Digital Commons Network^™

Differences In Patient Outcomes Of Prevalence, Interval, And Screen-Detected Lung Cancers In The Ct Arm Of The National Lung Screening Trial, Matthew B. Schabath, Pierre P. Massion, Zachary J. Thompson, Steven A. Eschrich, Yoganand Balagurunathan, Dmitry Goldof, Denise R. Aberle, Robert J. Gillies

Computer Science and Engineering Faculty Publications

Lung cancer screening identifies cancers with heterogeneous behaviors. Some lung cancers will be identified among patients who had prior negative CT screens and upon follow-up scans develop a de novo nodule that was determined to be cancerous. Other lung cancers will be identified among patients who had one or more prior stable positive scans that were not determined to be lung cancer (indeterminate pulmonary nodules), but in follow-up scans was diagnosed with an incidence lung cancer. Using data from the CT arm of the National Lung Screening Trial, this analysis investigated differences in patient characteristics and survival endpoints between prevalence-, …

Openthinning: Fast 3d Thinning Based On Local Neighborhood Lookups, Tobias Post, Christina Gillmann, Thomas Wischgoll, Hans Hagen

Computer Science and Engineering Faculty Publications

3D Thinning is an often required image processing task in order to perform shape analysis in various applications. For researchers in these domains, a fast, flexible and easy to access implementation is required. Open source solutions, as the Insights Segmentation and Registration Toolkit (ITK), are often used for image processing and visualization tasks, due to their wide range of provided algorithms. Unfortunately, ITK’s thinning implementation is computational expensive and allows solely one specific thinning approach. Therefore, this work presents OpenThinning, an open source thinning solution for 3D image data. The implemented algorithm evaluates a moving local neighborhood to find deletable …

Cardiovascular Dieseases: From Data Generation To Analysis, Thomas Wischgoll

Computer Science and Engineering Faculty Publications

Cardiovascular diseases remain the leading cause of death in Western societies. This presentation will provide insight into the use of expert knowledge and models to derive diagnostic tools that have the potential to aid in the diagnosis of diffuse cardiovascular diseases that tend to be more difficult to detect in CT angiograms. In order to develop these methods more basic research is needed to prove the validity of the approach, including validation of accuracy as well as approach itself. For that, specimens of porcine hearts were prepared and then analyzed followed by a statistical comparison between computed and optical measurements. …

Super-Resolution Reconstruction Of Mri, Sara Gharabaghi, Thomas Wischgoll, Nasser H. Kashou

Computer Science and Engineering Faculty Publications

Magnetic Resonance Imaging (MRI) is a non-invasive technique that is used in clinical applications such as diseases diagnosis and monitoring and treatment progress. Although, MRI scans typically have high in-plane resolution but they have very poor resolution in slice direction. Furthermore, in some applications with limited acquisition time or where the subject is moving, increased slice thickness or inter-slice space (slice gaps) may be used which results in poor resolution MRI.

In this research, we propose a novel Super Resolution (SR) technique for reconstructing High-Resolution (HR) MRI using a sequence of orthogonal Low-Resolution (LR) MRI scans.

The resolution of this …

Hpc Enabled Data Analytics For High-Throughput High-Content Cellular Analysis, Ross A. Smith, Rhonda J. Vickery, Jack Harris, Sara Gharabaghi, Thomas Wischgoll, David Short, Robert Trevino, Steven A. Kawamoto, Thomas J. Lamkin, Kevin Schoen, Eric E. Bardes, Scott C. Tabar, Bruce J. Aronow

Computer Science and Engineering Faculty Publications

Biologists doing high-throughput high-content cellular analysis are generally not computer scientists or high performance computing (HPC) experts, and they want their workflow to support their science without having to be. We describe a new HPC enabled data analytics workflow with a web interface, HPC pipeline for analysis, and both traditional and new analytics tools to help them transition from a single workstation mode of operation to power HPC users. This allows the processing of multiple plates over a short period of time to ensure timely query and analysis to match potential countermeasures to individual responses.

