Computer Sciences Commons^™

Provenir Ontology: Towards A Framework For Escience Provenance Management, Satya S. Sahoo, Amit P. Sheth

Kno.e.sis Publications

Provenance metadata describes the 'lineage' or history of an entity and necessary information to verify the quality of data, validate experiment protocols, and associate trust value with scientific results. eScience projects generate data and the associated provenance metadata in a distributed environment (such as myGrid) and on a very large scale that often precludes manual analysis. Given this scenario, provenance information should be, (a) interoperable across projects, research groups, and application domains, and (b) support analysis over large datasets using reasoning to discover implicit information. In this paper, we introduce an ontology-driven framework for eScience provenance management underpinned by an …

Venn, A Tool For Titrating Sequence Conservation Onto Protein Structures, Jay Vyas, Michael R. Gryk, Martin R. Schiller

Life Sciences Faculty Research

Residue conservation is an important, established method for inferring protein function, modularity and specificity. It is important to recognize that it is the 3D spatial orientation of residues that drives sequence conservation. Considering this, we have built a new computational tool, VENN that allows researchers to interactively and graphically titrate sequence homology onto surface representations of protein structures. Our proposed titration strategies reveal critical details that are not readily identified using other existing tools. Analyses of a bZIP transcription factor and receptor recognition of Fibroblast Growth Factor using VENN revealed key specificity determinants. Weblink: http://sbtools.uchc.edu/venn/.

Suggestions For Owl 3, Pascal Hitzler

Computer Science and Engineering Faculty Publications

With OWL 2 about to be completed, it is the right time to start discussions on possible future modifications of OWL. We present here a number of suggestions in order to discuss them with the OWL user community. They encompass expressive extensions on polynomial OWL 2 profiles, a suggestion for an OWL Rules language, and expressive extensions for OWL DL.

Ibm Altocumulus: A Cross-Cloud Middleware And Platform, E. Michael Maximilien, Ajith Harshana Ranabahu, Roy Engehausen, Laura Anderson

Kno.e.sis Publications

Cloud computing has become the new face of computing and promises to offer virtually unlimited, cheap, readily available, "utility type" computing resources. Many vendors have entered this market with different offerings ranging from infrastructure-as-a-service such as Amazon, to fully functional platform services such as Google App Engine. However, as a result of this heterogeneity, deploying applications to a cloud and managing them needs to be done using vendor specific methods. This "lock in" is seen as a major hurdle in adopting cloud technologies to the enterprise. IBM Altocumulus, the cloud middleware platform from IBM Almaden Services Research, aims to solve …

Paraconsistent Reasoning For Owl 2, Yue Ma, Pascal Hitzler

Computer Science and Engineering Faculty Publications

A four-valued description logic has been proposed to reason with description logic based inconsistent knowledge bases. This approach has a distinct advantage that it can be implemented by invoking classical reasoners to keep the same complexity as under the classical semantics. However, this approach has so far only been studied for the basid description logic ALC. In this paper, we further study how to extend the four-valued semantics to the more expressive description logic SROIQ which underlies the forthcoming revision of the Web Ontology Language, OWL 2, and also investigate how it fares when adapated to tractable description logics including …

A Preferential Tableaux Calculus For Circumscriptive Alco, Stephan Grimm, Pascal Hitzler

Computer Science and Engineering Faculty Publications

Nonmonotonic extensions of description logics (DLs) allow for default and local closed-world reasoning and are an acknowledged desired feature for applications, e.g. in the Semantic Web. A recent approach to such an extension is based on McCarthy's circumscription, which rests on the principle of minimising the extension of selected predicates to close off dedicated parts of a domain model. While decidability and complexity results have been established in the literature, no practical algorithmisation for circumscriptive DLs has been proposed so far. In this paper, we present a tableaux calculus that can be used as a decision procedure for concept satisfiability …

A Best Practice Model For Cloud Middleware Systems, Ajith Harshana Ranabahu, E. Michael Maximilien

Kno.e.sis Publications

Cloud computing is the latest trend in computing where the intention is to facilitate cheap, utility type computing resources in a service-oriented manner. However, the cloud landscape is still maturing and there are heterogeneities between the clouds, ranging from the application development paradigms to their service interfaces,and scaling approaches. These differences hinder the adoption of cloud by major enterprises. We believe that a cloud middleware can solve most of these issues to allow cross-cloud inter-operation. Our proposed system is Altocumulus, a cloud middleware that homogenizes the clouds. In order to provide the best use of the cloud resources and make …

Context And Domain Knowledge Enhanced Entity Spotting In Informal Text, Daniel Gruhl, Meena Nagarajan, Jan Pieper, Christine Robson, Amit P. Sheth

Kno.e.sis Publications

This paper explores the application of restricted relationship graphs (RDF) and statistical NLP techniques to improve named entity annotation in challenging Informal English domains. We validate our approach using on-line forums discussing popular music. Named entity annotation is particularly difficult in this domain because it is characterized by a large number of ambiguous entities, such as the Madonna album “Music” or Lilly Allen’s pop hit “Smile”.

