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 …

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

Computer Science Faculty Publications

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

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

Computer Science Faculty Publications

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

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

Computer Science Faculty Publications

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

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

Computer Science Faculty Publications

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

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 …

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

Computer Science Faculty Publications

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

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

Computer Science Faculty Publications

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

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

Computer Science Faculty Publications

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

Vulnerable, Recalcitrant And Resilient: A Foucauldian Discourse Analysis Of Risk And Older People Within The Context Of Covid-19 News Media, Marjorie Skoss, Rachel Batten, Patricia Cain, Mandy Stanley

Research outputs 2022 to 2026

Risk is an innate and integral part of everyday life and is present in simple, everyday occupations and complex actions. Age-related stereotypes can mean older people have little opportunity to engage in activities that present some degree of risk. The present study explores the discourse around risk and older people in the context of the COVID-19 pandemic. We investigated news media as a reflection of the dominant public discourse around older people's behaviour to identify how risk is represented in relation to occupational engagement. Texts relating to older people and COVID-19 were sourced from the West Australian newspaper for a …

Ecu-Mss-2 Dataset, A New Multi-Species Seagrass, Md K. Noman, Syed M. S. Islam, Seyed M. Jalali, Jumana Abu-Khalaf, Paul Lavery

Research Datasets

The "ECU-MSS-2' dataset contains four different habitats, 'Amphibolis' spp (hereafter 'Amphibolis"), 'Halophila' spp (hereafter 'Halophila'), 'Posidonia' spp (hereafter 'Posidonia') and 'Background'. We compiled this image dataset from different sources. The 'Halophila' images were collected by the Centre for Marine Ecosystems Research, Edith Cowan University, Western Australia.

The 'Amphibolis' 'Background' and 'Posidonia' images were collected by the Department of Biodiversity, Conservation and Attractions (DBCA), Australia. The 'Amphibolis' class includes the seagrass species Amphibolis griffithii and Amphibolis Antarctica. The 'Halophila' class includes Halophila ovalis, while the 'Posidonia' class includes Posidonia sinuosa, Posidonia coriacea, and Posidonia Australis. The 'Background' class includes coral, sand, …

A Comprehensive Investigation Of Shipping Business Performance And Corporate Governance Towards Maritime Sustainable Development, Evangelos Darousos

World Maritime University Ph.D. Dissertations

Shipping has always been associated with worldwide socioeconomic advancement, and it continues to be responsible for transporting 80% of all international trade. The shipping industry is undoubtedly one of the most globalized, and as such, it is governed by a comprehensive and dynamic regulatory framework that prioritizes the preservation of the maritime and coastal environment, the safety and security of the crew members and the vessels as primary company assets, and the proper conduct of all shipping operations. Nevertheless, there are frequently significant barriers to the adoption of practices allowing for the sustainable development of the shipping industry, a continuous …

Investigating Inland Waterway Transport Through A Sustainable Development Perspective: A Case Study Of Magdalena River (Colombia), Natalia Calderón-Rivera

World Maritime University Ph.D. Dissertations

The development of transport systems significantly influences economies, growth, and welfare of populations. However, these systems can have negative consequences, such as water and air pollution, traffic congestion, noise, and biodiversity loss. To address these challenges, it is essential to implement strategies that mitigate negative effects while improving the environmental, social, and economic conditions of the population. In this regard, inland water transport (IWT) is globally recognized as a more sustainable transport alternative due to its high cargo load capacities and comparatively lower environmental and social impacts. In Colombia, the Magdalena River – the country’s most important river basin – …

Outil D’Autodiagnostic (Audit) Pour Le Contenu D’Un Programme De Contrôle Des Énergies (Cadenassage Et Autres Méthodes), Damien Burlet-Vienney, Laurent Giraud, René Dufresne

Guides

No abstract provided.

Hand-Held Pneumatic Tools: Protect Your Ears And Your Hands, Isabelle Maguire, Pierre Marcotte

Guides

No abstract provided.

Chariot Élévateur Et Surfaceuse À Glace Au Propane : Un Entretien Préventif Pour Une Performance Sécuritaire, Isabelle Maguire, Capucine Ouellet

Guides

No abstract provided.

Les Coups De Chaleur, Comment Les Prévenir?, Marie-Hélène Poirier, Isabelle Maguire, Capucine Ouellet, Alireza Saidi

Guides

No abstract provided.

