using community-driven annotations of studies …

Artificial Intelligence For The Electron Ion Collider (Ai4eic), C. Allaire, R. Ammendola, E.-C. Aschenauer, M. Balandat, M. Battaglieri, J. Bernauer, M. Bondì, N. Branson, T. Britton, A. Butter, I. Chahrour, P. Chatagnon, E. Cisbani, E. W. Cline, S. Dash, C. Dean, W. Deconinck, A. Deshpande, M. Diefenthaler, R. Ent, C. Fanelli, M. Finger, M. Finger Jr., E. Fol, S. Furletov, Y. Gao, J. Giroux, N. C. Gunawardhana Waduge, O. Hassan, P. L. Hegde, R. J. Hernandez-Pinto, A. Hiller Blin, T. Horn, J. Huang, A. Jalotra, D. Jayakodige, B. Joo, M. Junaid, N. Kalantarians, P. Karande, B. Kriesten, R. Kunnawalkam Elayavalli, Y. Li, M. Lin, F. Liu, S. Liuti, G. Matousek, M. Mceneaney, D. Mcspadden, T. Menzo, T. Miceli, V. Mikuni, R. Montgomery, B. Nachman, R. R. Nair, J. Niestroy, S. A. Ochoa Oregon, J. Oleniacz, J. D. Osborn, C. Paudel, C. Pecar, C. Peng, G. N. Perdue, W. Phelps, M. L. Purschke, H. Rajendran, K. Rajput, Y. Ren, D. F. Renteria-Estrada, D. Richford, B. J. Roy, D. Roy, A. Saini, N. Sato, T. Satogata, G. Sborlini, M. Schram, D. Shih, J. Singh, R. Singh, A. Siodmok, J. Stevens, P. Stone, L. Suarez, K. Suresh, A. -N. Tawfik, F. Torales Acosta, N. Tran, R. Trotta, F. J. Twagirayezu, R. Tyson, S. Volkova, A. Vossen, E. Walter, D. Whiteson, M. Williams, S. Wu, N. Zachariou, P. Zurita

Computer Science Faculty Publications

The Electron-Ion Collider (EIC), a state-of-the-art facility for studying the strong force, is expected to begin commissioning its first experiments in 2028. This is an opportune time for artificial intelligence (AI) to be included from the start at this facility and in all phases that lead up to the experiments. The second annual workshop organized by the AI4EIC working group, which recently took place, centered on exploring all current and prospective application areas of AI for the EIC. This workshop is not only beneficial for the EIC, but also provides valuable insights for the newly established ePIC collaboration at EIC. …

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, …

Short: Can Citations Tell Us About A Paper's Reproducibility? A Case Study Of Machine Learning Papers, Rochana R. Obadage, Sarah M. Rajtmajer, Jian Wu

Computer Science Faculty Publications

The iterative character of work in machine learning (ML) and artificial intelligence (AI) and reliance on comparisons against benchmark datasets emphasize the importance of reproducibility in that literature. Yet, resource constraints and inadequate documentation can make running replications particularly challenging. Our work explores the potential of using downstream citation contexts as a signal of reproducibility. We introduce a sentiment analysis framework applied to citation contexts from papers involved in Machine Learning Reproducibility Challenges in order to interpret the positive or negative outcomes of reproduction attempts. Our contributions include training classifiers for reproducibility-related contexts and sentiment analysis, and exploring correlations between …

Archiving Digital Marketing: Examining Preservation Of Dynamic Content On The Web Through The Lens Of Online Advertisements, Christopher Rauch, Alex H. Poole, Travis Reid, Michele C. Weigle, Michael L. Nelson, Faryaneh Poursardar, Mat Kelly

Computer Science Faculty Publications

The transition to digital marketing has revolutionized advertising, reflecting and shaping societal norms and trends. The “Saving Ads” project addresses the challenges of preserving these ephemeral digital artifacts, essential for understanding the evolution of advertising and its socio-cultural impact. The initiative focuses on technical solutions for archiving dynamic online ads and enhancing access to these critical resources for future scholarship. By examining the preservation of online advertisements and suggesting improved approaches for archiving dynamic online content, this project contributes to the documentation of digital history.