A Semi-Automated Computer Program For Assessment Of Skeletal Maturity In Children, Sara Gharabaghi, Thomas Wischgoll

Computer Science and Engineering Faculty Publications

In pediatric patients, skeletal maturity is an important tool for detection of hormonal, growth or genetic disorders. The Fels method is a well-known visual assessment method in which the skeletal age is estimated by grading 98 skeletal indicators in the hand-wrist radiographic (x-ray) image. These indicators are features that reflect the three-dimensional shape of the bones and change during the maturation process. Generally, the Fels indicators could be categorized into three main groups of the status of ossification, the ratios of bone widths, and epiphysealdiaphyseal fusion.

Cognitive Networking For Next-G Wireless Communications, Qingqi Pei, Pin-Han Ho, Yao Liu, Qinghua Li, Lin Chen

Computer Science and Engineering Faculty Publications

No abstract provided.

Cognitive Networking For Next-G Wireless Communications, Qingqi Pei, Pin-Han Ho, Yao Liu, Qinghua Li, Lin Chen

Computer Science and Engineering Faculty Publications

No abstract provided.

Uncertainty-Awareness In Open Source Visualization Solutions, Christina Gillmann, Thomas Wischgoll, Hans Hagen

Computer Science and Engineering Faculty Publications

The popularity of open source tools is constantly increasing, as they offer the possibility to quickly create and use visualizations of arbitrary data sources. As the positive effects of uncertainty communication to all kinds of visualizations were discussed over the past years in the academic world, this work examines the uncertaintyawareness of open source solutions. Through a categorization and classification of available tools, this paper identifies the problems in uncertainty-awareness of available open source solutions. To solve this problem, a new paradigm of data handling that extends raw datasets by its uncertainty is suggested

On The Discovery Of Social Roles In Large Scale Social Systems, Derek Doran

Computer Science and Engineering Faculty Publications

The social role of a participant in a social system is a label conceptualizing the circumstances under which she interacts within it. They may be used as a theoretical tool that explains why and how users participate in an online social system. Social role analysis also serves practical purposes, such as reducing the structure of complex systems to relationships among roles rather than alters, and enabling a comparison of social systems that emerge in similar contexts. This article presents a data-driven approach for the discovery of social roles in large scale social systems. Motivated by an analysis of the present …

Stay Awhile And Listen: User Interactions In A Crowdsourced Platform Offering Emotional Support, Derek Doran, Samir P. Yelne, Luisa Massari, Maria-Carla Calzarossa, Latrelle D. Jackson, Glen Moriarty

Computer Science and Engineering Faculty Publications

Internet and online-based social systems are rising as the dominant mode of communication in society. However, the public or semi-private environment under which most online communications operate under do not make them suitable channels for speaking with others about personal or emotional problems. This has led to the emergence of online platforms for emotional support offering free, anonymous, and confidential conversations with live listeners. Yet very little is known about the way these platforms are utilized, and if their features and design foster strong user engagement. This paper explores the utilization and the interaction features of hundreds of thousands of …

Where Do We Develop? Discovering Regions For Urban Investment In Senegal, Derek Doran, Andrew Fox, Veena Mendiratta

Computer Science and Engineering Faculty Publications

The rate of urbanization in developing countries, defined as the speed with which a population shifts from rural to urban areas, is among the highest in the world. The disproportionate number of citizens that live in a small numbers of cities places incredible pressure on the largest cities in these countries, which may already be faced with limited resources, weak industrialization, and underdeveloped infrastructures. Urban planning researchers as well as policy makers have suggested that governments in developing countries make capital investments within and surrounding smaller cities to attract citizens away from large urban centers, thereby lowering the pressure placed …

