Physical Sciences and Mathematics Commons^™

Virtual Phd Courses – A New Mode Of Phd Education?, Bjørn Erik Munkvold, Ilze Zigurs, Deepak Khazanchi

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

This paper presents experiences from a joint virtual PhD course for doctoral students at a Norwegian and a US university. Based on an experiential learning approach, the course focused on practices for virtual research collaboration. Through six synchronous online sessions, interspersed with interaction in sub-teams, the participants worked on developing a joint conference publication. This gave the PhD students first-hand experience with working in a virtual research team. Based on our analysis of the experiences from the course, we discuss challenges of the virtual course setting and present guidelines for the design and conduct of similar virtual courses. Our results …

Bio-Logic Builder: A Non-Technical Tool For Building Dynamical, Qualitative Models, Tomáš Helikar, Brian Kowal, Alex Madrahimov, Manish Shrestha, Jay Pedersen, Kahani Limbu, Ishwor Thapa, Thaine Rowley, Rahul Satalkar, Naomi Kochi, John Konvalina, Jim A. Rogers

Mathematics Faculty Publications

Computational modeling of biological processes is a promising tool in biomedical research. While a large part of its potential lies in the ability to integrate it with laboratory research, modeling currently generally requires a high degree of training in mathematics and/or computer science. To help address this issue, we have developed a web-based tool, Bio-Logic Builder, that enables laboratory scientists to define mathematical representations (based on a discrete formalism) of biological regulatory mechanisms in a modular and non-technical fashion. As part of the user interface, generalized “bio-logic” modules have been defined to provide users with the building blocks for many …

Multi-Level Opinion Dynamics Under Bounded Confidence, Gang Kou, Yiyi Zhao, Yi Peng, Yong Shi

Information Systems and Quantitative Analysis Faculty Publications

Opinion dynamics focuses on the opinion evolution in a social community. Recently, some models of continuous opinion dynamics under bounded confidence were proposed by Deffuant and Krause, et al. In the literature, agents were generally assumed to have a homogeneous confidence level. This paper proposes an extended model for a group of agents with heterogeneous confidence levels. First, a social differentiation theory is introduced and a social group is divided into opinion subgroups with distinct confidence levels. Second, a multi-level heterogeneous opinion formation model is formulated under the framework of bounded confidence. Finally, computer simulations are conducted to study the …

Constraint Answer Set Programming, Yuliya Lierler

Computer Science Faculty Publications

Constraint answer set programming (CASP) is a novel, promising direction of research whose roots go back to propositional satisfiability (SAT). SAT solvers are efficient tools for solving boolean constraint satisfaction problems that arise in different areas of computer science, including software and hardware verification. Some constraints are more naturally expressed by non-boolean constructs. Satisfiability modulo theories (SMT) extends boolean satisfiability by the integration of non-boolean symbols defined by a background theory in another formalism, such as a constraint processing language. Answer set programming (ASP) extends computational methods of SAT in yet another way, inspired by ideas from knowledge representation, logic …

Experimental Determination Of Pka Values By Use Of Nmr Chemical Shifts, Revisited, Alan D. Gift

Chemistry Faculty Publications

This laboratory experiment, using proton NMR spectroscopy to determine the dissociation constant for heterocyclic bases, has been modified from a previously described experiment. A solution of a substituted pyridine is prepared using deuterium oxide (D2O) as the solvent. The pH of the solution is adjusted and proton NMR spectra are collected for a variety of pH values. The chemical shifts of the peaks in the NMR spectrum change depending on the degree of protonation of the pyridine ring. Analysis of the spectral data is used to calculate the dissociation constant of the substituted pyridine. This experiment is suitable for a …

The Cell Collective: Toward An Open And Collaborative Approach To Systems Biology., Tomáš Helikar, Brian Kowal, Sean Mcclenathan, Mitchell Bruckner, Thaine Rowley, Alex Madrahimov, Ben Wicks, Manish Shrestha, Kahani Limbu, Jim A. Rogers