Forecasting Crude Oil Price Using Multiple Factors, Hind Aldabagh, Xianrong Zheng, Mohammad Najand, Ravi Mukkamala

Computer Science Faculty Publications

In this paper, we predict crude oil price using various factors that may influence its price. The factors considered are physical market, financial, and trading market factors, including seven key factors and the dollar index. Firstly, we select the main factors that may greatly influence the prices. Then, we develop a hybrid model based on a convolutional neural network (CNN) and long short-term memory (LSTM) network to predict the prices. Lastly, we compare the CNN–LSTM model with other models, namely gradient boosting (GB), decision trees (DTs), random forests (RFs), neural networks (NNs), CNN, LSTM, and bidirectional LSTM (Bi–LSTM). The empirical …

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 …

Enhanced Skin Cancer Diagnosis Through Grid Search Algorithm-Optimized Deep Learning Models For Skin Lesion Analysis, Rudresh Pillai, Neha Sharma, Sheifali Gupta, Deepali Gupta, Sapna Juneja, Saurav Malik, Hong Qin, Mohammed S. Alqahtani, Amel Ksibi

Computer Science Faculty Publications

Skin cancer is a widespread and perilous disease that necessitates prompt and precise detection for successful treatment. This research introduces a thorough method for identifying skin lesions by utilizing sophisticated deep learning (DL) techniques. The study utilizes three convolutional neural networks (CNNs)-CNN1, CNN2, and CNN3-each assigned to a distinct categorization job. Task 1 involves binary classification to determine whether skin lesions are present or absent. Task 2 involves distinguishing between benign and malignant lesions. Task 3 involves multiclass classification of skin lesion images to identify the precise type of skin lesion from a set of seven categories. The most optimal …

The Combined Focal Loss And Dice Loss Function Improves The Segmentation Of Beta-Sheets In Medium-Resolution Cryo-Electron-Microscopy Density Maps, Yongcheng Mu, Thu Nguyen, Bryan Hawickhorst, Willy Wriggers, Jiangwen Sun, Jing He

Computer Science Faculty Publications

Although multiple neural networks have been proposed for detecting secondary structures from medium-resolution (5–10 Å) cryo-electron microscopy (cryo-EM) maps, the loss functions used in the existing deep learning networks are primarily based on cross-entropy loss, which is known to be sensitive to class imbalances. To monitor and tune the performance of various loss functions for the secondary structure detection problem, we investigated five loss functions: cross-entropy, Focal loss, Dice loss, and two combined loss functions. Using a U-Net architecture in our DeepSSETracer method and a dataset composed of 1,355 box-cropped atomic-structure/density-map pairs, we found that a newly designed loss function …

Evaluating Social Media Reach Via Mainstream Media Discourse, Himarsha R. Jayanetti

Computer Science Faculty Publications

This study examines the intersection between social media and mainstream television (TV) news with an aim to understand how social media content amplifies its impact through TV broadcasts. While many studies emphasize social media as a primary platform for information dissemination, they often underestimate its total influence by focusing solely on interactions within the platform. This research examines instances where social media posts gain prominence on TV broadcasts, reaching new audiences and prompting public discourse. By using TV news closed captions, on-screen text recognition, and social media logo detection, we analyze how social media is referenced in TV news. Our …

Defining 'Victim' Through Harm: Crime Victim Status In The Crime Victims' Rights Act And Other Victims' Rights Enactments, Paul Cassell, Michael Ray Morris

Utah Law Faculty Scholarship

Who qualifies as a “victim” is the foundational question for the Crime Victims’ Rights Act (“CVRA” or “Act”) and other crime victims’ rights laws. This article provides the first comprehensive exploration of this “victim” definition question. It traces how the CVRA (and many states) define “victim” as broadly covering anyone who has been harmed as the result of a crime. This article begins by reviewing how the definition of “victim” has evolved in the criminal justice system since the Nation’s founding. In the last several decades, as crime victims’ rights protections have proliferated, it has become necessary to define “victim” …

California, An Island?, Lincoln L. Davies, Stephanie Lenhart

Utah Law Faculty Scholarship

A monumental change quietly is unfolding in the American West. For decades, the region has lagged the rest of the nation in coordinating electricity operations. Multiple efforts to change this stalled or never got off the ground. Now, everything is different. In the face of climate uncertainty and deepening concern that the region is unprepared for its energy future, stakeholders—government, industry, interest groups—are posturing to create formal electricity markets that will transform the region’s infrastructure, resilience, and economy for the remainder of this century.

