Physical Sciences and Mathematics Commons^™

Optimizing Uncertainty Quantification Of Vision Transformers In Deep Learning On Novel Ai Architectures, Erik Pautsch, John Li, Silvio Rizzi, George K. Thiruvathukal, Maria Pantoja

Computer Science: Faculty Publications and Other Works

Deep Learning (DL) methods have shown substantial efficacy in computer vision (CV) and natural language processing (NLP). Despite their proficiency, the inconsistency in input data distributions can compromise prediction reliability. This study mitigates this issue by introducing uncertainty evaluations in DL models, thereby enhancing dependability through a distribution of predictions. Our focus lies on the Vision Transformer (ViT), a DL model that harmonizes both local and global behavior. We conduct extensive experiments on the ImageNet-1K dataset, a vast resource with over a million images across 1,000 categories. ViTs, while competitive, are vulnerable to adversarial attacks, making uncertainty estimation crucial for …

Unoapi: Balancing Performance, Portability, And Productivity (P3) In Hpc Education, Konstantin Laufer, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

oneAPI is a major initiative by Intel aimed at making it easier to program heterogeneous architectures used in high-performance computing using a unified application programming interface (API). While raising the abstraction level via a unified API represents a promising step for the current generation of students and practitioners to embrace high- performance computing, we argue that a curriculum of well- developed software engineering methods and well-crafted exem- plars will be necessary to ensure interest by this audience and those who teach them. We aim to bridge the gap by developing a curriculum—codenamed UnoAPI—that takes a more holistic approach by looking …

Mathematics And Programming Exercises For Educational Robot Navigation, Ronald I. Greenberg

Computer Science: Faculty Publications and Other Works

This paper points students towards ideas they can use towards developing a convenient library for robot navigation, with examples based on Botball primitives, and points educators towards mathematics and programming exercises they can suggest to students, especially advanced high school students.

A Survey Of Software Metric Use In Research Software Development, Nasir U. Eisty, George K. Thiruvathukal, Jeffrey C. Carver

Computer Science: Faculty Publications and Other Works

Background: Breakthroughs in research increasingly depend on complex software libraries, tools, and applications aimed at supporting specific science, engineering, business, or humanities disciplines. The complexity and criticality of this software motivate the need for ensuring quality and reliability. Software metrics are a key tool for assessing, measuring, and understanding software quality and reliability. Aims: The goal of this work is to better understand how research software developers use traditional software engineering concepts, like metrics, to support and evaluate both the software and the software development process. One key aspect of this goal is to identify how the set of metrics …

Software Engineering For Science, Jeffrey C. Carver, Neil P. Chue Hong, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

Software Engineering for Science provides an in-depth collection of peer-reviewed chapters that describe experiences with applying software engineering practices to the development of scientific software. It provides a better understanding of how software engineering is and should be practiced, and which software engineering practices are effective for scientific software.

The book starts with a detailed overview of the Scientific Software Lifecycle, and a general overview of the scientific software development process. It highlights key issues commonly arising during scientific software development, as well as solutions to these problems.

The second part of the book provides examples of the use of …

A Gene-Based Association Method For Mapping Traits Using Reference Transcriptome Data, Eric R. Gamazon, Heather Wheeler, Kaanan P. Shah, Sahar V. Mozaffari, Keston Aquino-Michaels, Robert J. Carroll, Anne E. Eyler, Joshua C. Denny, Gtex Consortium, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im

Bioinformatics Faculty Publications

Genome-wide association studies (GWAS) have identified thousands of variants robustly associated with complex traits. However, the biological mechanisms underlying these associations are, in general, not well understood. We propose a gene-based association method called PrediXcan that directly tests the molecular mechanisms through which genetic variation affects phenotype. The approach estimates the component of gene expression determined by an individual’s genetic profile and correlates ‘imputed’ gene expression with the phenotype under investigation to identify genes involved in the etiology of the phenotype. Genetically regulated gene expression is estimated using whole-genome tissue-dependent prediction models trained with reference transcriptome data sets. PrediXcan enjoys …

Natural Xml For Data Binding, Processing, And Persistence, George K. Thiruvathukal, Konstantin Läufer

Computer Science: Faculty Publications and Other Works

The article explains what you need to do to incorporate XML directly into your computational science application. The exploration involves the use of a standard parser to automatically build object trees entirely from application-specific classes. This discussion very much focuses on object-oriented programming languages such as Java and Python, but it can work for non-object-oriented languages as well. The ideas in the article provide a glimpse into the Natural XML research project.

Xml In Computational Science, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

In this first article in a series about XML in computational science, I present some background and lightweight examples of XML usage, describe some XML component frameworksalong with their purpose and applicability to computational science, and discuss some technical obstacles to overcome for the language to be taken seriously in computational science.

An Interval Newton Method, E R. Hansen, R I. Greenberg

Computer Science: Faculty Publications and Other Works

We introduce an interval Newton method for bounding solutions of systems of nonlinear equations. It entails three subalgorithms. The first is a Gauss-Seidel-type step. The second is a real (noninterval) Newton iteration. The third solves the linearized equations by elimination. We explain why each subalgorithm is desirable and how they fit together to provide solutions in as little as one-third or one-quarter the time required by Krawczyk's method [7] in our implementations.