Profit, Mission, And Protest At Work, Marion Crain

Scholarship@WashULaw

The classic understanding of capitalism maintains that the social responsibility of business is to increase its profits. But in the last decade, many firms have announced commitments to various social justice issues, folding them into corporate mission statements, codes of corporate social responsibility, and branding. Firms engaging in so-called “woke capitalism” signal their virtuous support for progressive social causes favored by both their consumer base and their idealistic young workers. This has become particularly important in a tight labor market: by targeting workers’ values, savvy firms increase recruiting yields, enhance productivity, and reduce training costs as retention rates rise, while …

Fragmented Futures: Publication Choices And The Evolution Of International Legal Scholarship, Melissa (M.J.) Durkee

Scholarship@WashULaw

How we produce and disseminate international legal scholarship affects can affect how international law itself develops. Fragmentation and siloing of international legal scholarship can diminish the coherence of international law as a shared social practice across national borders. It can also diminish the perceived salience of international law within the United States, contributing to U.S. propensities toward exceptionalism and isolationism. Non-traditional publication formats have equalizing and connecting functions, but there is still room for growth when it comes to aggregating scholarship across regional, linguistic, and disciplinary divides. Finding ways to do that will help international lawyers better accomplish the field’s …

Less Discriminatory Algorithms, Pauline Kim, Emily Black, John Logan Koepke, Solon Barocas, Mingwei Hsu

Scholarship@WashULaw

Entities that use algorithmic systems in traditional civil rights domains like housing, employment, and credit should have a duty to search for and implement less discriminatory algorithms (LDAs). Why? Work in computer science has established that, contrary to conventional wisdom, for a given prediction problem there are almost always multiple possible models with equivalent performance—a phenomenon termed model multiplicity. Critically for our purposes, different models of equivalent performance can produce different predictions for the same individual, and, in aggregate, exhibit different levels of impacts across demographic groups. As a result, when an algorithmic system displays a disparate impact, model multiplicity …

Lawyering In The Age Of Artificial Intelligence, Jonathan H. Choi, Monahan Amy, Daniel Schwarcz

Scholarship@WashULaw

We conducted the first randomized controlled trial to study the effect of AI assistance on human legal analysis. We randomly assigned law school students to complete realistic legal tasks either with or without the assistance of GPT-4, tracking how long the students took on each task and blind-grading the results. We found that access to GPT-4 only slightly and inconsistently improved the quality of participants’ legal analysis but induced large and consistent increases in speed. AI assistance improved the quality of output unevenly—where it was useful at all, the lowest-skilled participants saw the largest improvements. On the other hand, AI …

Social Relationships, Amyloid Burden, And Dementia: The Aric-Pet Study, Renée C Groechel, Albert C Liu, Chelsea Liu, David S Knopman, Silvia Koton, Anna M Kucharska-Newton, Pamela L Lutsey, Thomas H Mosley, Priya Palta, A Richey Sharrett, Keenan A Walker, Dean F Wong, Rebecca F Gottesman

2020-Current year OA Pubs

INTRODUCTION: This study aimed to assess whether social relationships in mid-life reduce the risk of dementia related to amyloid burden.

METHODS: Participants in the Atherosclerosis Risk in Communities (ARIC) study were assessed for social support and isolation (visit 2; 1990-1992). A composite measure, "social relationships," was generated. Brain amyloid was evaluated with florbetapir positron emission tomography (PET); (visit 5; 2012-2014). Incident dementia cases were identified following visit 5 through 2019 using ongoing surveillance. Relative contributions of mid-life social relationships and elevated brain amyloid to incident dementia were evaluated with Cox regression models.

RESULTS: Among 310 participants without dementia, strong mid-life …

Hippocampal Volumes In Uk Biobank Are Associated With Apoe Only In Older Adults, Ariya Chaloemtoem, Vera Thornton, Yoonhoo Chang, Andrey P Anokhin, Michaël E Belloy, Janine Bijsterbosch, Brian A Gordon, Sarah M Hartz, Laura J Bierut

2020-Current year OA Pubs

INTRODUCTION: The hippocampus atrophies with age and is implicated in neurodegenerative disorders including Alzheimer's disease (AD). We examined the interplay between age and apolipoprotein E (

METHODS: Using neuroimaging data from 37,463 UK Biobank participants, we applied linear regression to quantify the association of age and

RESULTS: Total hippocampal volume declined with age, with significant differences by

DISCUSSION: The association of

HIGHLIGHTS: Apolipoprotein E (

Law Enforcement Use Of Genetic Genealogy Databases In Criminal Investigations: Nomenclature, Definition And Scope, Oliver M Tuazon, Ray A Wickenheiser, Ricky Ansell, Christi J Guerrini, Gerrit-Jan Zwenne, Bart Custers

Center for Medical Ethics and Health Policy Staff Publications

Although law enforcement use of commercial genetic genealogy databases has gained prominence since the arrest of the Golden State Killer in 2018, and it has been used in hundreds of cases in the United States and more recently in Europe and Australia, it does not have a standard nomenclature and scope. We analyzed the more common terms currently being used and propose a common nomenclature: investigative forensic genetic genealogy (iFGG). We define iFGG as the use by law enforcement of genetic genealogy combined with traditional genealogy to generate suspect investigational leads from forensic samples in criminal investigations. We describe iFGG …