Two paths are on the table. In one, much if not all the West will join …

Abortion And The Extremism Of Bright Line Rules, Teneille R. Brown

Utah Law Faculty Scholarship

Rather than eliding the workability or necessity of bright-line rules in certain domains, this Essay is a rallying cry for epistemic humility regarding what biological criteria can and cannot say. Policymakers sometimes lean on the biosciences to offer “objective” solutions to thorny
moral and legal issues. But descriptive biological data cannot answer normative questions on their own. Cloaking the theoretical, normative scaffolding in biological criteria is a disingenuous but common phenomenon I refer to as the “bio-legal mismatch.”

In this Essay, I discuss various abortion-restrictive statutes and cases to elucidate the problems with the bio-legal mismatch. Specifically, I explore the …

A Global Crypto Code Of Conduct: Crafting An Internationally Centralized Regulatory Body For A Decentralized Asset, Mary Kavaloski

Vanderbilt Journal of Transnational Law

The advent of Bitcoin in 2009 presented a previously unfathomable possibility for the future of currency and monetary transactions. Now, cryptocurrency is ubiquitous; it is increasingly seizing media headlines, novel swathes of investors, institutional bank involvement, and most importantly of all, the attention of government regulators. Yet governments around the globe have failed to adequately keep up with the pace of cryptocurrency's evolution, particularly because of their lack of expertise in this unprecedented area. This Note discusses how cryptocurrency's truly global footprint warrants a partnership between national regulators and industry actors at the international level. Specifically, by exploring the approaches …

Addressing Unlawful Cyber Operations In Armed Conflict Through Human Rights Bodies Instead Of The International Criminal Court, Zachary R. Orr

Vanderbilt Journal of Transnational Law

Although the ICC-or other similarly-situated international criminal tribunals-could soon see the first cyber war crime prosecution, two glaring issues persist. First, the universe of conduct that could give rise to such a prosecution is limited. Second, heavy reliance on the war crimes framework fails to provide a forum for redress of many harms caused by other unlawful cyber operations in armed conflict. The fragmented nature of international law and its enforcement mechanisms requires solutions that harness the full range of the integrated architecture of the international system. Cyber operations might soon feature at the ICC, but only a fraction of …

Temporary Protection For Ukrainians In The European Union: Why Now And When Again?, Maryellen Fullerton

Vanderbilt Journal of Transnational Law

In 2022, the Russian invasion of Ukraine produced an unprecedented wave of temporary immigration protections throughout the European Union (EU). Within the first few months of the war in Ukraine, over 4 million displaced individuals had registered for temporary protection. EU States distant from Ukraine sheltered hundreds of thousands of displaced families, while Poland and other EU States that border Ukraine sheltered more than 2 million. This groundswell response marked a striking departure from just seven years earlier, when the EU Commission and EU Council failed to use readily available laws to provide a temporary protection program for Syrians displaced …

Justifying Aggression: Russia's 2020 Constitutional Amendments And The Invasion Of Ukraine, Robert C. Blitt

Vanderbilt Journal of Transnational Law

Beyond the alluring promise of an enhanced social safety net for Russian citizens, President Vladimir Putin's constitutional amendments of 2020 betrayed a distinct preoccupation with fortifying Russia's international standing and crafting a new national identity. By Putin's own account, these amendments were necessary to steel the country against the malevolent action of international conspirators committed to Russia's downfall. As this Article posits, these specific constitutional changes systematically entrenched an exceptionalist vision of Russian sovereignty and a civilizational identity that left the country constitutionally untethered from international norms and institutions, saturated in religious fervor and visions of imperial glory, and poised …

Book Review: From Thought To Action: Developing A Social Justice Orientation, Joy L. Daggs

Iowa Journal of Communication

In the second edition of From Thought to Action: Developing a Social Justice Orientation, Sanford helps to provide a framework for students’ first exposure to allyship and activism. In the preface of the book, Sanford (2024) articulates the three major purposes of the book, which include helping new allies, “a) focus on common humanity, b) feel less isolated on their social justice journey, c) figure out how to move from thought to action, either individually or collectively.” (p. xiv) The book could be used to supplement a course on Intercultural Communication, encouraging students to take their knowledge to collaborate with …