Mathematics Faculty Publications

Background: Despite decades of new discoveries in biomedical research, the overwhelming complexity of cells has been a significant barrier to a fundamental understanding of how cells work as a whole. As such, the holistic study of biochemical pathways requires computer modeling. Due to the complexity of cells, it is not feasible for one person or group to model the cell in its entirety. Results: The Cell Collective is a platform that allows the world-wide scientific community to create these models collectively. Its interface enables users to build and use models without specifying any mathematical equations or computer code - addressing …

Ethical Considerations For Virtual Worlds, Alanah Mitchell, Deepak Khazanchi

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

Metaverses, like Second Life and Teleplace, and the inherent technology capabilities that they offer continue to be of interest for researchers, practitioners, and educators. Due to this trend, and the uncertainty regarding immersive virtual experiences as contrasted with face-to-face experiences, there is a need to further understand the ethical challenges associated with this virtual context. This paper presents a starting point for discussing ethics in virtual worlds. Specifically, we review virtual worlds and their unique technology capabilities as well as the ethical considerations that arise due to these unique capabilities.

The Future Of Citizen Science: Emerging Technologies And Shifting Paradigms, Greg Newman, Andrea Wiggins, Alycia Crall, Eric Graham, Sarah Newman, Kevin Crowston

Information Systems and Quantitative Analysis Faculty Publications

Citizen science creates a nexus between science and education that, when coupled with emerging technologies, expands the frontiers of ecological research and public engagement. Using representative technologies and other examples, we examine the future of citizen science in terms of its research processes, program and participant cultures, and scientific communities. Future citizen‐science projects will likely be influenced by sociocultural issues related to new technologies and will continue to face practical programmatic challenges. We foresee networked, open science and the use of online computer/video gaming as important tools to engage non‐traditional audiences, and offer recommendations to help prepare project managers for …

A Multicriteria Decision Making Approach For Estimating The Number Of Clusters In A Data Set, Yi Peng, Yong Zhang, Gang Kou, Yong Shi

Information Systems and Quantitative Analysis Faculty Publications

Determining the number of clusters in a data set is an essential yet difficult step in cluster analysis. Since this task involves more than one criterion, it can be modeled as a multiple criteria decision making (MCDM) problem. This paper proposes a multiple criteria decision making (MCDM)-based approach to estimate the number of clusters for a given data set. In this approach, MCDM methods consider different numbers of clusters as alternatives and the outputs of any clustering algorithm on validity measures as criteria. The proposed method is examined by an experimental study using three MCDM methods, the well-known clustering algorithm–k-means, …

Evolutionary History And Phylodynamics Of Influenza A And B Neuraminidase (Na) Genes Inferred From Large-Scale Sequence Analyses, Haizhen Zhong

Chemistry Faculty Publications

Background: Influenza neuraminidase (NA) is an important surface glycoprotein and plays a vital role in viral replication and drug development. The NA is found in influenza A and B viruses, with nine subtypes classified in influenza A. The complete knowledge of influenza NA evolutionary history and phylodynamics, although critical for the prevention and control of influenza epidemics and pandemics, remains lacking.

Methodology/Principal findings: Evolutionary and phylogenetic analyses of influenza NA sequences using Maximum Likelihood and Bayesian MCMC methods demonstrated that the divergence of influenza viruses into types A and B occurred earlier than the divergence of influenza A …

An Energy-Aware Bioinformatics Application For Assembling Short Reads In High Performance Computing Systems, Julia Warnke, Sachin Pawaskar, Hesham Ali

Computer Science Faculty Proceedings & Presentations

Current biomedical technologies are producing massive amounts of data on an unprecedented scale. The increasing complexity and growth rate of biological data has made bioinformatics data processing and analysis a key and computationally intensive task. High performance computing (HPC) has been successfully applied to major bioinformatics applications to reduce computational burden. However, a naïve approach for developing parallel bioinformatics applications may achieve a high degree of parallelism while unnecessarily expending computational resources and consuming high levels of energy. As the wealth of biological data and associated computational burden continues to increase, there has become a need for the development of …

The Helium-Rich Subdwarf Cpd−20°1123: A Post-Common-Envelope Binary Evolving On To The Extended Horizontal Branch, Naslim N., S. Geier, C. S. Jeffery, N. T. Behara, V. M. Woolf, L. Classen