Compensatory Enlargement Of Ossabaw Miniature Swine Coronary Arteries In Diffuse Atherosclerosis, Jenny Susana Choy, Tong Luo, Yunlong Huo, Thomas Wischgoll, Kyle Schultz, Shawn D. Teague, Michael Sturek, Ghassan S. Kassab

Computer Science and Engineering Faculty Publications

Studies in human and non-human primates have confirmed the compensatory enlargement or positive remodeling (Glagov phenomenon) of coronary vessels in the presence of focal stenosis. To our knowledge, this is the first study to document arterial enlargement in a metabolic syndrome animal model with diffuse coronary artery disease (DCAD) in the absence of severe focal stenosis. Two different groups of Ossabaw miniature pigs were fed a high fat atherogenic diet for 4 months (Group I) and 12 months (Group II), respectively. Group I (6 pigs) underwent contrast enhanced computed tomographic angiography (CCTA) and intravascular ultrasound (IVUS) at baseline and after …

Survey On Fall Detection And Fall Prevention Using Wearable And External Sensors, Yueng Santiago Delahoz, Miguel Angel Labrador

Computer Science and Engineering Faculty Publications

According to nihseniorhealth.gov (a website for older adults), falling represents a great threat as people get older, and providing mechanisms to detect and prevent falls is critical to improve people’s lives. Over 1.6 million U.S. adults are treated for fall-related injuries in emergency rooms every year suffering fractures, loss of independence, and even death. It is clear then, that this problem must be addressed in a prompt manner, and the use of pervasive computing plays a key role to achieve this. Fall detection (FD) and fall prevention (FP) are research areas that have been active for over a decade, and …

Distributed Owl El Reasoning: The Story So Far, Raghava Mutharaju, Pascal Hitzler, Prabhaker Mateti

Computer Science and Engineering Faculty Publications

Automated generation of axioms from streaming data, such as traffic and text, can result in very large ontologies that single machine reasoners cannot handle. Reasoning with large ontologies requires distributed solutions. Scalable reasoning techniques for RDFS, OWL Horst and OWL 2 RL now exist. For OWL 2 EL, several distributed reasoning approaches have been tried, but are all perceived to be inefficient. We analyze this perception. We analyze completion rule based distributed approaches, using different characteristics, such as dependency among the rules, implementation optimizations, how axioms and rules are distributed. We also present a distributed queue approach for the classification …

Pushing The Boundaries Of Tractable Ontology Reasoning, David Carral, Cristina Feier, Bernardo Cuenca Grau, Pascal Hitzler, Ian Horrocks

Computer Science and Engineering Faculty Publications

We identify a class of Horn ontologies for which standard reasoning tasks such as instance checking and classification are tractable. The class is general enough to include the OWL 2 EL, QL, and RL profiles. Verifying whether a Horn ontology belongs to the class can be done in polynomial time. We show empirically that the class includes many real-world ontologies that are not included in any OWL 2 profile, and thus that polynomial time reasoning is possible for these ontologies.

Metabolomics Characterization Of U.S. And Japanese F-15 And C-130 Flight Line Crews Exposed To Jet Fuel Volatile Organic Compounds And Aerosols, Nicholas J. Delraso, David Mattie, Asao Kobayashi, Stephen W. Mitchell, Scott Dillard, Michael L. Raymer, Isaie Sibomana, Nicholas V. Reo

Computer Science and Engineering Faculty Publications

Air and ground crews transfer a significant amount of jet fuel, and as a result of transfers, breathe its volatile emission from residues. Working on the flight line also exposes maintainers to exhaust from the jet fuel as engines are tested or run before and after flight. Since little is known concerning level of exposure and the corresponding biological response associated with human jet fuel exposure, nuclear magnetic resonance (NMR)-based metabolomics analysis of human urine was utilized for characterization of metabolite profiles of flight line personnel for potential biomarker discovery. This project was a collaborative research effort between the US …