Synthesis And Characterization Of Thieno[3,4-B]Pyrazine-Based Near-Infrared Material, Spencer Gilman

Chemistry and Biochemistry

Since their first report in the 1800s, conjugated polymers have gained significant attention for their ability to exhibit the optical and electronic properties of inorganic semiconductors and the physical traits of organic plastics. This has led to the development of organic electronics with notable commercial applications, such as organic photovoltaics and organic light-emitting diodes. The tunability of these materials has also allowed for the production of materials that absorb and emit near-infrared (NIR) light, making them useful for NIR photodetection and bioimaging. NIR photodetection is important for several applications, including optical communication, artificial vision, and health monitoring. Commercially available NIR …

Common Data Set 2023-2024, University Of Minnesota, Morris Office Of Institutional Research

Institutional Effectiveness and Research Reports

No abstract provided.

Organizational Identity Management Policies, Alexander Rieger, Tamara Roth, Johannes Sedlmeir, Gilbert Fridgen, Amber Young

Information Systems Faculty Publications and Presentations

Effective identity management is essential for secure organizational processes, but organizations often do not approach it strategically. To break this trajectory, organizational policymakers need to define a clear and sustainable identity management strategy. This paper presents an overview and guidelines to help shape such strategy. It analyzes the key characteristics and trade-offs of today’s identity management models. Moreover, it offers practical recommendations for organizational policymakers when choosing among these models.

Immigration Detention Abolition And The Violence Of Digital Cages, Sarah R. Sherman-Stokes

Faculty Scholarship

The United States has a long history of devastating immigration enforcement and surveillance. Today, in addition to more than 34,000 people held in immigration detention, Immigration and Customs Enforcement (“ICE”) surveils an astounding 296,000 people under its “Alternatives to Detention” program. The number of people subjected to this surveillance has grown dramatically in the last two decades, from just 1,339 in 2005. ICE’s rapidly expanding Alternatives to Detention program is marked by “digital cages,” consisting of GPS-outfitted ankle shackles and invasive phone and location tracking. Government officials and some immigrant advocates have categorized these digital cages as a humane “reform”; …

Revisioning Algorithms As A Black Feminist Project, Ngozi Okidegbe

Faculty Scholarship

We live in an age of predictive algorithms.¹ Jurisdictions across the country are utilizing algorithms to make or influence life-altering decisions in a host of governmental decision-making processes—criminal justice, education, and social assistance to name a few.² One justification given for this algorithmic turn concerns redressing historical and current inequalities within governmental decision-making.³ The hope is that the predictions produced by these predictive systems can correct this problem by providing decision-makers with the information needed to make fairer, more accurate, and consistent decisions.⁴ For instance, jurisdictions claim that their turn to risk assessment algorithms in bail, …

Loper Bright And The Future Of Chevron Deference, Jack M. Beermann

Faculty Scholarship

The question presented in Loper Bright Industries v. Raimondo¹ is “[w]hether the Court should overrule Chevron or at least clarify that statutory silence concerning controversial powers expressly but narrowly granted elsewhere in the statute does not constitute an ambiguity requiring deference to the agency.” The Court denied certiorari on another question focused on the merits of the case,² indicating that at least four of the Justices are anxious to revisit or at least clarify Chevron. It’s about time, although it’s far from certain that the Court will actually follow through with the promise the certiorari grant indicates.^{3 …}

Constitutional Liberalism Through Thick And Thin: Reflections On Frank Michelman’S Constitutional Essentials, James E. Fleming, Linda C. Mcclain

Faculty Scholarship

In his new book, Constitutional Essentials, Frank Michelman provides a splendid elaboration and defense of “the constitutional theory of political liberalism” implicit in John Rawls’s classic work, Political Liberalism. In this essay, we make some observations about what a difference 30 years makes, comparing the political and constitutional climate in which Rawls wrote and published Political Liberalism in 1993 with the climate in which Frank wrote and published this exegesis of it. We focus on (1) changes in our circumstances of pluralism, including the accentuation of polarization and unreasonable views, and (2) the simultaneous breakdown of trust in the Supreme …