Physics Faculty Publications

Subluminous B stars come in a variety of flavours including single stars, close and wide binaries, and pulsating and non-pulsating variables. A majority have helium-poor surfaces (helium by number n_He < 1 per cent), whilst a minority have extremely helium rich surfaces (n_He > 90 per cent). A small number have an intermediate surface helium abundance (≈10–30 per cent), accompanied by peculiar abundances of other elements. The questions posed are (i) whether these abundance peculiarities are associated with radiatively driven and time-dependent stratification of elements within the photosphere as the star evolves from a helium-enriched progenitor to become a normal helium-poor sdB star and (ii) whether these phenomena occur only in …

Discontinuities And Best Practices In Virtual Research Collaboration, Vipin Arora, Deepak Khazanchi, Bjørn Erik Munkvold, Dawn Owens, Karen Stendal, Alvin Tarrell, Adeola Wale-Kolade, Sofi Westin, Ilze Zigurs

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

Research collaboration has become increasingly global, as collaboration technologies continue to advance and as research problems become more interdisciplinary and global. Virtual research teams have processes and challenges that are unique from a typical virtual team, and we need a better understanding of how such teams can utilize virtual research environments to their advantage. We examine this question from a review of the relevant literature and an analysis of experiences and reflections from a doctoral seminar that studied and experienced the process of virtual research collaboration.

Representing First-Order Causal Theories By Logic Programs, Paolo Ferrarris, Joohyung Lee, Yuliya Lierler, Vladimir Lifschitz, Fangkai Yang

Computer Science Faculty Publications

Nonmonotonic causal logic, introduced by McCain and Turner (McCain, N. and Turner, H. 1997. Causal theories of action and change. In Proceedings of National Conference on Artificial Intelligence (AAAI), Stanford, CA, 460–465) became the basis for the semantics of several expressive action languages. McCain's embedding of definite propositional causal theories into logic programming paved the way to the use of answer set solvers for answering queries about actions described in such languages. In this paper we extend this embedding to nondefinite theories and to the first-order causal logic.

The M Dwarf Problem In The Galaxy, Vincent M. Woolf, Andrew A. West

Physics Faculty Publications

We present evidence that there is an M dwarf problem similar to the previously identified G dwarf and K dwarf problems: the number of low-metallicity M dwarfs is not sufficient to match simple closed-box models of local Galactic chemical evolution. We estimated the metallicity of 4141 M dwarf stars with spectra from the Sloan Digital Sky Survey (SDSS) using a molecular band strength versus metallicity calibration developed using high resolution spectra of nearby M dwarfs. Using a sample of M dwarfs with measured magnitudes, parallaxes and metallicities, we derived a relation that describes the absolute magnitude variation as a function …

Mean-Field Boolean Network Model Of A Signal Transduction Network, Naomi Kochi, Mihaela Teodora Matache

Mathematics Faculty Publications

In this paper we provide a mean-field Boolean network model for a signal transduction network of a generic fibroblast cell. The network consists of several main signaling pathways, including the receptor tyrosine kinase, the G-protein coupled receptor, and the Integrin signaling pathway. The network consists of 130 nodes, each representing a signaling molecule (mainly proteins). Nodes are governed by Boolean dynamics including canalizing functions as well as totalistic Boolean functions that depend only on the overall fraction of active nodes. We categorize the Boolean functions into several different classes. Using a mean-field approach we generate a mathematical formula for the …

A Tarskian Informal Semantics For Answer Set Programming, Marc Denecker, Yuliya Lierler, Miroslaw Truszczyński, Joost Vennekens

Computer Science Faculty Proceedings & Presentations

In their seminal papers on stable model semantics, Gelfond and Lifschitz introduced ASP by casting programs as epistemic theories, in which rules represent statements about the knowledge of a rational agent. To the best of our knowledge, theirs is still the only published systematic account of the intuitive meaning of rules and programs under the stable semantics. In current ASP practice, however, we find numerous applications in which rational agents no longer seem to play any role. Therefore, we propose here an alternative explanation of the intuitive meaning of ASP programs, in which they are not viewed as statements about …

Weighted-Sequence Problem: Asp Vs Casp And Declarative Vs Problem-Oriented Solving, Yuliya Lierler, Shaden Smith