We evaluate improvements in annotation accuracy that can be obtained by restricting the set of possible entities using real-world constraints. We find that constrained domain entity extraction raises the annotation accuracy significantly, making an …

A Smart-Phone Application For Improving Communication Skills In Children With Autism, Lakshmi Padmaja Battagiri

Electrical & Computer Engineering Theses & Dissertations

The prevalence of autism, a complex neurobiological disorder, has grown at a staggering rate in the recent past. Today, one out of 150 American children is diagnosed with autism. Generally, the disorder appears during an individual's first three years of life of and persists through his/her entire life span. The individual faces various social interaction, communication and behavioral problems. Developmental disabilities, extreme withdrawal, lack of social behaviour, severe language and attention deficits, repetitive behaviours and limited interests are the characteristics of this disorder. There is no verified cure yet, but several therapies and intervention systems especially focused on the early …

Context Is Highly Contextual!, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

A Proposed Syntax For Minimotif Semantics, Version 1., Jay Vyas, Ronald J. Nowling, Mark W. Maciejewski, Sanguthevar Rajasekaran, Michael R. Gryk, Martin R. Schiller

Life Sciences Faculty Research

BACKGROUND:

One of the most important developments in bioinformatics over the past few decades has been the observation that short linear peptide sequences (minimotifs) mediate many classes of cellular functions such as protein-protein interactions, molecular trafficking and post-translational modifications. As both the creators and curators of a database which catalogues minimotifs, Minimotif Miner, the authors have a unique perspective on the commonalities of the many functional roles of minimotifs. There is an obvious usefulness in standardizing functional annotations both in allowing for the facile exchange of data between various bioinformatics resources, as well as the internal clustering of sets of …

“Best K”: Critical Clustering Structures In Categorical Datasets, Keke Chen, Ling Liu

Kno.e.sis Publications

The demand on cluster analysis for categorical data continues to grow over the last decade. A well-known problem in categorical clustering is to determine the best K number of clusters. Although several categorical clustering algorithms have been developed, surprisingly, none has satisfactorily addressed the problem of best K for categorical clustering. Since categorical data does not have an inherent distance function as the similarity measure, traditional cluster validation techniques based on geometric shapes and density distributions are not appropriate for categorical data. In this paper, we study the entropy property between the clustering results of categorical data with different K …

Tableau Algorithm For Concept Satisfiability In Description Logic Alch, Satya S. Sahoo, Krishnaprasad Thirunarayan

Kno.e.sis Publications

The provenir ontology is an upper-level ontology to facilitate interoperability of provenance information in scientific applications. The description logic (DL) expressivity of provenir ontology is ALCH, that is, it models role hierarchies (H) (without transitive roles and inverse roles). Even though the complexity results for concept satisfiability for numerous variants of DL such as ALC with transitively closed roles (ALC_R+ also called S), inverse roles SI, and role hierarchy SHI have been well-established, similar results for ALCH has been surprisingly missing from the literature. Here, we show that the complexity of the concept satisfiability problem for the ALCH variant …

Triangle Network Motifs Predict Complexes By Complementing High-Error Interactomes With Structural Information, Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder

Faculty Publications, Computer Science

BackgroundA lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs) were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs) representing binding evidence on proteins, forming PPI-SDDI-PPI triangles.ResultsWe find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with known complexes from …

Ontology Supported Knowledge Discovery In The Field Of Human Performance And Cognition, Christopher Thomas, Pablo N. Mendes, Delroy H. Cameron, Amit P. Sheth, Krishnaprasad Thirunarayan, Cartic Ramakrishnan

Kno.e.sis Publications

No abstract provided.

Analysis And Monetization Of Social Data, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Extending Sparql To Support Spatially And Temporally Related Information, Prateek Jain, Amit P. Sheth, Peter Z. Yeh, Kunal Verma

Kno.e.sis Publications

No abstract provided.