Is Your Ontology As Hard As You Think? Rewriting Ontologies Into Simpler Dls, David Carral, Cristina Feier, Ana Armas Romero, Bernardo Cuenca-Grau, Pascal Hitzler, Ian Horrocks

Computer Science and Engineering Faculty Publications

We investigate cases where an ontology expressed in a seemingly hard DL can be polynomially reduced to one in a simpler logic, while preserving reasoning outcomes for classification and fact entailment. Our transformations target the elimination of inverse roles, universal and existential restrictions, and in the best case allow us to rewrite the given ontology into one of the OWL 2 profiles. Even if an ontology cannot be fully rewritten into a profile, in many cases our transformations allow us to exploit further optimisation techniques. Moreover, the elimination of some out-of-profile axioms can improve the performance of modular reasoners, such …

El-Ifying Ontologies, David Carral, Cristina Feier, Bernardo Cuenca Grau, Pascal Hitzler, Ian Horrocks

Computer Science and Engineering Faculty Publications

The OWL 2 profiles are fragments of the ontology language OWL 2 for which standard reasoning tasks are feasible in polynomial time. Many OWL ontologies, however, contain a typically small number of out-of-profile axioms, which may have little or no influence on reasoning outcomes. We investigate techniques for rewriting axioms into the EL and RL profiles of OWL 2. We have tested our techniques on both classification and data reasoning tasks with encouraging results.

Accurate Local Estimation Of Geo-Coordinates For Social Media Posts, Derek Doran, Swapna S. Gokhale, Aldo Dagnino

Computer Science and Engineering Faculty Publications

Associating geo-coordinates with the content of social media posts can enhance many existing applications and services and enable a host of new ones. Unfortunately, a majority of social media posts are not tagged with geo-coordinates. Even when location data is available, it may be inaccurate, very broad or sometimes fictitious. Contemporary location estimation approaches based on analyzing the content of these posts can identify only broad areas such as a city, which limits their usefulness. To address these shortcomings, this paper proposes a methodology to narrowly estimate the geo-coordinates of social media posts with high accuracy. The methodology relies solely …

Visualization Support For Cognitive Sciences, Matt J. Marangoni, Thomas Wischgoll, Yue Zhou, Leslie M. Blaha, Ross Smith, Rhonda J. Vickery

Computer Science and Engineering Faculty Publications

The science of computer graphics and visualization is intertwined in many ways with Cognitive Sciences. On the one hand, computer graphics can lead to virtual environments in which a person is exposed to a virtual scenario. Typically, 3D-capable display technology combined with tracking systems, which are capable of identifying where the person is located at, are deployed to achieve maximal immersion in that the persons point of view is recreated in the virtual scenario. As a result, an impressive experience is created such that that person is navigating the virtual scenario as if it was real. On the other hand, …

Ivus Validation Of Patient Coronary Artery Lumen Area Obtained From Ct Images, Tong Luo, Thomas Wischgoll, Bon Kwon Koo, Yunlong Huo, Ghassan S. Kassab

Computer Science and Engineering Faculty Publications

Aims

Accurate computed tomography (CT)-based reconstruction of coronary morphometry (diameters, length, bifurcation angles) is important for construction of patient-specific models to aid diagnosis and therapy. The objective of this study is to validate the accuracy of patient coronary artery lumen area obtained from CT images based on intravascular ultrasound (IVUS).

Methods and Results

Morphometric data of 5 patient CT scans with 11 arteries from IVUS were reconstructed including the lumen cross sectional area (CSA), diameter and length. The volumetric data from CT images were analyzed at sub-pixel accuracy to obtain accurate vessel center lines and CSA. A new center line …

Supervised Categorical Principal Component Analysis For Genome-Wide Association Analyses, Meng Lu, Hye-Seung Lee, David Hadley, Jianhua Z. Huang, Xiaoning Qiao