Multimodal Prediction Of Obsessive-Compulsive Disorder And Comorbid Depression Severity And Energy Delivered By Deep Brain Electrodes, Saurabh Hinduja, Ali Darzi, Itir Onal Ertugrul, Nicole Provenza, Ron Gadot, Eric A Storch, Sameer A Sheth, Wayne K Goodman, Jeffrey F Cohn

Faculty, Staff and Students Publications

To develop reliable, valid, and efficient measures of obsessive-compulsive disorder (OCD) severity, comorbid depression severity, and total electrical energy delivered (TEED) by deep brain stimulation (DBS), we trained and compared random forests regression models in a clinical trial of participants receiving DBS for refractory OCD. Six participants were recorded during open-ended interviews at pre- and post-surgery baselines and then at 3-month intervals following DBS activation. Ground-truth severity was assessed by clinical interview and self-report. Visual and auditory modalities included facial action units, head and facial landmarks, speech behavior and content, and voice acoustics. Mixed-effects random forest regression with Shapley feature …

Prevalence Of Congenital Anomalies According To Maternal Race And Ethnicity, Texas, 1999–2018, Jeremy M Schraw, Elwin Jaime, Charles J Shumate, Mark A Canfield, Philip J Lupo

Faculty, Staff and Students Publications

BACKGROUND: Few studies of congenital anomalies provide prevalence estimates stratified by maternal race/ethnicity. We sought to determine whether the prevalence of a broad spectrum of anomalies varies among offspring of women from different race/ethnic groups.

METHODS: We obtained information on cases with anomalies from the population-based Texas Birth Defects Registry, and denominator data on livebirths among Texas residents during 1999-2018 from the Texas Center for Health Statistics. We estimated the prevalence ratio (PR) and 95% confidence interval (CI) of N = 145 anomalies among offspring of Hispanic and non-Hispanic Black relative to non-Hispanic White women using Poisson regression, adjusting for …

Combined Bioinformatic And Splicing Analysis Of Likely Benign Intronic And Synonymous Variants Reveals Evidence For Pathogenicity, Owen R Hirschi, Stephanie A Felker, Surya P Rednam, Kelly L Vallance, D Williams Parsons, Angshumoy Roy, Gregory M Cooper, Sharon E Plon

Faculty, Staff and Students Publications

PURPOSE: Clinical variant analysis pipelines likely have poor sensitivity to the effects on splicing from variants beyond 10 to 20 bases of exon-intron boundaries. Here, we demonstrate the value of SpliceAI to inform curation of rare variants previously classified as benign/likely benign (B/LB) under current guidelines.

METHODS: Exome sequencing data from 576 pediatric cancer patients enrolled in the Texas KidsCanSeq study were filtered for intronic or synonymous variants absent from population databases, predicted to alter splicing via SpliceAI (>0.20), and scored >10 by combined annotation-dependent depletion. Rare synonymous or intronic B/LB variants in 61 genes submitted to ClinVar were …

A Mini Chalk Talk Workshop For Fourth-Year Medical Students: Facilitating The Transition From Student To Resident Educator, Trevor Jamison, Zaven Sargsyan, Uma Ayyala, Stephanie Sherman, Holland Kaplan

Faculty, Staff and Students Publications

INTRODUCTION: There is increasing recognition that incoming interns benefit from formal training in teaching skills during UME. Many medical schools have capstone courses well suited for teacher-training content. Mini chalk talks (MCTs) are a common clinical teaching modality requiring a variety of teaching skills. We developed a session for our institution's capstone course in which students prepared and delivered MCTs.

METHODS: The voluntary flipped classroom session was offered virtually in 2021 and in person in 2022. Before the session, students reviewed materials on creating effective MCTs and developed and practiced their own MCT. During the 90-minute session, students presented their …

The Determinants Of Nonprofit Hospital Ceo Compensation, Derek Jenkins, Marah N Short, Vivian Ho

Center for Medical Ethics and Health Policy Staff Publications

Hospital CEO salaries have grown quickly over the past two decades. We investigate correlates of rising nonprofit hospital CEO pay between 2012 and 2019 by merging compensation data from Candid's IRS 990 forms with hospital data from the National Academy for State Health Policy Hospital Cost Tool. Almost half of the measured increase in CEO compensation (44.5%) accrued to a "base case" CEO, who was leading a non-teaching hospital system or independent hospital with fewer than 100 beds that earned 0 profits and provided no charity care. Another 28.5% of the measured salary increase resulted from changes in the generosity …