Trykipedia: Collaborative Bio-Ontology Development Using Wiki Environment, Pramod Anantharam, Satya S. Sahoo, Brent Weatherly, Flora Logan, Raghava Mutharaju, Amit P. Sheth, Rick L. Tarleton

Kno.e.sis Publications

Biomedical ontology development is an intensely collaborative process between biology experts and computer scientists. With the proliferation of ontology based approach to solve informatics problems in biological domain, there is a need for collaborative environment that is intuitive and widely accepted for modeling the ontology.

An Ontological Representation Of Time Series Observations On The Semantic Sensor Web, Cory Andrew Henson, Holger Neuhaus, Amit P. Sheth, Krishnaprasad Thirunarayan, Rajkumar Buyya

Kno.e.sis Publications

Time series observations are a common method of collecting sensor data. The Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) provides a standard representation for time series observations within the Observations and Measurements language, and therefore is in heavy use on the Sensor Web. By providing a common model, Observations and Measurements (O&M) facilitates syntax-level integration, but lacks the ability to facilitate semantic-level integration. This inability can cause problems with interoperability between disparate sensor networks that may have subtle variations in their sensing methods. An ontological representation of time series observations could provide a more expressive model and resolve problems …

Situation Awareness Via Abductive Reasoning For Semantic Sensor Data: A Preliminary Report, Krishnaprasad Thirunarayan, Cory Andrew Henson, Amit P. Sheth

Kno.e.sis Publications

Semantic sensor Web enhances raw sensor data with spatial, temporal, and thematic annotations to enable high-level reasoning. In this paper, we explore how abductive reasoning framework can benefit formalization and interpretation of sensor data to garner situation awareness. Specifically, we show how abductive logic programming techniques, in conjunction with symbolic knowledge rules, can be used to detect inconsistent sensor data and to generate human accessible description of the state of the world from consistent subset of the sensor data. We also show how trust/belief information can be incorporated into the interpreter to enhance reliability. For concreteness, we formalize weather domain …

Semsos: Semantic Sensor Observation Service, Cory Andrew Henson, Josh Pschorr, Amit P. Sheth, Krishnaprasad Thirunarayan

Kno.e.sis Publications

Sensor observation service (SOS) is a Web service specification defined by the Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) group in order to standardize the way sensors and sensor data are discovered and accessed on the Web. This standard goes a long way in providing interoperability between repositories of heterogeneous sensor data and applications that use this data. Many of these applications, however, are ill equipped at handling raw sensor data as provided by SOS and require actionable knowledge of the environment in order to be practically useful. There are two approaches to deal with this obstacle, make the …

Discrete Nondeterministic Modeling Of Biochemical Networks, John R. Jack

Doctoral Dissertations

The ideas expressed in this work pertain to biochemical modeling. We explore our technique, the Nondeterministic Waiting Time algorithm, for modeling molecular signaling cascades. The algorithm is presented with pseudocode along with an explanation of its implementation. The entire source code can be found in the Appendices. This algorithm builds on earlier work from the lab of Dr. Andrei Nun, the advisor for this dissertation. We discuss several important extensions including: (i) a heap with special maintenance functions for sorting reaction waiting times, (ii) a nondeterministic component for handling reaction competition, and (iii) a memory enhancement allowing slower reactions to …

Analysis Of Electroencephalogram Signals For The Identification Of Mental Tasks, My Thy Thi Tran

Electrical & Computer Engineering Theses & Dissertations

Electroencephalogram (EEG) signals can be used for implicit communication such as to control robots or medical equipment by brain activity or to detect an individual's intentions of committing premeditated crimes. An EEG based brain-computer interface allows paralyzed patients to express their thoughts. However, biological and technical artifacts heavily interfered with EEG signals due to blinking of the eyes, muscle activities and line noise. Sometimes the noise interference due to signal artifacts becomes more prominent than the information content. This thesis investigates novel feature extraction methodologies in EEG signals to represent different thought processes and employs neural network-based pattern classification techniques …

Volume 02, Joseph A. Mann, Kathryn J. Greenly, Scott E. Jenkins, Andrew E. Puckette, Daniel M. Honey, Jeffery P. Ravenhorst, Jamie Elizabeth Mesrobian, Thomas Scott, Jay Crowell, Sarah Spangenberg, Amy S. Eason, Kenny Wolfe, Liz Hale, Rachel Bouchard, Will Semonco, Carley York, Ryan Higgenbothom, Adrienne Heinbaugh, Melissa Dorton, Madeline Hunter, June Ashmore, Clark Barkley, Jay Haley