Computer Science Faculty Proceedings & Presentations

Search problems with large variable domains pose a challenge to current answer-set programming (ASP) systems as large variable domains make grounding take a long time, and lead to large ground theories that may make solving infeasible. To circumvent the “grounding bottleneck” researchers proposed to integrate constraint solving techniques with ASP in an approach called constraint ASP (CASP). In the paper, we evaluate an ASP system clingo and a CASP system clingcon on a handcrafted problem involving large integer domains that is patterned after the database task of determining the optimal join order. We find that search methods used by clingo …

On The Relation Of Constraint Answer Set Programming Languages And Algorithms, Yuliya Lierler

Computer Science Faculty Proceedings & Presentations

Recently a logic programming language AC was proposed by Mellarkod et al. (2008) to integrate answer set programming (ASP) and constraint logic programming. Similarly, Gebser et al. (2009) proposed a CLINGCON language integrating ASP and finite domain constraints. These languages allow new efficient inference algorithms that combine traditional ASP procedures and other methods in constraint programming. In this paper we show that a transition system introduced by Nieuwenhuis et al. (2006) to model SAT solvers can be extended to model the “hybrid” ACSOLVER algorithm by Mellarkod et al. developed for simple AC programs and the CLINGCON algorithm by Gebser et …

Practical And Methodological Aspects Of The Use Of Cutting-Edge Asp Tools, Marcello Balduccini, Yuliya Lierler

Computer Science Faculty Proceedings & Presentations

In the development of practical applications of answer set programming (ASP), encodings that use well-established solvers such as CLASP and DLV are sometimes affected by scalability issues. In those situations, one can resort to more sophisticated ASP tools exploiting, for instance, incremental and constraint ASP. However, today there is no specific methodology for the selection or use of such tools. In this paper we describe how we used such cutting-edge ASP tools on challenging problems from the Third Answer Set Programming Competition. We view this paper as a first step in the development of a general methodology for the use …

Surviving Solver Sensitivity: An Asp Practitioner’S Guide, Bryan Silverthorn, Yuliya Lierler, Marius Schneider

Computer Science Faculty Proceedings & Presentations

Answer set programming (ASP) is a declarative programming formalism that allows a practitioner to specify a problem without describing an algorithm for solving it. In ASP, the tools for processing problem specifications are called answer set solvers. Because specified problems are often NP complete, these systems often require significant computational effort to succeed. Furthermore, they offer different heuristics, expose numerous parameters, and their running time is sensitive to the configuration used. Portfolio solvers and automatic algorithm configuration systems are recent attempts to automate the problem of manual parameter tuning, and to mitigate the burden of identifying the right solver configuration. …

Establishing A Foundation For Automated Human Credibility Screening, Jay F. Nunamaker Jr., Judee K. Burgoon, Nathan W. Twyman, Jeffrey Gainer Proudfoot, Ryan M. Schuetzler, Justin Scott Giboney

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

Automated human credibility screening is an emerging research area that has potential for high impact in fields as diverse as homeland security and accounting fraud detection. Systems that conduct interviews and make credibility judgments can provide objectivity, improved accuracy, and greater reliability to credibility assessment practices, need to be built. This study establishes a foundation for developing automated systems for human credibility screening.

Countermeasures And Eye Tracking Deception Detection, Ryan M. Schuetzler

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

A new development in the field of deception detection is been the development of rapid, noncontact tools for automated detection. This research in progress paper describes a method for assessing the robustness of eye tracker-based deception detection to countermeasures employed by knowledgeable participants.