Computer Science and Engineering Faculty Publications

In order to have a better understanding of unexplained heritability for complex diseases in conventional Genome-Wide Association Studies (GWAS), aggregated association analyses based on predefined functional regions, such as genes and pathways, become popular recently as they enable evaluating joint effect of multiple Single-Nucleotide Polymorphisms (SNPs), which helps increase the detection power, especially when investigating genetic variants with weak individual effects. In this paper, we focus on aggregated analysis methods based on the idea of Principal Component Analysis (PCA). The past approaches using PCA mostly make some inherent genotype data and/or risk effect model assumptions, which may hinder the accurate …

Joint Clustering Of Protein Interaction Networks Through Markov Random Walk, Yijie Wang, Xiaoning Qian

Computer Science and Engineering Faculty Publications

Biological networks obtained by high-throughput profiling or human curation are typically noisy. For functional module identification, single network clustering algorithms may not yield accurate and robust results. In order to borrow information across multiple sources to alleviate such problems due to data quality, we propose a new joint network clustering algorithm ASModel in this paper. We construct an integrated network to combine network topological information based on protein-protein interaction (PPI) datasets and homological information introduced by constituent similarity between proteins across networks. A novel random walk strategy on the integrated network is developed for joint network clustering and an optimization …

Ontology Design Patterns For Ocean Science Data Discovery, Pascal Hitzler

Computer Science and Engineering Faculty Publications

No abstract provided.

Why The Data Train Needs Semantic Rails, Krzysztof Janowicz, Frank Van Harmelen, James A. Hendler, Pascal Hitzler

Computer Science and Engineering Faculty Publications

While catchphrases such as big data, smart data, data intensive science, or smart dust highlight different aspects, they share a common theme: Namely, a shift towards a data-centric perspective in which the synthesis and analysis of data at an ever-increasing spatial, temporal, and thematic resolution promises new insights, while, at the same time, reducing the need for strong domain theories as starting points. In terms of the envisioned methodologies, those catchphrases tend to emphasize the role of predictive analytics, i.e., statistical techniques including data mining and machine learning, as well as supercomputing. Interestingly, however, while this perspective takes the availability …

An Ontology Pattern For Oceanographic Cruises: Towards An Oceanographer's Dream Of Integrated Knowledge Discovery, Adila Krisnadhi, Robert Arko, Suzanne Carbotte, Cynthia Chandler, Michelle Cheatham, Timothy Finin, Pascal Hitzler, Krzysztof Janowicz, Thomas Narock, Lisa Raymond, Adam Shepherd, Peter Wiebe

Computer Science and Engineering Faculty Publications

EarthCube is a major effort of the National Science Foundation to establish a next-generation knowledge architecture for the broader geosciences. Data storage, retrieval, access, and reuse are central parts of this new effort. Currently, EarthCube is organized around several building blocks and research coordination networks. OceanLink is a semantics enabled building block that aims at improving data retrieval and reuse via ontologies, Semantic Web technologies, and Linked Data for the ocean sciences. Cruises, in the sense of research expeditions, are central events for ocean scientists. Consequently, information about these cruises and the involved vessels has to be shared and made …

Web Ontology Language (Owl), Kunal Sengupta, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Web Ontology Language (OWL) is a core world wide web consortium [W3C] standard Knowledge representation language for the Semantic Web.

Description Logics, Adila Krisnadhi, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Description logics (DLs) is a family of knowledge representation (KR) languages which represent knowledge in a domain of interest using formal, logic-based semantics through knowledge bases (KBs) containing general assertions of describing relevant concepts - hence, the term description - and specific assertions about individuals and relationships among them.

Enhancing Ocean Research Data Access, Cyndy Chandler, Robert Groman, Adam Shepherd, Molly Allison, Robert Arko, Yu Chen, Peter Fox, David Glover, Pascal Hitzler, Adam Leadbetter, Thomas Narock, Patrick West, Peter Wiebe

Computer Science and Engineering Faculty Publications

No abstract provided.