Incite: The Journal of Undergraduate Scholarship

Introduction from Dean Dr. Charles Ross

Mike's Nite: New Jazz for an Old Instrument by Joseph A. Mann

Investigation of the use of Cucumis Sativus for Remediation Of Chromium from Contaminated Environmental Matrices: An Interdisciplinary Instrumental Analysis Project by Kathryn J. Greenly, Scott E. Jenkins, and Andrew E. Puckette

Development of GC-MS and Chemometric Methods for the Analysis of Accelerants in Arson Cases by Scott Jenkins

Building and Measuring Scalable Computing Systems by Daniel M. Honey and Jeffery P. Ravenhorst

Nomini Hall: A Case Study in the Use of Archival Resources as Guides for Excavation at An Archaeological Site by …

Using Gis To Locate Areas For Growing Quality Coffee In Honduras, Ellen Mickle

Department of Environmental Studies: Undergraduate Student Theses

Abstract Small-scale coffee producers worldwide remain vulnerable to price fluctuations after the 1999-2003 coffee crisis. One way to increase small-scale farmer economic resilience is to produce a more expensive product, such as quality coffee. There is growing demand in coffee-producing and coffee-importing countries for user-friendly tools that facilitate the marketing of quality coffee. The purpose of this study is to develop a prototypical quality coffee marketing tool in the form of a GIS model that identifies regions for producing quality coffee in a country not usually associated with quality coffee, Honduras. Maps of areas for growing quality coffee were produced …

Catena-Poly[[(Pyridine-Κn)Copper(Ii)]-Μ3-Pyridine-2,6-Dicarboxylato-Κ3o2:O2′,N,O6:O6′], Manoj Trivedi, Daya Pandey, Nigam Rath

Chemistry & Biochemistry Faculty Works

In the title compound, [Cu(C7H3NO4)(C5H5N)]n, the CuII atom is in a slightly distorted octa­hedral coordination environment. Each CuII atom is bound to two N atoms and one O atom of the pyridine­dicarboxyl­ate (PDA) ligand in a tridentate manner, one N atom of the pyridine mol­ecule and two bridging carboxyl­ate O atoms of adjacent PDA ligands, leading to a linear one-dimensional chain running along the c axis. These chains are further assembled via weak C-H...O and [pi]-[pi] inter­actions into a three-dimensional supra­molecular network structure. The centroid-centroid distance between the [pi]-[pi] inter­acting pyridine rings is 3.9104 (13) Å. The two N atoms …

Reconstructability Analysis In Biomedical Research, Martin Zwick

Complex Systems Faculty Publications and Presentations

This talk explains reconstructability analysis (RA), a graphical modeling methodology based in information theory & graph theory which overlaps more familiar machine learning & statistical methods such as log-linear models & Bayesian networks. The talk reports on the use of RA in a recent bioinformatics study of human gene (SNP) - disease (diabetes) association & epistasis & in some other biomedical applications of RA.

Keywords: Reconstructability Analysis, biomedical research, bioinformatics, categorical data, multivariate statistics, exploratory modeling, confirmatory modeling

Semantic Integration Of Citizen Sensor Data And Multilevel Sensing: A Comprehensive Path Towards Event Monitoring And Situational Awareness, Amit P. Sheth

Kno.e.sis Publications

No abstract provided.

Computing For Human Experience: Sensors, Perception, Semantics, Web N.0, And Beyond, Amit P. Sheth

Kno.e.sis Publications

Traditionally there has been a strong separation between computing and human activities in the real world. The approach has largely been that of mapping the complexity and richness of the real world to constrained computer models and languages for more efficient computation, and then transferring the results for use in the real world. I think the time is ripe to reverse the situation, for computing and communication to transparently enrich and enhance human experience. Today, devices enable something more than a 'human instructs machine' paradigm. We are seeing computing and communication engage transparently in human activities by enriching them in …

Rna Secondary Structure Detection Programs With An Emphasis On Covariance Models, Justin Slotman

Theses

RNA secondary structure prediction requires a different approach from traditional alignment methods. Functional RNAs often have their secondary structure better conserved than their primary structure. Covariance models, probabilistic models that utilize stochastic-context-free grammars, are one approach. CMs allow for homology to be detected where purely sequence-based methods would fail. A background on CMs is given, as well as a background of the major classes of non-coding RNAs (ncRNAs). Comparisons are made between some CM-using tools (the Infernal suite and CMfinder) and some other RNA secondary structure tools (CARNAC, miRNAminer, Pfold, Mfold) as well as between Infernal and the primary alignment …