Can Information And Communication Technologies Lead To Community Capital? An Analysis Of Development, Dave Kocsis, Sajda Qureshi, Jie Xiong

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

While it is widely accepted that the increasing interconnectedness of the world economy has been fueled by the innovative uses of Information and Communication Technologies (ICTs), little attention has been paid to the increasing inequalities within developed and developing countries. These inequalities manifest themselves in the form of communities in which incomes are considerably below the rest of the country and there is a rise in poverty. This paper investigates this trend by taking a community capital perspective to investigate how ICTs may or may not enable businesses to grow. As micro-enterprises are seen to contribute to the growth of …

Factors Affecting Information And Communications Technology Adoption Of Small Businesses: Studies In China And United States, Jie Xiong, Sajda Qureshi

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

Small businesses in China and United States generate the largest share of economic activity and employment. As the driving force behind the economic growth of both countries, Information and Communications Technology (ICTs) has fundamentally shaped the two countries. This research-in-progress paper reports the research model we conduct to analyze the factors that will affect ICTs adoption of small businesses in both countries. The purpose of the paper is to (1) report proposals of the current status of the research project (2) build an understanding of ICTs adoption in both countries (3) build the framework to explore the relationship between ICTs …

Analysis Of Information And Communications Technology Adoption Between Small Businesses In China And The United States, Jie Xiong, Sajda Qureshi

Information Systems and Quantitative Analysis Faculty Proceedings & Presentations

This paper reports on two case studies, the Information and Communications Technology (ICT) adoption among small businesses conducted in both United States and China. One small business from Nebraska (United States of America) and one small business from Sichuan (China) were chosen for comparison. The purpose of this paper is to conduct a comparative case study based on the ICT adoption among small businesses in China and the United States. This paper will: (i) build an understanding of small business ICT in both areas, (ii) explore the relationship between the ICT development in less cutting-edge areas of China and the …

A Novel Multithreaded Algorithm For Extracting Maximal Chordal Subgraphs, Mahantesh Halappanavar, John Feo, Kathryn Dempsey Cooper, Hesham Ali, Sanjukta Bhowmick

Interdisciplinary Informatics Faculty Proceedings & Presentations

Chordal graphs are triangulated graphs where any cycle larger than three is bisected by a chord. Many combinatorial optimization problems such as computing the size of the maximum clique and the chromatic number are NP-hard on general graphs but have polynomial time solutions on chordal graphs. In this paper, we present a novel multithreaded algorithm to extract a maximal chordal sub graph from a general graph. We develop an iterative approach where each thread can asynchronously update a subset of edges that are dynamically assigned to it per iteration and implement our algorithm on two different multithreaded architectures - Cray …

On The Design Of Advanced Filters For Biological Networks Using Graph Theoretic Properties, Kathryn Dempsey Cooper, Tzu-Yi Chen, Sanjukta Bhowmick, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

Network modeling of biological systems is a powerful tool for analysis of high-throughput datasets by computational systems biologists. Integration of networks to form a heterogeneous model requires that each network be as noise-free as possible while still containing relevant biological information. In earlier work, we have shown that the graph theoretic properties of gene correlation networks can be used to highlight and maintain important structures such as high degree nodes, clusters, and critical links between sparse network branches while reducing noise. In this paper, we propose the design of advanced network filters using structurally related graph theoretic properties. While spanning …

The Development Of Parallel Adaptive Sampling Algorithms For Analyzing Biological Networks, Kathryn Dempsey Cooper, Kanimathi Duraisamy, Sanjukta Bhowmick, Hesham Ali

Interdisciplinary Informatics Faculty Proceedings & Presentations

The availability of biological data in massive scales continues to represent unlimited opportunities as well as great challenges in bioinformatics research. Developing innovative data mining techniques and efficient parallel computational methods to implement them will be crucial in extracting useful knowledge from this raw unprocessed data, such as in discovering significant cellular subsystems from gene correlation networks. In this paper, we present a scalable combinatorial sampling technique, based on identifying maximum chordal subgraphs, that reduces noise from biological correlation networks, thereby making it possible to find biologically relevant clusters from the filtered network. We show how selecting the appropriate filter …

Proof-Of-Concept For A Green Energy Linear Program For Optimizing Deployments, James M. Taylor, Betty Love

Mathematics Faculty Proceedings & Presentations

The US military has spent billions of dollars and sacrificed many lives in the effort to bring electrical power services and the fuel that drives the generators to forward-deployed bases in Afghanistan and Iraq over the past 10 years. In an effort to reduce some of these tremendous costs, the US military has considered using alternative energy sources to generate electricity and reduce costs and exposure of fuel truck convoys. While some research [10] has used detailed software packages to model the electrical demand and renewable energy production tradeoffs in this environment, the impact of operational constraints is not readily …